motifs

Bindings for protocols::motifs namespace

pyrosetta.rosetta.protocols.motifs.add_motif_bb_constraints(cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, this_pos: int, inv_rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: protocols::motifs::add_motif_bb_constraints(class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, class core::pose::Pose &, unsigned long, const class core::conformation::Residue &) –> void

pyrosetta.rosetta.protocols.motifs.add_motif_sc_constraints(cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, this_pos: int, inv_rotamer: pyrosetta.rosetta.core.conformation.Residue, this_motif: pyrosetta.rosetta.protocols.motifs.Motif, is_it_forward: bool) → None

C++: protocols::motifs::add_motif_sc_constraints(class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, class core::pose::Pose &, unsigned long, const class core::conformation::Residue &, class std::shared_ptr<const class protocols::motifs::Motif>, const bool) –> void

pyrosetta.rosetta.protocols.motifs.atom_specific_rms(*args, **kwargs)

Overloaded function.

1. atom_specific_rms(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_std_string) -> float

C++: protocols::motifs::atom_specific_rms(const class core::conformation::Residue &, const class core::conformation::Residue &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> double

2. atom_specific_rms(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

C++: protocols::motifs::atom_specific_rms(const class core::conformation::Residue &, const class core::conformation::Residue &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> double

pyrosetta.rosetta.protocols.motifs.backbone_stub_match(r1: pyrosetta.rosetta.core.conformation.Residue, r2: pyrosetta.rosetta.core.conformation.Residue) → float

C++: protocols::motifs::backbone_stub_match(const class core::conformation::Residue &, const class core::conformation::Residue &) –> double

pyrosetta.rosetta.protocols.motifs.bools_from_sizes(nres: int, v: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::motifs::bools_from_sizes(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.motifs.bpdefs2map(pose: pyrosetta.rosetta.core.pose.Pose, targets: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_std_less_std_string_std_allocator_std_string_t

C++: protocols::motifs::bpdefs2map(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &) –> class std::map<unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > >

pyrosetta.rosetta.protocols.motifs.build_rotamers_lite(*args, **kwargs)

Overloaded function.

1. build_rotamers_lite(pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, aa_info: pyrosetta.rosetta.utility.vector1_bool, ex_: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet
2. build_rotamers_lite(pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, aa_info: pyrosetta.rosetta.utility.vector1_bool, ex_: int, bump_check: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: protocols::motifs::build_rotamers_lite(class core::pose::Pose &, const unsigned long, class utility::vector1<bool, class std::allocator<bool> >, const unsigned long, bool) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

pyrosetta.rosetta.protocols.motifs.defs2map(pose: pyrosetta.rosetta.core.pose.Pose, targets: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_std_less_std_string_std_allocator_std_string_t

C++: protocols::motifs::defs2map(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &) –> class std::map<unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > >

pyrosetta.rosetta.protocols.motifs.defs2vector(pose: pyrosetta.rosetta.core.pose.Pose, targeted_dna: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::motifs::defs2vector(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.motifs.get_LigandMotifLibrary_user() → pyrosetta.rosetta.protocols.motifs.MotifLibrary

C++: protocols::motifs::get_LigandMotifLibrary_user() –> const class protocols::motifs::MotifLibrary

pyrosetta.rosetta.protocols.motifs.get_MotifLibrary_user() → pyrosetta.rosetta.protocols.motifs.MotifLibrary

C++: protocols::motifs::get_MotifLibrary_user() –> const class protocols::motifs::MotifLibrary

pyrosetta.rosetta.protocols.motifs.get_filenames(listnames: pyrosetta.rosetta.utility.vector1_utility_file_FileName) → pyrosetta.rosetta.utility.vector1_utility_file_FileName

C++: protocols::motifs::get_filenames(const class utility::vector1<class utility::file::FileName, class std::allocator<class utility::file::FileName> > &) –> class utility::vector1<class utility::file::FileName, class std::allocator<class utility::file::FileName> >

pyrosetta.rosetta.protocols.motifs.get_motif_build_position_defs_user() → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t

C++: protocols::motifs::get_motif_build_position_defs_user() –> class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > >

pyrosetta.rosetta.protocols.motifs.get_motif_build_positions_user(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::motifs::get_motif_build_positions_user(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.motifs.get_target_position_map_make_dna_mutations(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_std_less_std_string_std_allocator_std_string_t

