rotamers

Bindings for core::pack::rotamers namespace

class pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

A simple Rotamer library, which serves as a default for ResidueTypes which don’t have some other more specific rotamer library.

In practice just diversifies the proton chi records.

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, : pyrosetta.rosetta.numeric.random.RandomGenerator, : pyrosetta.rosetta.utility.vector1_double, : bool) None

C++: core::pack::rotamers::SingleBasicRotamerLibrary::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &, 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.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::rotamers::SingleBasicRotamerLibrary::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.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

C++: core::pack::rotamers::SingleBasicRotamerLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

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.SingleBasicRotamerLibrary, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.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

Adheres to the contract from SingleBasicRotamerLibrary

C++: core::pack::rotamers::SingleBasicRotamerLibrary::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

rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

Adheres to the contract from SingleBasicRotamerLibrary

C++: core::pack::rotamers::SingleBasicRotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

Adheres to the contract from SingleBasicRotamerLibrary

C++: core::pack::rotamers::SingleBasicRotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

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_file(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, out: pyrosetta.rosetta.utility.io.ozstream) None

Adheres to the contract from SingleBasicRotamerLibrary

C++: core::pack::rotamers::SingleBasicRotamerLibrary::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator, : pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator) pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator

C++: core::pack::rotamers::SingleBasicRotamerLibraryCreator::operator=(const class core::pack::rotamers::SingleBasicRotamerLibraryCreator &) –> class core::pack::rotamers::SingleBasicRotamerLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::rotamers::SingleBasicRotamerLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator) str

C++: core::pack::rotamers::SingleBasicRotamerLibraryCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

A fixed library of conformations for some residue type (doesn’t have to be a ligand).

Reads residue conformations in PDB format separated by mandatory TER records. “Included” from a residue .params file with the PDB_ROTAMERS keyword.

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, : pyrosetta.rosetta.numeric.random.RandomGenerator, : pyrosetta.rosetta.utility.vector1_double, : bool) None

C++: core::pack::rotamers::SingleLigandRotamerLibrary::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &, 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.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::rotamers::SingleLigandRotamerLibrary::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.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

C++: core::pack::rotamers::SingleLigandRotamerLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

build_base_rotamers(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, restype: pyrosetta.rosetta.core.chemical.ResidueType, base_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) None

Build a set of rotamers for the given ResidueType

C++: core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(const class core::chemical::ResidueType &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

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.SingleLigandRotamerLibrary, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.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

Adheres to the contract from SingleLigandRotamerLibrary

C++: core::pack::rotamers::SingleLigandRotamerLibrary::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_atom_positions(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary) pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t

@ brief getter for our contained data. Not meant for use by Rosetta proper; this enables a simpler unit test.

C++: core::pack::rotamers::SingleLigandRotamerLibrary::get_atom_positions() const –> const class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &

get_reference_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary) float

C++: core::pack::rotamers::SingleLigandRotamerLibrary::get_reference_energy() const –> double

init_from_file(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, filename: str, restype: pyrosetta.rosetta.core.chemical.ResidueType) None

Reads conformers from PDB-format file (must be separated by TER records!)

C++: core::pack::rotamers::SingleLigandRotamerLibrary::init_from_file(const std::string &, const class core::chemical::ResidueType &) –> void

init_from_vector(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, coordinates: pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t) None

Reads conformers from a vector of name:coordinate maps

C++: core::pack::rotamers::SingleLigandRotamerLibrary::init_from_vector(const class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &) –> void

rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

Adheres to the contract from SingleLigandRotamerLibrary

C++: core::pack::rotamers::SingleLigandRotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) float

Adheres to the contract from SingleLigandRotamerLibrary

C++: core::pack::rotamers::SingleLigandRotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

set_reference_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, ref_E_in: float) None

C++: core::pack::rotamers::SingleLigandRotamerLibrary::set_reference_energy(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_file(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, out: pyrosetta.rosetta.utility.io.ozstream) None

Adheres to the contract from SingleLigandRotamerLibrary

C++: core::pack::rotamers::SingleLigandRotamerLibrary::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator, : pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator) pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator

C++: core::pack::rotamers::SingleLigandRotamerLibraryCreator::operator=(const class core::pack::rotamers::SingleLigandRotamerLibraryCreator &) –> class core::pack::rotamers::SingleLigandRotamerLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator) str

C++: core::pack::rotamers::SingleLigandRotamerLibraryCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator, : pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator) pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator

