dunbrack

• cenrot

Bindings for core::pack::dunbrack namespace

class pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepNRChiSample<double>::operator=(const class core::pack::dunbrack::BBDepNRChiSample<double> &) –> class core::pack::dunbrack::BBDepNRChiSample<double> &

property nrchi_bin_

property nrchi_mean_

property nrchi_sd_

property packed_rotno_

property prob_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t

C++: core::pack::dunbrack::BBDepNRChiSample<float>::operator=(const class core::pack::dunbrack::BBDepNRChiSample<float> &) –> class core::pack::dunbrack::BBDepNRChiSample<float> &

property nrchi_bin_

property nrchi_mean_

property nrchi_sd_

property packed_rotno_

property prob_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t

C++: core::pack::dunbrack::BBDepScoreInterpData<1>::operator=(const struct core::pack::dunbrack::BBDepScoreInterpData<1> &) –> struct core::pack::dunbrack::BBDepScoreInterpData<1> &

property n_derivs_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t

C++: core::pack::dunbrack::BBDepScoreInterpData<2>::operator=(const struct core::pack::dunbrack::BBDepScoreInterpData<2> &) –> struct core::pack::dunbrack::BBDepScoreInterpData<2> &

property n_derivs_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t

C++: core::pack::dunbrack::BBDepScoreInterpData<3>::operator=(const struct core::pack::dunbrack::BBDepScoreInterpData<3> &) –> struct core::pack::dunbrack::BBDepScoreInterpData<3> &

property n_derivs_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t

C++: core::pack::dunbrack::BBDepScoreInterpData<4>::operator=(const struct core::pack::dunbrack::BBDepScoreInterpData<4> &) –> struct core::pack::dunbrack::BBDepScoreInterpData<4> &

property n_derivs_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t

C++: core::pack::dunbrack::BBDepScoreInterpData<5>::operator=(const struct core::pack::dunbrack::BBDepScoreInterpData<5> &) –> struct core::pack::dunbrack::BBDepScoreInterpData<5> &

property n_derivs_

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t

Bases: RotamericData_1_1_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 1>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<1, 1> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<1, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t

C++: core::pack::dunbrack::RotamericData<1, 1>::operator=(const class core::pack::dunbrack::RotamericData<1, 1> &) –> class core::pack::dunbrack::RotamericData<1, 1> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 1>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t

C++: core::pack::dunbrack::RotamericData<1, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t

Bases: RotamericData_1_2_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 2>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<1, 2> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<1, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t

C++: core::pack::dunbrack::RotamericData<1, 2>::operator=(const class core::pack::dunbrack::RotamericData<1, 2> &) –> class core::pack::dunbrack::RotamericData<1, 2> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 2>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t

C++: core::pack::dunbrack::RotamericData<1, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t

Bases: RotamericData_1_3_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 3>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<1, 3> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<1, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t

C++: core::pack::dunbrack::RotamericData<1, 3>::operator=(const class core::pack::dunbrack::RotamericData<1, 3> &) –> class core::pack::dunbrack::RotamericData<1, 3> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 3>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t

C++: core::pack::dunbrack::RotamericData<1, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t

Bases: RotamericData_1_4_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 4>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<1, 4> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<1, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t

C++: core::pack::dunbrack::RotamericData<1, 4>::operator=(const class core::pack::dunbrack::RotamericData<1, 4> &) –> class core::pack::dunbrack::RotamericData<1, 4> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 4>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t

C++: core::pack::dunbrack::RotamericData<1, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t

Bases: RotamericData_1_5_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 5>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<1, 5> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<1, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t

C++: core::pack::dunbrack::RotamericData<1, 5>::operator=(const class core::pack::dunbrack::RotamericData<1, 5> &) –> class core::pack::dunbrack::RotamericData<1, 5> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<1, 5>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t

C++: core::pack::dunbrack::RotamericData<1, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t

Bases: RotamericData_2_1_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 1>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<2, 1> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<2, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t

C++: core::pack::dunbrack::RotamericData<2, 1>::operator=(const class core::pack::dunbrack::RotamericData<2, 1> &) –> class core::pack::dunbrack::RotamericData<2, 1> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 1>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t

C++: core::pack::dunbrack::RotamericData<2, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t

Bases: RotamericData_2_2_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 2>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<2, 2> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<2, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t

C++: core::pack::dunbrack::RotamericData<2, 2>::operator=(const class core::pack::dunbrack::RotamericData<2, 2> &) –> class core::pack::dunbrack::RotamericData<2, 2> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 2>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t

C++: core::pack::dunbrack::RotamericData<2, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t

Bases: RotamericData_2_3_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 3>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<2, 3> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<2, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t

C++: core::pack::dunbrack::RotamericData<2, 3>::operator=(const class core::pack::dunbrack::RotamericData<2, 3> &) –> class core::pack::dunbrack::RotamericData<2, 3> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 3>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t

C++: core::pack::dunbrack::RotamericData<2, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t

Bases: RotamericData_2_4_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 4>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<2, 4> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<2, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t

C++: core::pack::dunbrack::RotamericData<2, 4>::operator=(const class core::pack::dunbrack::RotamericData<2, 4> &) –> class core::pack::dunbrack::RotamericData<2, 4> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 4>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t

C++: core::pack::dunbrack::RotamericData<2, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t

Bases: RotamericData_2_5_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t, : pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 5>::operator=(const class core::pack::dunbrack::BBDepSemiRotamericData<2, 5> &) –> class core::pack::dunbrack::BBDepSemiRotamericData<2, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t

C++: core::pack::dunbrack::RotamericData<2, 5>::operator=(const class core::pack::dunbrack::RotamericData<2, 5> &) –> class core::pack::dunbrack::RotamericData<2, 5> &

3. assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

bbdep_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t) → pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t

C++: core::pack::dunbrack::BBDepSemiRotamericData<2, 5>::bbdep_nrchi_sample() const –> const class core::pack::dunbrack::BBDepNRChiSample<double> &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t

C++: core::pack::dunbrack::RotamericData<2, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t, : pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t) → pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t

C++: core::pack::dunbrack::BBIndNRChiSample<float>::operator=(const class core::pack::dunbrack::BBIndNRChiSample<float> &) –> class core::pack::dunbrack::BBIndNRChiSample<float> &

property left_

property median_

property prob_

property right_

class pyrosetta.rosetta.core.pack.dunbrack.ChiSet

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ChiSet, : pyrosetta.rosetta.core.pack.dunbrack.ChiSet) → pyrosetta.rosetta.core.pack.dunbrack.ChiSet

C++: core::pack::dunbrack::ChiSet::operator=(const class core::pack::dunbrack::ChiSet &) –> class core::pack::dunbrack::ChiSet &

property chi

property ex_chi_steps

property probability

property rot

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

Bases: pybind11_object

A small structure to hold overview parameters about the Dunbrack Libraries

property astr

static get_dun02_aa_parameters() → pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

C++: core::pack::dunbrack::DunbrackAAParameterSet::get_dun02_aa_parameters() –> struct core::pack::dunbrack::DunbrackAAParameterSet

static get_dun10_aa_parameters() → pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

C++: core::pack::dunbrack::DunbrackAAParameterSet::get_dun10_aa_parameters() –> struct core::pack::dunbrack::DunbrackAAParameterSet

property rotameric_amino_acids

property rotameric_n_bb

property rotameric_n_chi

property sampind

property scind

property sraa

property srnbb

property srnchi

property sym

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint

Bases: Constraint

atom(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID

C++: core::pack::dunbrack::DunbrackConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

bin_matches(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, resi: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: core::pack::dunbrack::DunbrackConstraint::bin_matches(const class core::conformation::Residue &) const –> bool

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) → int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::dunbrack::DunbrackConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

1. dist(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

2. dist(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, xyz: core::scoring::func::XYZ_Func) -> float

Will return 1.0 if the bonus will be added, 0.0 otherwise

C++: core::pack::dunbrack::DunbrackConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) → int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: core::scoring::func::XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::DunbrackConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint) → int

C++: core::pack::dunbrack::DunbrackConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) → None

This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None

initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: core::scoring::func::FuncFactory) → None

C++: core::pack::dunbrack::DunbrackConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

apply a resid remapping to this constraint, returns the remapped

constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

C++: core::scoring::constraints::Constraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

Copies the data from this Constraint into a new object and returns

an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool

C++: core::pack::dunbrack::DunbrackConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

2. score(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

3. score(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::pack::dunbrack::DunbrackConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint, out: pyrosetta.rosetta.std.ostream) → None

This gets used to compare one constraint to

another, so it should uniquely reflect all the parameters.

