modifications

Bindings for core::chemical::modifications namespace

class pyrosetta.rosetta.core.chemical.modifications.ChemistryBase

Bases: pybind11_object

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Modify the passed ResidueType

C++: core::chemical::modifications::ChemistryBase::apply(class core::chemical::MutableResidueType &) –> void

assign(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, : pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryBase

C++: core::chemical::modifications::ChemistryBase::operator=(const class core::chemical::modifications::ChemistryBase &) –> class core::chemical::modifications::ChemistryBase &

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType

Get additional generated ResidueTypes, if any.

This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

Get the vertex mapping that was used for the last apply() or get_additional_output()

This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping.

C++: core::chemical::modifications::ChemistryBase::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool

Are there alternate ResidueTypes which are availible from the last time we called apply?

(That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus

Bases: pybind11_object

What was the status of the last call to apply (or get_additional_output)

Members:

SUCCESS

FAIL_RETRY

FAIL_DO_NOT_RETRY

FAIL_BAD_INPUT

FAIL_BAD_SETTINGS

FAIL_BAD_INPUT = <ChemistryStatus.FAIL_BAD_INPUT: 3>

FAIL_BAD_SETTINGS = <ChemistryStatus.FAIL_BAD_SETTINGS: 4>

FAIL_DO_NOT_RETRY = <ChemistryStatus.FAIL_DO_NOT_RETRY: 2>

FAIL_RETRY = <ChemistryStatus.FAIL_RETRY: 1>

SUCCESS = <ChemistryStatus.SUCCESS: 0>

_pybind11_conduit_v1_()

property name

property value

class pyrosetta.rosetta.core.chemical.modifications.Reprotonate

Bases: ChemistryBase

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.core.chemical.modifications.Reprotonate, res: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Search the provided ResidueType for protons which should be added/removed

in order to conform to the protonation state in neutral (pH 7-ish) aqueous solution. This is done heuristically, assuming that protons have already been added. The geometry of any existing hydrogen atoms will be adjusted, but not any heavy atoms.

C++: core::chemical::modifications::Reprotonate::apply(class core::chemical::MutableResidueType &) –> void

assign(self: pyrosetta.rosetta.core.chemical.modifications.Reprotonate, : pyrosetta.rosetta.core.chemical.modifications.Reprotonate) → pyrosetta.rosetta.core.chemical.modifications.Reprotonate

C++: core::chemical::modifications::Reprotonate::operator=(const class core::chemical::modifications::Reprotonate &) –> class core::chemical::modifications::Reprotonate &

static class_name() → str

C++: core::chemical::modifications::Reprotonate::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType

Get additional generated ResidueTypes, if any.

This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.core.chemical.modifications.Reprotonate) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

C++: core::chemical::modifications::Reprotonate::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool

Are there alternate ResidueTypes which are availible from the last time we called apply?

(That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

pyrosetta.rosetta.core.chemical.modifications.angle_coordinates(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_C: pyrosetta.rosetta.numeric.xyzVector_double_t, DISTANCE_XA: float, ANGLE_XAB: float, ANGLE_XAC: float, SIDE: bool, VECTOR_SIDE: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

calculates coordinates using angle information (point X in B,C->A->X)

first point

second point

third point

distance between X and VECTOR_A

angle between X, VECTOR_A, and VECTOR_B

angle between X, VECTOR_A, and VECTOR_C

true if on a side

vector of the side

point X in B,C->A->X

C++: core::chemical::modifications::angle_coordinates(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double, const double, const double, const bool, const class numeric::xyzVector<double> &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.chemical.modifications.determine_coordinates(res: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::chemical::modifications::determine_coordinates(const class core::chemical::MutableResidueType &, void *const &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

pyrosetta.rosetta.core.chemical.modifications.dihedral_coordinates(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_C: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_D: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

dihedral angle between four points (A->B -x-> C->D)

see http://en.wikipedia.org/wiki/Dihedral_angle for reference

first vector (point)

second vector (point)

third vector (point)

fourth vector (point)

dihedral angle between four points

C++: core::chemical::modifications::dihedral_coordinates(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.core.chemical.modifications.linear_coordinates(vector_a: pyrosetta.rosetta.numeric.xyzVector_double_t, vector_b: pyrosetta.rosetta.numeric.xyzVector_double_t, distance_xa: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

point X in B->A->X where A, B and X are on the same line

calculates point X in B->A->X where A, B and X are on the same line

first point

second point

distance between X and VECTOR_A

point X in B->A->X where A, B and X are on the same line

C++: core::chemical::modifications::linear_coordinates(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.chemical.modifications.projection_angle(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

calculates projection angle between two linal::Vector3D

first vector (point)

second vector (point)

projection angle between two linal::Vector3D

C++: core::chemical::modifications::projection_angle(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.core.chemical.modifications.projection_angle_cosin(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::chemical::modifications::projection_angle_cosin(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.core.chemical.modifications.tetrahedral_coordinates(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_C: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_D: pyrosetta.rosetta.numeric.xyzVector_double_t, DISTANCE_XA: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

point X in B,C,D->A->X

calculates point X in B,C,D->A->X

first point

second point

third point

fourth point

distance between X and VECTOR_A

point X in B,C,D->A->X

C++: core::chemical::modifications::tetrahedral_coordinates(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.chemical.modifications.triganol_coordinates(VECTOR_A: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_B: pyrosetta.rosetta.numeric.xyzVector_double_t, VECTOR_C: pyrosetta.rosetta.numeric.xyzVector_double_t, DISTANCE_XA: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

calculates the unit vector starting from one linal::Vector3D to another

vector of origin

target vector

the unit vector between ORIGIN and TARGET

C++: core::chemical::modifications::triganol_coordinates(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double) –> class numeric::xyzVector<double>