C++: core::pack::rotamers::SingleNCAARotamerLibraryCreator::operator=(const class core::pack::rotamers::SingleNCAARotamerLibraryCreator &) –> class core::pack::rotamers::SingleNCAARotamerLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator) str

C++: core::pack::rotamers::SingleNCAARotamerLibraryCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

Bases: pybind11_builtins.pybind11_object

SingleResidueRotamerLibrary pure virtual base class

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace, 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 core::pack::dunbrack::RotamerLibraryScratchSpace &, 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, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) 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, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

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

rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) float

C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) float

C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

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_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.rotamers.SingleResidueRotamerLibraryCreator

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator, : pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator) pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator

C++: core::pack::rotamers::SingleResidueRotamerLibraryCreator::operator=(const class core::pack::rotamers::SingleResidueRotamerLibraryCreator &) –> class core::pack::rotamers::SingleResidueRotamerLibraryCreator &

create(*args, **kwargs)

Overloaded function.

  1. create(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::rotamers::SingleResidueRotamerLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

  1. create(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator, restype: pyrosetta.rosetta.core.chemical.ResidueType, : pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

Base class implementation ignores passed Residue object.

C++: core::pack::rotamers::SingleResidueRotamerLibraryCreator::create(const class core::chemical::ResidueType &, const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator) str

C++: core::pack::rotamers::SingleResidueRotamerLibraryCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_core_pack_rotamers_SingleResidueRotamerLibraryFactory_t

factory_register(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, creator: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator) None

C++: core::pack::rotamers::SingleResidueRotamerLibraryFactory::factory_register(class std::shared_ptr<class core::pack::rotamers::SingleResidueRotamerLibraryCreator>) –> void

get(*args, **kwargs)

Overloaded function.

  1. get(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, : pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

  2. get(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, : pyrosetta.rosetta.core.chemical.ResidueType, forcebasic: bool) -> pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

Get the SingleResidueRotamerLibrary coresponding to the given ResidueType.

If forcebasic is true, a SingleBasicRotamerLibrary will be returned instead of a null pointer.

If a cachetag exists for the ResidueType, store the information in the cache. If not, always regenerate the RotamerLibrary

Rocco Moretti

Vikram K. Mulligan (vmullig.edu) – implemented more efficient locking scheme.

C++: core::pack::rotamers::SingleResidueRotamerLibraryFactory::get(const class core::chemical::ResidueType &, const bool) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

  1. get(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, : pyrosetta.rosetta.core.chemical.ResidueType, : pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

Get the SingleResidueRotamerLibrary coresponding to the given ResidueType

C++: core::pack::rotamers::SingleResidueRotamerLibraryFactory::get(const class core::chemical::ResidueType &, const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

static get_instance() core::pack::rotamers::SingleResidueRotamerLibraryFactory

C++: utility::SingletonBase<core::pack::rotamers::SingleResidueRotamerLibraryFactory>::get_instance() –> class core::pack::rotamers::SingleResidueRotamerLibraryFactory *

has_type(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, : str) bool

C++: core::pack::rotamers::SingleResidueRotamerLibraryFactory::has_type(const std::string &) const –> bool

type_for_residuetype(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory, restype: pyrosetta.rosetta.core.chemical.ResidueType) str

C++: core::pack::rotamers::SingleResidueRotamerLibraryFactory::type_for_residuetype(const class core::chemical::ResidueType &) const –> std::string

class pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator

Bases: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator, : pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator) pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator

C++: core::pack::rotamers::StoredRotamerLibraryCreator::operator=(const class core::pack::rotamers::StoredRotamerLibraryCreator &) –> class core::pack::rotamers::StoredRotamerLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::rotamers::StoredRotamerLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator) str

C++: core::pack::rotamers::StoredRotamerLibraryCreator::keyname() const –> std::string

pyrosetta.rosetta.core.pack.rotamers.rotamer_information_from_PDB_stream(conformers_stream: pyrosetta.rosetta.std.istream, restype: pyrosetta.rosetta.core.chemical.ResidueType, atom_positions: pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t, e_ref: float) None
read an istream containing conformers (formatted as concatenated PDBs) into the data types held by SingleLigandRotamerLibrary

atom_positions and e_ref are return values

refactored by Steven Lewis smlewi.com

C++: core::pack::rotamers::rotamer_information_from_PDB_stream(std::istream &, const class core::chemical::ResidueType &, class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &, double &) –> void