C++: core::pack::dunbrack::DunbrackConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

Prints the definition of a Constraint to the given std::ostream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) → None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str

Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint) → str

C++: core::pack::dunbrack::DunbrackConstraint::type() const –> std::string

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator

Bases: ConstraintCreator

Mover creator for the DunbrackConstraint constraint

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator

C++: core::pack::dunbrack::DunbrackConstraintCreator::operator=(const class core::pack::dunbrack::DunbrackConstraintCreator &) –> class core::pack::dunbrack::DunbrackConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::dunbrack::DunbrackConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → str

C++: core::pack::dunbrack::DunbrackConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy

Bases: ContextIndependentOneBodyEnergy

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy

C++: core::pack::dunbrack::DunbrackEnergy::operator=(const class core::pack::dunbrack::DunbrackEnergy &) –> class core::pack::dunbrack::DunbrackEnergy &

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: core::pack::dunbrack::DunbrackEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, p: pyrosetta.rosetta.core.pose.Pose) → bool

Yes. The DunbrackEnergy defines derivatives

for phi/psi and the chi dihedrals.

C++: core::pack::dunbrack::DunbrackEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

defines_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

C++: core::scoring::methods::OneBodyEnergy::defines_score_for_residue(const class core::conformation::Residue &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_residue_dof_derivative(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

Evaluate the phi/psi and chi dihedral derivatives

for the input residue.

C++: core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → None

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

C++: core::scoring::methods::EnergyMethod::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?

Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

indicate_required_context_graphs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

DunbrackEnergy is context independent; indicates that no

context graphs are required

C++: core::pack::dunbrack::DunbrackEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

C++: core::scoring::methods::ContextIndependentOneBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::pack::dunbrack::DunbrackEnergy::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

residue_energy(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::DunbrackEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work necessary before evaluating the derivatives for this residue

C++: core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None

if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

1. setup_for_packing() is called for all energy methods

2. rotamers are built

3. setup_for_packing_with_rotsets() is called for all energy methods

4. prepare_rotamers_for_packing() is called for all energy methods

5. The energy methods are asked to score all rotamers and rotamer pairs

6. Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) → None

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → int

Return the version of the energy method

C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator

C++: core::pack::dunbrack::DunbrackEnergyCreator::operator=(const class core::pack::dunbrack::DunbrackEnergyCreator &) –> class core::pack::dunbrack::DunbrackEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new DunbrackEnergy

C++: core::pack::dunbrack::DunbrackEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: core::pack::dunbrack::DunbrackEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

Bases: pybind11_object

assign_random_chi(*args, **kwargs)

Overloaded function.

1. assign_random_chi(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles: pyrosetta.rosetta.utility.vector1_double, RG: numeric::random::RandomGenerator) -> None

2. assign_random_chi(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles: pyrosetta.rosetta.utility.vector1_double, RG: numeric::random::RandomGenerator, factor: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::assign_random_chi(class utility::vector1<double, class std::allocator<double> > &, class numeric::random::RandomGenerator &, double) const –> void

chi_is_nonrotameric(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi: int) → bool

C++: core::pack::dunbrack::DunbrackRotamerSampleData::chi_is_nonrotameric(unsigned long) const –> bool

chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean() const –> const class utility::fixedsizearray1<double, 5> &

chi_probability(*args, **kwargs)

Overloaded function.

1. chi_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles: pyrosetta.rosetta.utility.vector1_double) -> float

2. chi_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles: pyrosetta.rosetta.utility.vector1_double, factor: float) -> float

C++: core::pack::dunbrack::DunbrackRotamerSampleData::chi_probability(const class utility::vector1<double, class std::allocator<double> > &, double) const –> double

chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd() const –> const class utility::fixedsizearray1<double, 5> &

nchi(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → int

C++: core::pack::dunbrack::DunbrackRotamerSampleData::nchi() const –> unsigned long

nrchi_lower_boundary(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → float

C++: core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary() const –> double

nrchi_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → float

C++: core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_probability() const –> double

nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → bool

C++: core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_sample() const –> bool

nrchi_upper_boundary(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → float

C++: core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary() const –> double

probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → float

C++: core::pack::dunbrack::DunbrackRotamerSampleData::probability() const –> double

rot_well(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) → pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t

C++: core::pack::dunbrack::DunbrackRotamerSampleData::rot_well() const –> const class utility::fixedsizearray1<unsigned long, 5> &

set_chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index: int, mean: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_mean(unsigned long, double) –> void

set_chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index: int, sd: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_sd(unsigned long, double) –> void

set_nchi(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, nchi: int) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi(unsigned long) –> void

set_nrchi_lower_boundary(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, low: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_lower_boundary(double) –> void

set_nrchi_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, nrchi_prob: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_probability(double) –> void

set_nrchi_sample(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, setting: bool) → None

Setters

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_sample(bool) –> void

set_nrchi_upper_boundary(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, high: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_upper_boundary(double) –> void

set_prob(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, probability: float) → None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_prob(double) –> void

set_rotwell(*args, **kwargs)

Overloaded function.

1. set_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index: int, rotwell: int) -> None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_rotwell(unsigned long, unsigned long) –> void

2. set_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::DunbrackRotamerSampleData::set_rotwell(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t

Bases: DunbrackRotamerMeanSD_1_1_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t

C++: core::pack::dunbrack::DunbrackRotamer<1, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<1, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamer<1, 1, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 1, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 1, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t

Bases: DunbrackRotamerMeanSD_1_1_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 1, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 1, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t

Bases: DunbrackRotamerMeanSD_1_2_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t

C++: core::pack::dunbrack::DunbrackRotamer<1, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<1, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamer<1, 2, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 2, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 2, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t

Bases: DunbrackRotamerMeanSD_1_2_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 2, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 2, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t

Bases: DunbrackRotamerMeanSD_1_3_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t

C++: core::pack::dunbrack::DunbrackRotamer<1, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<1, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamer<1, 3, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 3, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 3, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t

Bases: DunbrackRotamerMeanSD_1_3_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 3, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 3, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t

Bases: DunbrackRotamerMeanSD_1_4_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t

C++: core::pack::dunbrack::DunbrackRotamer<1, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<1, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamer<1, 4, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 4, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 4, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t

Bases: DunbrackRotamerMeanSD_1_4_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 4, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 4, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t

Bases: DunbrackRotamerMeanSD_1_5_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t

C++: core::pack::dunbrack::DunbrackRotamer<1, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<1, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamer<1, 5, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 5, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 5, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t

Bases: DunbrackRotamerMeanSD_1_5_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<1, 5, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<1, 5, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t

Bases: DunbrackRotamerMeanSD_2_1_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t

C++: core::pack::dunbrack::DunbrackRotamer<2, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<2, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamer<2, 1, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 1, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 1, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t

Bases: DunbrackRotamerMeanSD_2_1_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 1, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 1, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t

Bases: DunbrackRotamerMeanSD_2_2_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t

C++: core::pack::dunbrack::DunbrackRotamer<2, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<2, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamer<2, 2, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 2, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 2, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t

Bases: DunbrackRotamerMeanSD_2_2_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 2, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 2, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t

Bases: DunbrackRotamerMeanSD_2_3_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t

C++: core::pack::dunbrack::DunbrackRotamer<2, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<2, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamer<2, 3, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 3, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 3, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t

Bases: DunbrackRotamerMeanSD_2_3_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 3, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 3, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t

Bases: DunbrackRotamerMeanSD_2_4_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t

C++: core::pack::dunbrack::DunbrackRotamer<2, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<2, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamer<2, 4, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 4, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 4, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t

Bases: DunbrackRotamerMeanSD_2_4_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 4, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 4, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t

Bases: DunbrackRotamerMeanSD_2_5_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t

C++: core::pack::dunbrack::DunbrackRotamer<2, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<2, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamer<2, 5, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 5, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 5, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t

Bases: DunbrackRotamerMeanSD_2_5_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<2, 5, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<2, 5, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t

Bases: DunbrackRotamerMeanSD_3_1_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t

C++: core::pack::dunbrack::DunbrackRotamer<3, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<3, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamer<3, 1, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 1, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 1, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t

Bases: DunbrackRotamerMeanSD_3_1_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 1, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 1, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t

Bases: DunbrackRotamerMeanSD_3_2_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t

C++: core::pack::dunbrack::DunbrackRotamer<3, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<3, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamer<3, 2, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 2, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 2, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t

Bases: DunbrackRotamerMeanSD_3_2_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 2, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 2, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t

Bases: DunbrackRotamerMeanSD_3_3_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t