C++: protocols::motifs::get_target_position_map_make_dna_mutations(class core::pose::Pose &) –> class std::map<unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > >

pyrosetta.rosetta.protocols.motifs.get_target_positions_make_dna_mutations(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::motifs::get_target_positions_make_dna_mutations(class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.motifs.get_targetconformers_user() → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

C++: protocols::motifs::get_targetconformers_user() –> const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

pyrosetta.rosetta.protocols.motifs.load_build_position_data(*args, **kwargs)

Overloaded function.

1. load_build_position_data(bp: pyrosetta.rosetta.protocols.motifs.BuildPosition, filename: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. load_build_position_data(bp: pyrosetta.rosetta.protocols.motifs.BuildPosition, filename: str, pose: pyrosetta.rosetta.core.pose.Pose, ligand_marker: int) -> None

C++: protocols::motifs::load_build_position_data(class protocols::motifs::BuildPosition &, const class std::basic_string<char> &, class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.motifs.make_base_pair_mutation(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, na: pyrosetta.rosetta.core.chemical.AA) → None

C++: protocols::motifs::make_base_pair_mutation(class core::pose::Pose &, const unsigned long, const enum core::chemical::AA &) –> void

pyrosetta.rosetta.protocols.motifs.make_dna_mutations(*args, **kwargs)

Overloaded function.

1. make_dna_mutations(pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::motifs::make_dna_mutations(class core::pose::Pose &) –> void

2. make_dna_mutations(pose: pyrosetta.rosetta.core.pose.Pose, targeted_dna: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> None

C++: protocols::motifs::make_dna_mutations(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::dna::DnaDesignDef>, class std::allocator<class std::shared_ptr<class protocols::dna::DnaDesignDef> > > &) –> void

pyrosetta.rosetta.protocols.motifs.mutate_loops_for_search(pose: pyrosetta.rosetta.core.pose.Pose, flex_regions: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::motifs::mutate_loops_for_search(class core::pose::Pose &, class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.motifs.mutate_position_vector_for_search(pose: pyrosetta.rosetta.core.pose.Pose, trim_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::motifs::mutate_position_vector_for_search(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.motifs.name3_from_oneletter(oneletter: str) → str

C++: protocols::motifs::name3_from_oneletter(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.motifs.parallel_base_test(pose_dna: pyrosetta.rosetta.core.conformation.Residue, motif_dna: pyrosetta.rosetta.core.conformation.Residue) → float

C++: protocols::motifs::parallel_base_test(const class core::conformation::Residue &, const class core::conformation::Residue &) –> double

pyrosetta.rosetta.protocols.motifs.setup_conformer_map(conformerOPs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t

C++: protocols::motifs::setup_conformer_map(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> const class std::map<std::string, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > > > >

pyrosetta.rosetta.protocols.motifs.single_ligand_motif_from_stream(motif_info: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::single_ligand_motif_from_stream(class std::basic_istream<char> &) –> class std::shared_ptr<class protocols::motifs::SingleMotif>

pyrosetta.rosetta.protocols.motifs.single_motif_from_filename(motif_filename: pyrosetta.rosetta.utility.file.FileName) → pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::single_motif_from_filename(const class utility::file::FileName &) –> class std::shared_ptr<class protocols::motifs::SingleMotif>

pyrosetta.rosetta.protocols.motifs.single_motif_from_stream(*args, **kwargs)

Overloaded function.

1. single_motif_from_stream(motif_info: pyrosetta.rosetta.utility.io.izstream) -> pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::single_motif_from_stream(class utility::io::izstream &) –> class std::shared_ptr<class protocols::motifs::SingleMotif>

2. single_motif_from_stream(motif_info: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::single_motif_from_stream(class std::basic_istream<char> &) –> class std::shared_ptr<class protocols::motifs::SingleMotif>

pyrosetta.rosetta.protocols.motifs.single_residue_from_stream(residueinfo: pyrosetta.rosetta.utility.io.izstream) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::motifs::single_residue_from_stream(class utility::io::izstream &) –> class std::shared_ptr<class core::conformation::Residue>