motifs

Bindings for protocols::motifs namespace

class pyrosetta.rosetta.protocols.motifs.BuildPosition

Bases: pybind11_object

allowed_types(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.std.set_std_string_t

C++: protocols::motifs::BuildPosition::allowed_types() const –> const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &

assign(self: pyrosetta.rosetta.protocols.motifs.BuildPosition, : pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.protocols.motifs.BuildPosition

C++: protocols::motifs::BuildPosition::operator=(const class protocols::motifs::BuildPosition &) –> class protocols::motifs::BuildPosition &

best_motifhits(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_MotifHit_t

C++: protocols::motifs::BuildPosition::best_motifhits() const –> const class utility::vector1<class std::shared_ptr<const class protocols::motifs::MotifHit>, class std::allocator<class std::shared_ptr<const class protocols::motifs::MotifHit> > > &

best_motifs(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_Motif_t

C++: protocols::motifs::BuildPosition::best_motifs() const –> const class utility::vector1<class std::shared_ptr<const class protocols::motifs::Motif>, class std::allocator<class std::shared_ptr<const class protocols::motifs::Motif> > > &

best_rotamers(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

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

clear_data(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → None

C++: protocols::motifs::BuildPosition::clear_data() –> void

clear_rots(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → None

C++: protocols::motifs::BuildPosition::clear_rots() –> void

clone(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.protocols.motifs.BuildPosition

C++: protocols::motifs::BuildPosition::clone() const –> class std::shared_ptr<class protocols::motifs::BuildPosition>

keep_motif(self: pyrosetta.rosetta.protocols.motifs.BuildPosition, motif: protocols::motifs::Motif) → None

C++: protocols::motifs::BuildPosition::keep_motif(const class protocols::motifs::Motif &) –> void

keep_motifhit(self: pyrosetta.rosetta.protocols.motifs.BuildPosition, motifhit: protocols::motifs::MotifHit) → None

C++: protocols::motifs::BuildPosition::keep_motifhit(const class protocols::motifs::MotifHit &) –> void

keep_rotamer(self: pyrosetta.rosetta.protocols.motifs.BuildPosition, res: pyrosetta.rosetta.core.conformation.Residue) → None

C++: protocols::motifs::BuildPosition::keep_rotamer(const class core::conformation::Residue &) –> void

seqpos(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → int

C++: protocols::motifs::BuildPosition::seqpos() const –> const unsigned long &

target_positions(self: pyrosetta.rosetta.protocols.motifs.BuildPosition) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

class pyrosetta.rosetta.protocols.motifs.IRCollection

Bases: pybind11_object

find_closest_backbone(self: pyrosetta.rosetta.protocols.motifs.IRCollection, pose: pyrosetta.rosetta.core.pose.Pose, flexible_positions: pyrosetta.rosetta.protocols.loops.Loops, closest_pos: pyrosetta.rosetta.utility.vector1_unsigned_long, closest_rmsd: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::motifs::IRCollection::find_closest_backbone(class core::pose::Pose &, const class std::shared_ptr<class protocols::loops::Loops>, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

incorporate_motifs(self: pyrosetta.rosetta.protocols.motifs.IRCollection, pose: pyrosetta.rosetta.core.pose.Pose, flexible_positions: pyrosetta.rosetta.protocols.loops.Loops, trim_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::motifs::IRCollection::incorporate_motifs(class core::pose::Pose &, const class std::shared_ptr<class protocols::loops::Loops>, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

increment_unique_id(self: pyrosetta.rosetta.protocols.motifs.IRCollection) → None

C++: protocols::motifs::IRCollection::increment_unique_id() –> void

nirotamers(self: pyrosetta.rosetta.protocols.motifs.IRCollection) → int

C++: protocols::motifs::IRCollection::nirotamers() const –> unsigned long

reset_unique_id(self: pyrosetta.rosetta.protocols.motifs.IRCollection) → None

C++: protocols::motifs::IRCollection::reset_unique_id() –> void

unique_id(self: pyrosetta.rosetta.protocols.motifs.IRCollection) → int

C++: protocols::motifs::IRCollection::unique_id() –> unsigned long

class pyrosetta.rosetta.protocols.motifs.LigandMotifSearch

Bases: pybind11_object

BuildPosition_from_Size(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BP: int) → None