C++: core::pack::dunbrack::DunbrackRotamer<3, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<3, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamer<3, 3, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 3, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 3, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t

Bases: DunbrackRotamerMeanSD_3_3_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 3, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 3, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t

Bases: DunbrackRotamerMeanSD_3_4_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t

C++: core::pack::dunbrack::DunbrackRotamer<3, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<3, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamer<3, 4, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 4, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 4, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t

Bases: DunbrackRotamerMeanSD_3_4_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 4, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 4, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t

Bases: DunbrackRotamerMeanSD_3_5_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t

C++: core::pack::dunbrack::DunbrackRotamer<3, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<3, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamer<3, 5, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 5, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 5, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t

Bases: DunbrackRotamerMeanSD_3_5_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<3, 5, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<3, 5, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t

Bases: DunbrackRotamerMeanSD_4_1_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t

C++: core::pack::dunbrack::DunbrackRotamer<4, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<4, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamer<4, 1, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 1, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 1, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t

Bases: DunbrackRotamerMeanSD_4_1_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 1, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 1, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t

Bases: DunbrackRotamerMeanSD_4_2_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t

C++: core::pack::dunbrack::DunbrackRotamer<4, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<4, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamer<4, 2, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 2, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 2, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t

Bases: DunbrackRotamerMeanSD_4_2_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 2, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 2, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t

Bases: DunbrackRotamerMeanSD_4_3_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t

C++: core::pack::dunbrack::DunbrackRotamer<4, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<4, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamer<4, 3, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 3, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 3, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t

Bases: DunbrackRotamerMeanSD_4_3_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 3, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 3, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t

Bases: DunbrackRotamerMeanSD_4_4_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t

C++: core::pack::dunbrack::DunbrackRotamer<4, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<4, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamer<4, 4, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 4, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 4, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t

Bases: DunbrackRotamerMeanSD_4_4_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 4, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 4, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t

Bases: DunbrackRotamerMeanSD_4_5_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t

C++: core::pack::dunbrack::DunbrackRotamer<4, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<4, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamer<4, 5, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 5, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 5, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t

Bases: DunbrackRotamerMeanSD_4_5_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<4, 5, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<4, 5, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t

Bases: DunbrackRotamerMeanSD_5_1_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t

C++: core::pack::dunbrack::DunbrackRotamer<5, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<5, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamer<5, 1, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 1, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 1, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t

Bases: DunbrackRotamerMeanSD_5_1_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 1, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 1, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t

Bases: DunbrackRotamerMeanSD_5_2_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t

C++: core::pack::dunbrack::DunbrackRotamer<5, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<5, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamer<5, 2, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 2, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 2, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t

Bases: DunbrackRotamerMeanSD_5_2_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 2, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 2, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t

Bases: DunbrackRotamerMeanSD_5_3_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t

C++: core::pack::dunbrack::DunbrackRotamer<5, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<5, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamer<5, 3, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 3, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 3, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t

Bases: DunbrackRotamerMeanSD_5_3_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 3, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 3, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t

Bases: DunbrackRotamerMeanSD_5_4_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t

C++: core::pack::dunbrack::DunbrackRotamer<5, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<5, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamer<5, 4, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 4, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 4, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t

Bases: DunbrackRotamerMeanSD_5_4_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 4, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 4, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t

Bases: DunbrackRotamerMeanSD_5_5_double_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t

C++: core::pack::dunbrack::DunbrackRotamer<5, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamer<5, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamer<5, 5, double> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability(double) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 5, double>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 5, double>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t

Bases: DunbrackRotamerMeanSD_5_5_float_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability(float) –> void

rotwell(*args, **kwargs)

Overloaded function.

1. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int) -> int

C++: core::pack::dunbrack::DunbrackRotamer<5, 5, float>::rotwell(unsigned long) –> unsigned long &

2. rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t, which_chi: int, rotwell_in: int) -> None

C++: core::pack::dunbrack::DunbrackRotamer<5, 5, float>::rotwell(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter

Bases: ResidueDOFReporter

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, : pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter) → pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

C++: core::pack::dunbrack::ResidueDOFReporter::operator=(const class core::pack::dunbrack::ResidueDOFReporter &) –> class core::pack::dunbrack::ResidueDOFReporter &

get_dof(self: pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::pack::dunbrack::MainchainTorsionReporter::get_dof(const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

insert_atoms_defining_dof(self: pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) → None

C++: core::pack::dunbrack::MainchainTorsionReporter::insert_atoms_defining_dof(const class core::conformation::Residue &, const class core::pose::Pose &, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t

Bases: DunbrackRotamerMeanSD_1_1_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 1, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 1, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t

Bases: DunbrackRotamerMeanSD_1_1_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 1, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<1, 1, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<1, 1, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 1, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 1, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t

Bases: DunbrackRotamerMeanSD_1_2_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 2, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 2, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t

Bases: DunbrackRotamerMeanSD_1_2_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 2, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<1, 2, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<1, 2, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 2, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 2, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t

Bases: DunbrackRotamerMeanSD_1_3_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 3, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 3, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t

Bases: DunbrackRotamerMeanSD_1_3_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 3, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<1, 3, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<1, 3, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 3, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 3, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t

Bases: DunbrackRotamerMeanSD_1_4_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 4, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 4, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t

Bases: DunbrackRotamerMeanSD_1_4_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 4, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<1, 4, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<1, 4, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 4, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 4, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t

Bases: DunbrackRotamerMeanSD_1_5_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 5, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 5, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t

Bases: DunbrackRotamerMeanSD_1_5_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 5, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<1, 5, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<1, 5, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 5, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<1, 5, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<1, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t

Bases: DunbrackRotamerMeanSD_2_1_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 1, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 1, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t

Bases: DunbrackRotamerMeanSD_2_1_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 1, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<2, 1, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<2, 1, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 1, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 1, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t

Bases: DunbrackRotamerMeanSD_2_2_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 2, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 2, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t

Bases: DunbrackRotamerMeanSD_2_2_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 2, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<2, 2, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<2, 2, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 2, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 2, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t

Bases: DunbrackRotamerMeanSD_2_3_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 3, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 3, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t

Bases: DunbrackRotamerMeanSD_2_3_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 3, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<2, 3, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<2, 3, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 3, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 3, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t

Bases: DunbrackRotamerMeanSD_2_4_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 4, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 4, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t

Bases: DunbrackRotamerMeanSD_2_4_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 4, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<2, 4, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<2, 4, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 4, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 4, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t

Bases: DunbrackRotamerMeanSD_2_5_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 5, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 5, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t

Bases: DunbrackRotamerMeanSD_2_5_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 5, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<2, 5, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<2, 5, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 5, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<2, 5, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<2, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t

Bases: DunbrackRotamerMeanSD_3_1_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 1, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 1, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t

Bases: DunbrackRotamerMeanSD_3_1_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 1, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<3, 1, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<3, 1, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 1, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 1, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t

Bases: DunbrackRotamerMeanSD_3_2_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 2, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 2, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t

Bases: DunbrackRotamerMeanSD_3_2_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 2, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<3, 2, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<3, 2, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 2, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 2, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t

Bases: DunbrackRotamerMeanSD_3_3_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 3, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 3, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t

Bases: DunbrackRotamerMeanSD_3_3_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 3, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<3, 3, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<3, 3, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 3, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 3, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t

Bases: DunbrackRotamerMeanSD_3_4_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 4, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 4, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t

Bases: DunbrackRotamerMeanSD_3_4_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 4, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<3, 4, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<3, 4, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 4, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 4, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t

Bases: DunbrackRotamerMeanSD_3_5_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 5, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 5, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t

Bases: DunbrackRotamerMeanSD_3_5_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 5, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<3, 5, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<3, 5, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 5, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<3, 5, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<3, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t

Bases: DunbrackRotamerMeanSD_4_1_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 1, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 1, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t

Bases: DunbrackRotamerMeanSD_4_1_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 1, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<4, 1, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<4, 1, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 1, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 1, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t

Bases: DunbrackRotamerMeanSD_4_2_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 2, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 2, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t

Bases: DunbrackRotamerMeanSD_4_2_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 2, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<4, 2, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<4, 2, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 2, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 2, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t

Bases: DunbrackRotamerMeanSD_4_3_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 3, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 3, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t

Bases: DunbrackRotamerMeanSD_4_3_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 3, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<4, 3, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<4, 3, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 3, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 3, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t

Bases: DunbrackRotamerMeanSD_4_4_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 4, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 4, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t

Bases: DunbrackRotamerMeanSD_4_4_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 4, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<4, 4, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<4, 4, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 4, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 4, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t

