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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, : pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) → bool¶

Equality test for equivalence.: Two SingleResidueRotamerLibraries test equal if and only if they represent the exact same behavior

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

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, 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.

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
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, 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 &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, 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.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, : pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) → bool¶

Equality test for equivalence.: Two SingleResidueRotamerLibraries test equal if and only if they represent the exact same behavior

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

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, 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.

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
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 class std::basic_string<char> &, 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<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > > > > &) –> void

rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, 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.SingleResidueRotamerLibrary¶

Bases: pybind11_builtins.pybind11_object

SingleResidueRotamerLibrary pure virtual base class

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, : pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) → bool¶

Equality test for equivalence.: Two SingleResidueRotamerLibraries test equal if and only if they represent the exact same behavior

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

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: pyrosetta.rosetta.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

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, 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 &, 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.

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
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, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) → float¶: C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy(const class core::conformation::Residue &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) → float¶: C++: core::pack::rotamers::SingleResidueRotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, 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

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(class std::basic_istream<char> &, const class core::chemical::ResidueType &, class utility::vector1<class std::map<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > > > > &, double &) –> void