C++: protocols::motifs::LigandMotifSearch::BuildPosition_from_Size(const class core::pose::Pose &, const unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, src: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.protocols.motifs.LigandMotifSearch

C++: protocols::motifs::LigandMotifSearch::operator=(const class protocols::motifs::LigandMotifSearch &) –> class protocols::motifs::LigandMotifSearch &

bp_rotamers(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, seqpos: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

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

build_positionOPs(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_motifs_BuildPosition_t

C++: protocols::motifs::LigandMotifSearch::build_positionOPs() const –> const class utility::vector1<class std::shared_ptr<class protocols::motifs::BuildPosition>, class std::allocator<class std::shared_ptr<class protocols::motifs::BuildPosition> > > &

defs2BuildPositions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → None

C++: protocols::motifs::LigandMotifSearch::defs2BuildPositions(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> > > &) –> void

defs2BuildPositions_findts(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → None

C++: protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts(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> > > &) –> void

dna_positions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

dtest_cutoff(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → float

C++: protocols::motifs::LigandMotifSearch::dtest_cutoff() const –> const double &

get_rotamers(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

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

get_sphere_aa(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, cut1: float) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

identify_motif_BuildPositions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions(const class core::pose::Pose &) –> void

identify_motif_build_positions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

incorporate_motifs(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::LigandMotifSearch::incorporate_motifs(const class core::pose::Pose &) –> void

initialize(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BPs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

map2keyvector(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, mappositions: pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::motifs::LigandMotifSearch::map2keyvector(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 > > > > >) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

minimize(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → bool

C++: protocols::motifs::LigandMotifSearch::minimize() const –> const bool &

motif_library(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_Motif_t

C++: protocols::motifs::LigandMotifSearch::motif_library() const –> const class utility::vector1<class std::shared_ptr<const class protocols::motifs::Motif>, class std::allocator<class std::shared_ptr<const class protocols::motifs::Motif> > > &

output_build_positions_only(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → bool

C++: protocols::motifs::LigandMotifSearch::output_build_positions_only() const –> const bool &

override_option_input(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, r1: float, z1: float, r2: float, z2: float, d1: float, rlevel: int) → None

C++: protocols::motifs::LigandMotifSearch::override_option_input(const double &, const double &, const double &, const double &, const double &, const unsigned long &) –> void

position_vector_setup(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::LigandMotifSearch::position_vector_setup(const class core::pose::Pose &) –> void

protein_DNA_motif_build_positions_JA(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, target_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

protein_DNA_motif_target_positions_JA(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, target_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, short_tl: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

protein_dna_motif(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → bool

C++: protocols::motifs::LigandMotifSearch::protein_dna_motif() –> bool

protein_positions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

reset_option_input(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → None

C++: protocols::motifs::LigandMotifSearch::reset_option_input() –> void

rmsd_cutoff_1(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → float

C++: protocols::motifs::LigandMotifSearch::rmsd_cutoff_1() const –> const double &

rmsd_cutoff_2(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → float

C++: protocols::motifs::LigandMotifSearch::rmsd_cutoff_2() const –> const double &

rot_level(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → int

C++: protocols::motifs::LigandMotifSearch::rot_level() const –> const unsigned long &

run(*args, **kwargs)

Overloaded function.