Bases: DunbrackRotamerMeanSD_4_5_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 5, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 5, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t

Bases: DunbrackRotamerMeanSD_4_5_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 5, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<4, 5, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<4, 5, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 5, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<4, 5, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<4, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t

Bases: DunbrackRotamerMeanSD_5_1_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 1, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 1, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t

Bases: DunbrackRotamerMeanSD_5_1_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 1, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<5, 1, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<5, 1, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_2_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::n_derivs() –> class utility::fixedsizearray1<double, 2> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 1, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 1, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 1, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t

Bases: DunbrackRotamerMeanSD_5_2_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 2, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 2, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t

Bases: DunbrackRotamerMeanSD_5_2_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 2, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<5, 2, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<5, 2, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::n_derivs() –> class utility::fixedsizearray1<double, 4> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 2, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 2, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 2, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t

Bases: DunbrackRotamerMeanSD_5_3_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 3, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 3, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t

Bases: DunbrackRotamerMeanSD_5_3_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 3, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<5, 3, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<5, 3, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_8_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::n_derivs() –> class utility::fixedsizearray1<double, 8> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 3, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 3, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 3, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t

Bases: DunbrackRotamerMeanSD_5_4_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 4, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 4, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t

Bases: DunbrackRotamerMeanSD_5_4_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 4, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<5, 4, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<5, 4, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_16_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::n_derivs() –> class utility::fixedsizearray1<double, 16> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 4, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 4, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 4, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t

Bases: DunbrackRotamerMeanSD_5_5_double_t

assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long) –> double &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_mean(unsigned long, double) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long) –> double &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::chi_sd(unsigned long, double) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 5, double>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 5, double>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability() –> double &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, double>::rotamer_probability(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t

Bases: DunbrackRotamerMeanSD_5_5_float_t

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 5, float>::operator=(const class core::pack::dunbrack::PackedDunbrackRotamer<5, 5, float> &) –> class core::pack::dunbrack::PackedDunbrackRotamer<5, 5, float> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::operator=(const class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &) –> class core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float> &

chi_mean(*args, **kwargs)

Overloaded function.

1. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long) –> float &

2. chi_mean(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, which_chi: int, chi_mean_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_mean(unsigned long, float) –> void

chi_sd(*args, **kwargs)

Overloaded function.

1. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, which_chi: int) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long) –> float &

2. chi_sd(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, which_chi: int, chi_sd_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::chi_sd(unsigned long, float) –> void

n_derivs(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_32_t

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::n_derivs() –> class utility::fixedsizearray1<double, 32> &

packed_rotno(*args, **kwargs)

Overloaded function.

1. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t) -> int

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 5, float>::packed_rotno() –> unsigned long &

2. packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, packed_rotno_in: int) -> None

C++: core::pack::dunbrack::PackedDunbrackRotamer<5, 5, float>::packed_rotno(unsigned long) –> void

rotamer_probability(*args, **kwargs)

Overloaded function.

1. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t) -> float

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability() –> float &

2. rotamer_probability(self: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t, rotprob_in: float) -> None

C++: core::pack::dunbrack::DunbrackRotamerMeanSD<5, 5, float>::rotamer_probability(float) –> void

class pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter

Bases: ResidueDOFReporter

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, : pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter) → pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

C++: core::pack::dunbrack::ResidueDOFReporter::operator=(const class core::pack::dunbrack::ResidueDOFReporter &) –> class core::pack::dunbrack::ResidueDOFReporter &

get_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::pack::dunbrack::PeptideTorsionReporter::get_dof(const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

insert_atoms_defining_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) → None

C++: core::pack::dunbrack::PeptideTorsionReporter::insert_atoms_defining_dof(const class core::conformation::Residue &, const class core::pose::Pose &, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter

Bases: ResidueDOFReporter

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, : pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter) → pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

C++: core::pack::dunbrack::ResidueDOFReporter::operator=(const class core::pack::dunbrack::ResidueDOFReporter &) –> class core::pack::dunbrack::ResidueDOFReporter &

get_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::pack::dunbrack::PeptoidGeneralDOFReporter::get_dof(const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

insert_atoms_defining_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) → None

C++: core::pack::dunbrack::PeptoidGeneralDOFReporter::insert_atoms_defining_dof(const class core::conformation::Residue &, const class core::pose::Pose &, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter

Bases: ResidueDOFReporter

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, : pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter) → pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

C++: core::pack::dunbrack::ResidueDOFReporter::operator=(const class core::pack::dunbrack::ResidueDOFReporter &) –> class core::pack::dunbrack::ResidueDOFReporter &

get_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::pack::dunbrack::PeptoidOmegaReporter::get_dof(const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

insert_atoms_defining_dof(self: pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) → None

C++: core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(const class core::conformation::Residue &, const class core::pose::Pose &, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass

Bases: pybind11_object

property index_

property probability_

class pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, : pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter) → pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter

C++: core::pack::dunbrack::ResidueDOFReporter::operator=(const class core::pack::dunbrack::ResidueDOFReporter &) –> class core::pack::dunbrack::ResidueDOFReporter &

get_dof(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::pack::dunbrack::ResidueDOFReporter::get_dof(const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

insert_atoms_defining_dof(self: pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) → None

C++: core::pack::dunbrack::ResidueDOFReporter::insert_atoms_defining_dof(const class core::conformation::Residue &, const class core::pose::Pose &, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

Bases: pybind11_object

a simple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast.

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) → pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

class pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint

Bases: Constraint

This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.

Specifically, the given rotamer well(s) receive a bonus equal to the difference between their minimum energy (for the ideal rotamer in this well) and the minimum energy of any rotamer (at the current phi,psi). This class is used to implement the scoring component of the -unboundrot flag; actually adding those rotamers to the library occurs in core/pack/rotamer_set/UnboundRotamersOperation.

add_residue(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, rsd: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::dunbrack::RotamerConstraint::add_residue(const class core::conformation::Residue &) –> void

atom(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID

C++: core::pack::dunbrack::RotamerConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) → int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::dunbrack::RotamerConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

1. dist(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

2. dist(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, : core::scoring::func::XYZ_Func) -> float

Is ithere a “distance” that we can give for RotamerConstraints?

C++: core::pack::dunbrack::RotamerConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) → int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: core::scoring::func::XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::RotamerConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → int

C++: core::pack::dunbrack::RotamerConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) → None

This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None

initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None

Reads the definition of a Constraint from the given std::istream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

apply a resid remapping to this constraint, returns the remapped

constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

C++: core::scoring::constraints::Constraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

Copies the data from this Constraint into a new object and returns

an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool

C++: core::pack::dunbrack::RotamerConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

2. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

3. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::pack::dunbrack::RotamerConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, out: pyrosetta.rosetta.std.ostream) → None

This gets used to compare one constraint to another, so it should

uniquely reflect all the parameters.

C++: core::pack::dunbrack::RotamerConstraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

Prints the definition of a Constraint to the given std::ostream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) → None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str

Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → str

C++: core::pack::dunbrack::RotamerConstraint::type() const –> std::string

class pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

Bases: SingletonBase_core_pack_dunbrack_RotamerLibrary_t

A class to manage the Dunbrack Rotamer Libraries

This class no longer manages arbitrary rotamer libraries. Use core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_instance()->get( restype ); to get rotamer libraries for an arbitrary ResidueType.

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

C++: core::pack::dunbrack::RotamerLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

decide_read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → bool

C++: core::pack::dunbrack::RotamerLibrary::decide_read_from_binary() const –> bool

get_binary_name(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → str

C++: core::pack::dunbrack::RotamerLibrary::get_binary_name() const –> std::string

static get_instance() → core::pack::dunbrack::RotamerLibrary

C++: utility::SingletonBase<core::pack::dunbrack::RotamerLibrary>::get_instance() –> class core::pack::dunbrack::RotamerLibrary *

get_library_by_aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, aa: pyrosetta.rosetta.core.chemical.AA) → core::pack::rotamers::SingleResidueRotamerLibrary

C++: core::pack::dunbrack::RotamerLibrary::get_library_by_aa(const enum core::chemical::AA &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

static initialize_dun02_aa_parameters(nchi_for_aa: pyrosetta.rosetta.utility.vector1_unsigned_long, nbb_for_aa: pyrosetta.rosetta.utility.vector1_unsigned_long, n_rotameric_aas: int) → None

C++: core::pack::dunbrack::RotamerLibrary::initialize_dun02_aa_parameters(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long &) –> void

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: core::pack::rotamers::TorsionEnergy) → float

C++: core::pack::dunbrack::RotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: core::pack::rotamers::TorsionEnergy) → None

to do:

C++: core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

validate_dunbrack_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → bool

Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary.

Return true if the binary file is valid, false if the binary is invalid. NOTE WELL: This is not a const function, as reloading from ASCII modifies internals. It’s also VERY thread unsafe. Never call this function from a multithreaded context.

C++: core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary() –> bool

class pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch

Bases: pybind11_object

A scratch-space class to store the information needed for Dunbrack Rotamer interpolation

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, : pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::operator=(const class core::pack::dunbrack::RotamerLibraryInterpolationScratch &) –> class core::pack::dunbrack::RotamerLibraryInterpolationScratch &

chimean(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::chimean() –> class utility::fixedsizearray1<double, 5> &

chisd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::chisd() –> class utility::fixedsizearray1<double, 5> &

dchimean_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dchimean_dbb() –> class utility::fixedsizearray1<class utility::fixedsizearray1<double, 5>, 5> &

dchisd_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dchisd_dbb() –> class utility::fixedsizearray1<class utility::fixedsizearray1<double, 5>, 5> &

dentropy_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dentropy_dbb() –> class utility::fixedsizearray1<double, 5> &

dneglnrotprob_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dneglnrotprob_dbb() –> class utility::fixedsizearray1<double, 5> &

drotprob_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::drotprob_dbb() –> class utility::fixedsizearray1<double, 5> &

entropy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::entropy() –> double &

negln_rotprob(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::negln_rotprob() –> double &

rotprob(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::rotprob() –> double &

class pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace

Bases: RotamerLibraryInterpolationScratch

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, : pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::operator=(const class core::pack::dunbrack::RotamerLibraryScratchSpace &) –> class core::pack::dunbrack::RotamerLibraryScratchSpace &

chidev(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::chidev() –> class utility::fixedsizearray1<double, 5> &

chidevpen(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::chidevpen() –> class utility::fixedsizearray1<double, 5> &

chimean(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::chimean() –> class utility::fixedsizearray1<double, 5> &

chisd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::chisd() –> class utility::fixedsizearray1<double, 5> &

dE_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb() –> class utility::fixedsizearray1<double, 5> &

dE_dbb_dev(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev() –> class utility::fixedsizearray1<double, 5> &

dE_dbb_dev_perchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev_perchi() –> class utility::fixedsizearray1<class utility::fixedsizearray1<double, 5>, 5> &

dE_dbb_rot(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_rot() –> class utility::fixedsizearray1<double, 5> &

dE_dbb_semi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_semi() –> class utility::fixedsizearray1<double, 5> &

dE_dchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi() –> class utility::fixedsizearray1<double, 5> &

dE_dchi_dev(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_dev() –> class utility::fixedsizearray1<double, 5> &

dE_dchi_semi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi_semi() –> class utility::fixedsizearray1<double, 5> &

dchidevpen_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dbb() –> class utility::fixedsizearray1<double, 5> &

dchidevpen_dchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dchidevpen_dchi() –> class utility::fixedsizearray1<double, 5> &

dchimean_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dchimean_dbb() –> class utility::fixedsizearray1<class utility::fixedsizearray1<double, 5>, 5> &

dchimean_domg(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dchimean_domg() –> class utility::fixedsizearray1<double, 5> &

dchisd_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dchisd_dbb() –> class utility::fixedsizearray1<class utility::fixedsizearray1<double, 5>, 5> &

dchisd_domg(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::dchisd_domg() –> class utility::fixedsizearray1<double, 5> &

dentropy_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dentropy_dbb() –> class utility::fixedsizearray1<double, 5> &

dneglnrotprob_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::dneglnrotprob_dbb() –> class utility::fixedsizearray1<double, 5> &

drotprob_dbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → pyrosetta.rosetta.utility.fixedsizearray1_double_5_t

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::drotprob_dbb() –> class utility::fixedsizearray1<double, 5> &

entropy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::entropy() –> double &

extract_torsion_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, tor_id: pyrosetta.rosetta.core.id.TorsionID, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::extract_torsion_deriv(const class core::id::TorsionID &, const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> void

fa_dun_dev(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_dev() –> double &

fa_dun_rot(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_rot() –> double &

fa_dun_semi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_semi() –> double &

fa_dun_tot(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibraryScratchSpace::fa_dun_tot() –> double &

negln_rotprob(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::negln_rotprob() –> double &

rotprob(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch) → float

C++: core::pack::dunbrack::RotamerLibraryInterpolationScratch::rotprob() –> double &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t

C++: core::pack::dunbrack::RotamericData<1, 1>::operator=(const class core::pack::dunbrack::RotamericData<1, 1> &) –> class core::pack::dunbrack::RotamericData<1, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t

C++: core::pack::dunbrack::RotamericData<1, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t

C++: core::pack::dunbrack::RotamericData<1, 2>::operator=(const class core::pack::dunbrack::RotamericData<1, 2> &) –> class core::pack::dunbrack::RotamericData<1, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t

C++: core::pack::dunbrack::RotamericData<1, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t

C++: core::pack::dunbrack::RotamericData<1, 3>::operator=(const class core::pack::dunbrack::RotamericData<1, 3> &) –> class core::pack::dunbrack::RotamericData<1, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t

C++: core::pack::dunbrack::RotamericData<1, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t

C++: core::pack::dunbrack::RotamericData<1, 4>::operator=(const class core::pack::dunbrack::RotamericData<1, 4> &) –> class core::pack::dunbrack::RotamericData<1, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t

C++: core::pack::dunbrack::RotamericData<1, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t

C++: core::pack::dunbrack::RotamericData<1, 5>::operator=(const class core::pack::dunbrack::RotamericData<1, 5> &) –> class core::pack::dunbrack::RotamericData<1, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t

C++: core::pack::dunbrack::RotamericData<1, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<1, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t

C++: core::pack::dunbrack::RotamericData<2, 1>::operator=(const class core::pack::dunbrack::RotamericData<2, 1> &) –> class core::pack::dunbrack::RotamericData<2, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t

C++: core::pack::dunbrack::RotamericData<2, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t

C++: core::pack::dunbrack::RotamericData<2, 2>::operator=(const class core::pack::dunbrack::RotamericData<2, 2> &) –> class core::pack::dunbrack::RotamericData<2, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t

C++: core::pack::dunbrack::RotamericData<2, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t

C++: core::pack::dunbrack::RotamericData<2, 3>::operator=(const class core::pack::dunbrack::RotamericData<2, 3> &) –> class core::pack::dunbrack::RotamericData<2, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t

C++: core::pack::dunbrack::RotamericData<2, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t

C++: core::pack::dunbrack::RotamericData<2, 4>::operator=(const class core::pack::dunbrack::RotamericData<2, 4> &) –> class core::pack::dunbrack::RotamericData<2, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t

C++: core::pack::dunbrack::RotamericData<2, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t

C++: core::pack::dunbrack::RotamericData<2, 5>::operator=(const class core::pack::dunbrack::RotamericData<2, 5> &) –> class core::pack::dunbrack::RotamericData<2, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t

C++: core::pack::dunbrack::RotamericData<2, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<2, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t

C++: core::pack::dunbrack::RotamericData<3, 1>::operator=(const class core::pack::dunbrack::RotamericData<3, 1> &) –> class core::pack::dunbrack::RotamericData<3, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t

C++: core::pack::dunbrack::RotamericData<3, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<3, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t

C++: core::pack::dunbrack::RotamericData<3, 2>::operator=(const class core::pack::dunbrack::RotamericData<3, 2> &) –> class core::pack::dunbrack::RotamericData<3, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t

C++: core::pack::dunbrack::RotamericData<3, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<3, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t

C++: core::pack::dunbrack::RotamericData<3, 3>::operator=(const class core::pack::dunbrack::RotamericData<3, 3> &) –> class core::pack::dunbrack::RotamericData<3, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t

C++: core::pack::dunbrack::RotamericData<3, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<3, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t

C++: core::pack::dunbrack::RotamericData<3, 4>::operator=(const class core::pack::dunbrack::RotamericData<3, 4> &) –> class core::pack::dunbrack::RotamericData<3, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t

C++: core::pack::dunbrack::RotamericData<3, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<3, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t

C++: core::pack::dunbrack::RotamericData<3, 5>::operator=(const class core::pack::dunbrack::RotamericData<3, 5> &) –> class core::pack::dunbrack::RotamericData<3, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t

C++: core::pack::dunbrack::RotamericData<3, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<3, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t

C++: core::pack::dunbrack::RotamericData<4, 1>::operator=(const class core::pack::dunbrack::RotamericData<4, 1> &) –> class core::pack::dunbrack::RotamericData<4, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t

C++: core::pack::dunbrack::RotamericData<4, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<4, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t

C++: core::pack::dunbrack::RotamericData<4, 2>::operator=(const class core::pack::dunbrack::RotamericData<4, 2> &) –> class core::pack::dunbrack::RotamericData<4, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t

C++: core::pack::dunbrack::RotamericData<4, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<4, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t

C++: core::pack::dunbrack::RotamericData<4, 3>::operator=(const class core::pack::dunbrack::RotamericData<4, 3> &) –> class core::pack::dunbrack::RotamericData<4, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t

C++: core::pack::dunbrack::RotamericData<4, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<4, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t

C++: core::pack::dunbrack::RotamericData<4, 4>::operator=(const class core::pack::dunbrack::RotamericData<4, 4> &) –> class core::pack::dunbrack::RotamericData<4, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t

C++: core::pack::dunbrack::RotamericData<4, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<4, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t

C++: core::pack::dunbrack::RotamericData<4, 5>::operator=(const class core::pack::dunbrack::RotamericData<4, 5> &) –> class core::pack::dunbrack::RotamericData<4, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t

C++: core::pack::dunbrack::RotamericData<4, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<4, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t

C++: core::pack::dunbrack::RotamericData<5, 1>::operator=(const class core::pack::dunbrack::RotamericData<5, 1> &) –> class core::pack::dunbrack::RotamericData<5, 1> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t

C++: core::pack::dunbrack::RotamericData<5, 1>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<5, 1, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t

C++: core::pack::dunbrack::RotamericData<5, 2>::operator=(const class core::pack::dunbrack::RotamericData<5, 2> &) –> class core::pack::dunbrack::RotamericData<5, 2> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t

C++: core::pack::dunbrack::RotamericData<5, 2>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<5, 2, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t

C++: core::pack::dunbrack::RotamericData<5, 3>::operator=(const class core::pack::dunbrack::RotamericData<5, 3> &) –> class core::pack::dunbrack::RotamericData<5, 3> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t

C++: core::pack::dunbrack::RotamericData<5, 3>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<5, 3, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t

C++: core::pack::dunbrack::RotamericData<5, 4>::operator=(const class core::pack::dunbrack::RotamericData<5, 4> &) –> class core::pack::dunbrack::RotamericData<5, 4> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t

C++: core::pack::dunbrack::RotamericData<5, 4>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<5, 4, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t

Bases: RotamerBuildingData

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t) -> pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t

C++: core::pack::dunbrack::RotamericData<5, 5>::operator=(const class core::pack::dunbrack::RotamericData<5, 5> &) –> class core::pack::dunbrack::RotamericData<5, 5> &

2. assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) -> pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t

C++: core::pack::dunbrack::RotamericData<5, 5>::rotamer() const –> const class core::pack::dunbrack::DunbrackRotamer<5, 5, double> &

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

Bases: pybind11_object

A helper class to assist in parsing rotamer libraries.

Vikram K. Mulligan (vmullig.edu).

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, : pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::operator=(const class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser &) –> class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser &

calc_product(*args, **kwargs)

Overloaded function.

1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 1>) const –> unsigned long

2. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 2>) const –> unsigned long

3. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 3>) const –> unsigned long

4. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 4>) const –> unsigned long

5. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 5>) const –> unsigned long

clear_imporated_data(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → None

Clear all of the data read from a file.

Also resets read_file_was_called_ to false.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clear_imporated_data() –> void

clone(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clone() const –> class std::shared_ptr<class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser>

configure_rotameric_single_residue_dunbrack_library(*args, **kwargs)

Overloaded function.

1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

2. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

4. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

5. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

6. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

7. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

8. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

9. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

10. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

11. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

12. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

13. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

14. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

15. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

16. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

17. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

18. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

19. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

20. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

21. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

22. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

23. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

24. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

25. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

read_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, aa: pyrosetta.rosetta.core.chemical.AA) → str

Read an input stream to set up this object.

The RotamericSingleResidueDunbrackLibraryParser stores the information from the rotamer library in a very one-to-one format, and can subsequently be used to configure a RotamericSingleResidueDunbrackLibrary object (requiring some interpretation of the data).

We might be starting the read in the middle of the file, and the three-letter code from the first line might already have been read.

The name of the next amino acid specified in the input stream, or alternatively an empty string if EOF is reached.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(class utility::io::izstream &, bool, const enum core::chemical::AA) –> std::string

write_rotamer_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::write_rotamer_library() const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<3, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<3, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<3, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<3, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<3, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<4, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<4, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<4, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<4, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<4, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<5, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<5, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<5, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<5, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t

Bases: SingleResidueDunbrackLibrary

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<5, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t, : pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t

Bases: RotamericSingleResidueDunbrackLibrary_1_1_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<double, 1> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 1>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t

Bases: RotamericSingleResidueDunbrackLibrary_1_2_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<double, 2> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 2>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t

Bases: RotamericSingleResidueDunbrackLibrary_1_3_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<double, 3> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 3>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t

Bases: RotamericSingleResidueDunbrackLibrary_1_4_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<double, 4> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 4>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t

Bases: RotamericSingleResidueDunbrackLibrary_1_5_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<double, 5> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<1, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<1, 5>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t

Bases: RotamericSingleResidueDunbrackLibrary_2_1_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<unsigned long, 1> &, class utility::fixedsizearray1<double, 1> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::fixedsizearray1<double, 1> &, class utility::fixedsizearray1<unsigned long, 1> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer(class utility::fixedsizearray1<double, 1>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<double, 1> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 1, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 1>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 1>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t

Bases: RotamericSingleResidueDunbrackLibrary_2_2_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<unsigned long, 2> &, class utility::fixedsizearray1<double, 2> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::fixedsizearray1<double, 2> &, class utility::fixedsizearray1<unsigned long, 2> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer(class utility::fixedsizearray1<double, 2>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<double, 2> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 2, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 2>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 2>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t

Bases: RotamericSingleResidueDunbrackLibrary_2_3_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<unsigned long, 3> &, class utility::fixedsizearray1<double, 3> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::fixedsizearray1<double, 3> &, class utility::fixedsizearray1<unsigned long, 3> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer(class utility::fixedsizearray1<double, 3>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<double, 3> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 3, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 3>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 3>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t

Bases: RotamericSingleResidueDunbrackLibrary_2_4_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<unsigned long, 4> &, class utility::fixedsizearray1<double, 4> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::fixedsizearray1<double, 4> &, class utility::fixedsizearray1<unsigned long, 4> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer(class utility::fixedsizearray1<double, 4>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<double, 4> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 4, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 4>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 4>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t

Bases: RotamericSingleResidueDunbrackLibrary_2_5_t

property BB_BINRANGE

property BIN_EQUIVALENTS

property N_BB_BINS

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(*args, **kwargs)

Overloaded function.

1. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

2. assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(*args, **kwargs)

Overloaded function.

1. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

2. best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) -> float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(*args, **kwargs)

Overloaded function.

1. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

2. fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

find_another_representative_for_unlikely_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) → int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::find_another_representative_for_unlikely_rotamer(const class core::conformation::Residue &, const class core::pose::Pose &, class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

get_all_rotamer_samples(*args, **kwargs)

Overloaded function.

1. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

2. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs2: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular backbone bin.

For N-terminus residues, hand in the first bb value SingleResidueDunbrackLibrary::NEUTRAL_PHI and for C-terminus residues, hand in the final bb value SingleResidueDunbrackLibrary::NEUTRAL_PSI. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower torsion bin that the input backbone torsions prescribe.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

3. get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_bb_bins(*args, **kwargs)

Overloaded function.

1. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<unsigned long, 5> &, class utility::fixedsizearray1<double, 5> &) const –> void

2. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::fixedsizearray1<double, 5> &, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. get_bb_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.vector1_double, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Version for external, non-template classes to access.

Converts to fixedsizearrays internally.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_bb_bins(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_probability_for_rotamer(*args, **kwargs)

Overloaded function.

1. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

2. get_probability_for_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> float

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_probability_for_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer(*args, **kwargs)

Overloaded function.

1. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

2. get_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, rot_ind: int) -> pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer(class utility::fixedsizearray1<double, 5>, unsigned long) const –> class core::pack::dunbrack::DunbrackRotamerSampleData

get_rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

3. get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

interpolate_nrchi_values(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin_next: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_alpha: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, packed_rotno: int, interpolated_nrchi_distribution: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::interpolate_nrchi_values(const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<double, 5> &, unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

interpolate_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch, packed_rotno: int, interpolated_rotamer: pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t) → None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::interpolate_rotamers(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryInterpolationScratch &, unsigned long, class core::pack::dunbrack::PackedDunbrackRotamer<2, 5, double> &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::n_rotamer_bins() const –> unsigned long

2. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::n_rotamer_bins() const –> unsigned long

3. n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(*args, **kwargs)

Overloaded function.

1. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::nbb() const –> unsigned long

2. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::nbb() const –> unsigned long

3. nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(*args, **kwargs)

Overloaded function.

1. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::nchi() const –> unsigned long

2. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::nchi() const –> unsigned long

3. nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t) -> int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(*args, **kwargs)

Overloaded function.

1. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

2. probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, buried: bool) -> float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(*args, **kwargs)

Overloaded function.

1. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::read_from_binary(class utility::io::izstream &) –> void

2. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::read_from_binary(class utility::io::izstream &) –> void

3. read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, in: pyrosetta.rosetta.utility.io.izstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

read_from_file(*args, **kwargs)

Overloaded function.

1. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) -> str

2. read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, write_out: bool) -> str

Read from input stream; stream may contain data for other amino acids.

Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it’s already been extracted from the input stream). Return the empty string if no other amino acid is specified.

Returns the three letter string of the next amino acid specified in the input library.

Rewritten on 8 January 2018 by Vikram K. Mulligan (vmullig.edu).

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::read_from_file(class utility::io::izstream &, bool, bool) –> std::string

read_from_files(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, in_rotdef: pyrosetta.rosetta.utility.io.izstream, in_rotameric: pyrosetta.rosetta.utility.io.izstream, in_continmin_bbdep: pyrosetta.rosetta.utility.io.izstream) → None

Initialize a backbone-dependent SRSRDL from the set of three files

which describe it.

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::read_from_files(class utility::io::izstream &, class utility::io::izstream &, class utility::io::izstream &) –> void

rotamer_energy(*args, **kwargs)

Overloaded function.

1. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

2. rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> float

Virtual functions required by the base classes

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(*args, **kwargs)

Overloaded function.

1. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

2. rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_nonrotameric_chi_bbdep_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, step_size_in_degrees: float) → None

What is the angular step size of the bbdep score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::set_nonrotameric_chi_bbdep_scoring_step_size(double) –> void

set_nonrotameric_chi_bbind_scoring_step_size(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, step_size_in_degrees: float) → None

What is the angular step size of the bbind score?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::set_nonrotameric_chi_bbind_scoring_step_size(double) –> void

set_nonrotameric_chi_start_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, angle_in_degrees: float) → None

What angle do the interpolation data start from?

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::set_nonrotameric_chi_start_angle(double) –> void

set_nrchi_periodicity(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, angle_in_degrees: float) → None

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::set_nrchi_periodicity(double) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(*args, **kwargs)

Overloaded function.

1. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::write_to_binary(class utility::io::ozstream &) const –> void

2. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::write_to_binary(class utility::io::ozstream &) const –> void

3. write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, out: pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary<2, 5>::write_to_file(class utility::io::ozstream &) const –> void

2. write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t, : pyrosetta.rosetta.utility.io.ozstream) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2, 5>::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary

Bases: SingleResidueRotamerLibrary

aa(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) → pyrosetta.rosetta.core.chemical.AA

The amino acid this library is representing

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: numeric::random::RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

Pick a rotamer for the input residue according to the rotamer probability

distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle’s standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe’s interpretation.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

Return the set of atoms ids (or, if they come from another residue, PartialAtomIDs)

for the set of atoms that are used in defining the DOF derivatives for a particular residue

C++: core::pack::rotamers::SingleResidueRotamerLibrary::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::rotamers::SingleResidueRotamerLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bin_angle(*args, **kwargs)

Overloaded function.

1. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, angle_start: float, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

2. bin_angle(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, angle_start: float, bin_equivs: pyrosetta.rosetta.utility.vector1_unsigned_long, angle_step: float, : float, nbins: int, ang: float, bin_lower: int, bin_upper: int, angle_alpha: float) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle(const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const double, const unsigned long, const double, unsigned long &, unsigned long &, double &) const –> void

bin_rotameric_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, chi: float, which_chi: int) → int

, Turns out, when non-rotameric chi are taken out of the picture,

all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(double, unsigned long) const –> unsigned long

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamers::SingleResidueRotamerLibrary::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

get_all_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, bbs: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) → pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData

Return all of the rotamer sample data given a particular phi/psi.

For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples(class utility::fixedsizearray1<double, 5>) const –> class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> >

get_phi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd(const class core::conformation::Residue &) const –> double

get_psi_from_rsd(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd(const class core::conformation::Residue &) const –> double

get_rotamer_from_chi(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.

Derived class should be consistent, but may be arbitrary in how wells divide angle space.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

memory_usage_in_bytes(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) → int

Derived classes should invoke base class function as well.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes() const –> unsigned long

n_rotamer_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) → int

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins() const –> unsigned long

static n_rotamer_bins_for_aa(*args, **kwargs)

Overloaded function.

1. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. n_rotamer_bins_for_aa(rt: pyrosetta.rosetta.core.chemical.ResidueType, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) -> None

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType

and store it in rot.

Rewritten by Vikram K. Mulligan (vmullig.edu) to make this general and to remove hard-coded information about canonical amino acids.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

3. n_rotamer_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

The number of wells for canonical amino acids defined for the 08 library; includes

the number of wells for the semi-rotameric chi (arbitrarily chosen).

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotamer_bins_for_aa_02(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

To continue supporting the 2002 Dunbrack library, we

need to preserve the rotamer well definitions for canonical amino acids that it made.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

static n_rotameric_bins_for_aa(aa: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long, dun02: bool) → None

For the rotameric chi – not all chi are rotameric

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa(const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

nbb(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) → int

the number of backbone dihedrals represented by the library

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nbb() const –> unsigned long

nchi(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) → int

The number of chi represented by the library.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi() const –> unsigned long

packed_rotno_2_rotwell(*args, **kwargs)

Overloaded function.

1. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Convert from the packed rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

2. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno: int, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) const –> void

3. packed_rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

probability_to_accumulate_while_building_rotamers(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, task: core::pack::task::PackerTask, buried: bool) → float

When creating rotamer, what position in the CDF should one build until?

Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers(const class core::pack::task::PackerTask &, bool) const –> double

read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, in: pyrosetta.rosetta.utility.io.izstream) → None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary(class utility::io::izstream &) –> void

rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

rotno_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotno: int) → int

Convert from the rotamer number to the compacted

“packed rotamer number”. Returns 0 if rotno has no corresponding packed rotno.

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno(const unsigned long) const –> unsigned long

rotno_2_rotwell(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotno: int, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Convert from the rotamer number to the rotamer well

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

rotwell_2_packed_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_packed_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

compacted “packed rotamer number.” Returns 0 if rotwell has no corresponding packed rotno

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

rotwell_2_rotno(*args, **kwargs)

Overloaded function.

1. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

2. rotwell_2_rotno(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

Convert from the rotamer bin indices for each chi to the

(non-compact) “rotamer number”

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno(const class utility::fixedsizearray1<unsigned long, 5> &) const –> unsigned long

set_n_chi_bins(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Tell the base class the number of chi bins for each rotameric

chi dimension

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_binary(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, out: pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary(class utility::io::ozstream &) const –> void

write_to_file(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, out: pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::rotamers::SingleResidueRotamerLibrary::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator

Bases: SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator, : pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator) → pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator

C++: core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::operator=(const class core::pack::dunbrack::SingleResidueDunbrackLibraryCreator &) –> class core::pack::dunbrack::SingleResidueDunbrackLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator) → str

C++: core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::keyname() const –> std::string

pyrosetta.rosetta.core.pack.dunbrack.bit_is_set(num: int, num_len: int, pos: int) → bool

C++: core::pack::dunbrack::bit_is_set(unsigned long, unsigned long, unsigned long) –> bool

pyrosetta.rosetta.core.pack.dunbrack.interpolate_polylinear_by_value(*args, **kwargs)

Overloaded function.

1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 1> &, const class utility::fixedsizearray1<double, 1> &, bool, double &, class utility::fixedsizearray1<double, 1> &) –> void

2. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 2> &, bool, double &, class utility::fixedsizearray1<double, 2> &) –> void

3. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_8_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 8> &, const class utility::fixedsizearray1<double, 3> &, const class utility::fixedsizearray1<double, 3> &, bool, double &, class utility::fixedsizearray1<double, 3> &) –> void

4. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_16_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 16> &, const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 4> &, bool, double &, class utility::fixedsizearray1<double, 4> &) –> void

5. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_32_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 32> &, const class utility::fixedsizearray1<double, 5> &, const class utility::fixedsizearray1<double, 5> &, bool, double &, class utility::fixedsizearray1<double, 5> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.interpolate_polylinear_by_value_angles_degrees(*args, **kwargs)

Overloaded function.

1. interpolate_polylinear_by_value_angles_degrees(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 2> &, double &, class utility::fixedsizearray1<double, 2> &) –> void

2. interpolate_polylinear_by_value_angles_degrees(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_8_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(const class utility::fixedsizearray1<double, 8> &, const class utility::fixedsizearray1<double, 3> &, const class utility::fixedsizearray1<double, 3> &, double &, class utility::fixedsizearray1<double, 3> &) –> void

3. interpolate_polylinear_by_value_angles_degrees(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_16_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(const class utility::fixedsizearray1<double, 16> &, const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 4> &, double &, class utility::fixedsizearray1<double, 4> &) –> void

4. interpolate_polylinear_by_value_angles_degrees(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_32_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(const class utility::fixedsizearray1<double, 32> &, const class utility::fixedsizearray1<double, 5> &, const class utility::fixedsizearray1<double, 5> &, double &, class utility::fixedsizearray1<double, 5> &) –> void

5. interpolate_polylinear_by_value_angles_degrees(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

Interpolate polylinearly in N dimensions, for outputs that are angles (and have to handle wraparound properly).

This version is for the special N=1 case. It is ultimately the end of the recusive call chain for the version below.

Original author unknown.

Angle interpolation rewritten by Vikram K. Mulligan (vmulligan.org) and Andy Watkins, 12 Sept. 2018.

We assume that angles are in DEGREES.

The values at the corners of the gridpoints. This vector should have N^2 points.

Coordinate within the grid square/cube/hypercube, with each dimension ranging from 0 to 1.

Size of each bin. For example, 10 degrees by 10 degrees by 10 degrees…

The interpolated value.

The derivatives of the interpolated value, with respect to the degrees of freedom over which the grid is defined.

C++: core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 1> &, const class utility::fixedsizearray1<double, 1> &, double &, class utility::fixedsizearray1<double, 1> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.interpolate_polylinear_by_value_noangles(*args, **kwargs)

Overloaded function.

1. interpolate_polylinear_by_value_noangles(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_noangles(const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 1> &, const class utility::fixedsizearray1<double, 1> &, double &, class utility::fixedsizearray1<double, 1> &) –> void

2. interpolate_polylinear_by_value_noangles(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_noangles(const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 2> &, double &, class utility::fixedsizearray1<double, 2> &) –> void

3. interpolate_polylinear_by_value_noangles(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_8_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_noangles(const class utility::fixedsizearray1<double, 8> &, const class utility::fixedsizearray1<double, 3> &, const class utility::fixedsizearray1<double, 3> &, double &, class utility::fixedsizearray1<double, 3> &) –> void

4. interpolate_polylinear_by_value_noangles(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_16_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_noangles(const class utility::fixedsizearray1<double, 16> &, const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 4> &, double &, class utility::fixedsizearray1<double, 4> &) –> void

5. interpolate_polylinear_by_value_noangles(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_32_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value_noangles(const class utility::fixedsizearray1<double, 32> &, const class utility::fixedsizearray1<double, 5> &, const class utility::fixedsizearray1<double, 5> &, double &, class utility::fixedsizearray1<double, 5> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.load_unboundrot(*args, **kwargs)

Overloaded function.

1. load_unboundrot(pose: pyrosetta.rosetta.core.pose.Pose) -> None

Convenience function adds constraints to the supplied pose based on

the -unboundrot command line flag.

C++: core::pack::dunbrack::load_unboundrot(class core::pose::Pose &) –> void

2. load_unboundrot(pose: pyrosetta.rosetta.core.pose.Pose, unboundrot_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t) -> None

Convenience function adds constraints to the supplied pose based on

the list of provided poses.

C++: core::pack::dunbrack::load_unboundrot(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &) –> void

pyrosetta.rosetta.core.pack.dunbrack.make_conditional_index(*args, **kwargs)

Overloaded function.

1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 1>, unsigned long, class utility::fixedsizearray1<unsigned long, 1>, class utility::fixedsizearray1<unsigned long, 1>) –> unsigned long

2. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 2>, unsigned long, class utility::fixedsizearray1<unsigned long, 2>, class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

3. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 3>, unsigned long, class utility::fixedsizearray1<unsigned long, 3>, class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

4. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 4>, unsigned long, class utility::fixedsizearray1<unsigned long, 4>, class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

5. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 5>, unsigned long, class utility::fixedsizearray1<unsigned long, 5>, class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.make_index(*args, **kwargs)

Overloaded function.

1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<unsigned long, 1> &) –> unsigned long

2. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<unsigned long, 2> &) –> unsigned long

3. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<unsigned long, 3> &) –> unsigned long

4. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<unsigned long, 4> &) –> unsigned long

5. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<unsigned long, 5> &) –> unsigned long

6. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::fixedsizearray1<unsigned long, 2> &) –> unsigned long

7. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::fixedsizearray1<unsigned long, 3> &) –> unsigned long

8. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::fixedsizearray1<unsigned long, 4> &) –> unsigned long

9. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::fixedsizearray1<unsigned long, 5> &) –> unsigned long

10. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::fixedsizearray1<unsigned long, 6> &) –> unsigned long

11. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 1> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

12. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 2> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

13. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 3> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

14. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 4> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

15. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(const class utility::fixedsizearray1<unsigned long, 5> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.polycubic_interpolation(*args, **kwargs)

Overloaded function.

1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_2_2_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 2>, 2>, class utility::fixedsizearray1<double, 1>, class utility::fixedsizearray1<double, 1>, double &, class utility::fixedsizearray1<double, 1> &) –> void

2. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_4_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 4>, 4>, class utility::fixedsizearray1<double, 2>, class utility::fixedsizearray1<double, 2>, double &, class utility::fixedsizearray1<double, 2> &) –> void

3. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_8_8_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 8>, 8>, class utility::fixedsizearray1<double, 3>, class utility::fixedsizearray1<double, 3>, double &, class utility::fixedsizearray1<double, 3> &) –> void

4. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_16_16_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 16>, 16>, class utility::fixedsizearray1<double, 4>, class utility::fixedsizearray1<double, 4>, double &, class utility::fixedsizearray1<double, 4> &) –> void

5. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_32_32_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 32>, 32>, class utility::fixedsizearray1<double, 5>, class utility::fixedsizearray1<double, 5>, double &, class utility::fixedsizearray1<double, 5> &) –> void

6. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_64_64_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 64>, 64>, class utility::fixedsizearray1<double, 6>, class utility::fixedsizearray1<double, 6>, double &, class utility::fixedsizearray1<double, 6> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.positive_pow(mantissa: int, exponent: int) → int

C++: core::pack::dunbrack::positive_pow(unsigned long, unsigned long) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.product(*args, **kwargs)

Overloaded function.

1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 1>) –> unsigned long

2. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

3. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

4. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

5. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.psc_compare(left: pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass, right: pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass) → bool

C++: core::pack::dunbrack::psc_compare(class core::pack::dunbrack::ProbSortClass, class core::pack::dunbrack::ProbSortClass) –> bool

pyrosetta.rosetta.core.pack.dunbrack.rotamer_from_chi(*args, **kwargs)

Overloaded function.

1. rotamer_from_chi(rsd: pyrosetta.rosetta.core.conformation.Residue, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::rotamer_from_chi(const class core::conformation::Residue &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. rotamer_from_chi(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::rotamer_from_chi(const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.pack.dunbrack.rotamer_from_chi_02(*args, **kwargs)

Overloaded function.

1. rotamer_from_chi_02(chi: pyrosetta.rosetta.utility.vector1_double, res: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Do not bother calling this function if you’re interested in staying

up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true.

C++: core::pack::dunbrack::rotamer_from_chi_02(const class utility::vector1<double, class std::allocator<double> > &, const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. rotamer_from_chi_02(chi: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, res: pyrosetta.rosetta.core.chemical.AA, nchi: int, rot: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::rotamer_from_chi_02(const class utility::fixedsizearray1<double, 5> &, const enum core::chemical::AA, unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.subtract_chi_angles(chi1: float, chi2: float, aa: pyrosetta.rosetta.core.chemical.AA, chino: int) → float

Find the difference in angles between two chi values using hard-coded

symmetry information for the symmetric amino acids. Disappears for 2010 library.

C++: core::pack::dunbrack::subtract_chi_angles(double, double, const enum core::chemical::AA &, int) –> double