1. run(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BPs: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

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

2. run(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::motifs::LigandMotifSearch::run(const class core::pose::Pose &, class core::pack::task::PackerTask &) –> void

3. run(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, ligand_motif_sphere: float) -> None

C++: protocols::motifs::LigandMotifSearch::run(const class core::pose::Pose &, double &) –> void

set_motif_library(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, motiflibrary: pyrosetta.rosetta.protocols.motifs.MotifLibrary) → None

C++: protocols::motifs::LigandMotifSearch::set_motif_library(class protocols::motifs::MotifLibrary &) –> void

shorten_target_list(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, bp: int, full_tl: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

specific_build_position(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → int

C++: protocols::motifs::LigandMotifSearch::specific_build_position() const –> const unsigned long &

target_conformers_map(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t

C++: protocols::motifs::LigandMotifSearch::target_conformers_map() const –> 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> > > > > > &

target_positions(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t

C++: protocols::motifs::LigandMotifSearch::target_positions() const –> const 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 > > > > > &

ztest_cutoff_1(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → float

C++: protocols::motifs::LigandMotifSearch::ztest_cutoff_1() const –> const double &

ztest_cutoff_2(self: pyrosetta.rosetta.protocols.motifs.LigandMotifSearch) → float

C++: protocols::motifs::LigandMotifSearch::ztest_cutoff_2() const –> const double &

class pyrosetta.rosetta.protocols.motifs.Motif

Bases: pybind11_object

apply_check(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, pos: int) → bool

C++: protocols::motifs::Motif::apply_check(const class core::pose::Pose &, const unsigned long) const –> bool

assign(self: pyrosetta.rosetta.protocols.motifs.Motif, : pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.protocols.motifs.Motif

C++: protocols::motifs::Motif::operator=(const class protocols::motifs::Motif &) –> class protocols::motifs::Motif &

backward_check(self: pyrosetta.rosetta.protocols.motifs.Motif, check_res: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: protocols::motifs::Motif::backward_check(const class core::conformation::Residue &) const –> bool

backward_jump(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::motifs::Motif::backward_jump() const –> const class core::kinematics::Jump &

build_inverted_rotamers(*args, **kwargs)

Overloaded function.

1. build_inverted_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, motif_anchor_position: int, use_forward: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

2. build_inverted_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, motif_anchor_position: int, use_forward: bool, rotamer_build_position: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

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

build_rotamers(*args, **kwargs)

Overloaded function.

1. build_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, ex_: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

2. build_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, ex_: int, res2: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

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

clone(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.protocols.motifs.Motif

C++: protocols::motifs::Motif::clone() const –> class std::shared_ptr<class protocols::motifs::Motif>

forward_check(self: pyrosetta.rosetta.protocols.motifs.Motif, check_res: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: protocols::motifs::Motif::forward_check(const class core::conformation::Residue &) const –> bool

forward_jump(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::motifs::Motif::forward_jump() const –> const class core::kinematics::Jump &

has_path(self: pyrosetta.rosetta.protocols.motifs.Motif) → bool

C++: protocols::motifs::Motif::has_path() const –> bool

has_remark(self: pyrosetta.rosetta.protocols.motifs.Motif) → bool

C++: protocols::motifs::Motif::has_remark() const –> bool

path(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::path() const –> const std::string &

place_atom(*args, **kwargs)

Overloaded function.

1. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom) -> None

2. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool) -> None

3. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool, atomtype: str) -> None

C++: protocols::motifs::Motif::place_atom(const class core::conformation::Residue &, class core::conformation::Residue &, class core::conformation::Atom &, bool, const std::string &) const –> void

4. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int) -> None

5. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atom(const class core::conformation::Residue &, class core::conformation::Residue &, class core::conformation::Atom &, const unsigned long &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atom_(*args, **kwargs)

Overloaded function.

1. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom) -> None

2. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool) -> None

3. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool, atomtype: str) -> None

C++: protocols::motifs::Motif::place_atom_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, class core::conformation::Atom &, bool, const std::string &) const –> void

4. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int) -> None

5. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atom_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, class core::conformation::Atom &, const unsigned long &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atoms(*args, **kwargs)

Overloaded function.

1. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_std_string, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool) const –> void

3. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atoms_(*args, **kwargs)

Overloaded function.

1. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_std_string, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool) const –> void

3. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_residue(*args, **kwargs)

Overloaded function.

1. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue) -> None

2. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue(const class core::conformation::Residue &, class core::conformation::Residue &, bool) const –> void

3. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue(const class core::conformation::Residue &, class core::conformation::Residue &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_residue_(*args, **kwargs)

Overloaded function.

1. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool) -> None

2. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, bool) const –> void

3. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

print(*args, **kwargs)

Overloaded function.

1. print(self: pyrosetta.rosetta.protocols.motifs.Motif, os: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::motifs::Motif::print(std::ostream &) const –> void

2. print(self: pyrosetta.rosetta.protocols.motifs.Motif) -> str

C++: protocols::motifs::Motif::print() const –> std::string

remark(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::remark() const –> const std::string &

res1_atom1_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom1_index() const –> const unsigned long &

res1_atom1_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

WARNING res*_atom*_int() values are not consistently initialized in constructors

C++: protocols::motifs::Motif::res1_atom1_int() const –> const int &

res1_atom1_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom1_name() const –> const std::string &

res1_atom2_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom2_index() const –> const unsigned long &

res1_atom2_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom2_int() const –> const int &

res1_atom2_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom2_name() const –> const std::string &

res1_atom3_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom3_index() const –> const unsigned long &

res1_atom3_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom3_int() const –> const int &

res1_atom3_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom3_name() const –> const std::string &

res2_atom1_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom1_index() const –> const unsigned long &

res2_atom1_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

WARNING res*_atom*_int() values are not consistently initialized in constructors

C++: protocols::motifs::Motif::res2_atom1_int() const –> const int &

res2_atom1_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom1_name() const –> const std::string &

res2_atom2_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom2_index() const –> const unsigned long &

res2_atom2_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom2_int() const –> const int &

res2_atom2_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom2_name() const –> const std::string &

res2_atom3_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom3_index() const –> const unsigned long &

res2_atom3_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom3_int() const –> const int &

res2_atom3_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom3_name() const –> const std::string &

restype_name1(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::restype_name1() const –> const std::string &

restype_name2(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::restype_name2() const –> const std::string &

store_path(self: pyrosetta.rosetta.protocols.motifs.Motif, path_in: str) → None

C++: protocols::motifs::Motif::store_path(const std::string &) –> void

store_remark(self: pyrosetta.rosetta.protocols.motifs.Motif, remark_in: str) → None

C++: protocols::motifs::Motif::store_remark(const std::string &) –> void

class pyrosetta.rosetta.protocols.motifs.MotifDnaPacker

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPacker, : pyrosetta.rosetta.core.pose.Pose) → None

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

assign(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPacker, : pyrosetta.rosetta.protocols.motifs.MotifDnaPacker) → pyrosetta.rosetta.protocols.motifs.MotifDnaPacker

C++: protocols::motifs::MotifDnaPacker::operator=(const class protocols::motifs::MotifDnaPacker &) –> class protocols::motifs::MotifDnaPacker &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPacker) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::motifs::MotifDnaPacker::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPacker) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::motifs::MotifDnaPacker::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPacker) → str

C++: protocols::motifs::MotifDnaPacker::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str

C++: protocols::motifs::MotifDnaPacker::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

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

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

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::motifs::MotifDnaPacker::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator, : pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator) → pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator

C++: protocols::motifs::MotifDnaPackerCreator::operator=(const class protocols::motifs::MotifDnaPackerCreator &) –> class protocols::motifs::MotifDnaPackerCreator &

create_mover(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::motifs::MotifDnaPackerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator) → str

C++: protocols::motifs::MotifDnaPackerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::motifs::MotifDnaPackerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.motifs.MotifHit

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.motifs.MotifHit, : pyrosetta.rosetta.protocols.motifs.MotifHit) → pyrosetta.rosetta.protocols.motifs.MotifHit

C++: protocols::motifs::MotifHit::operator=(const class protocols::motifs::MotifHit &) –> class protocols::motifs::MotifHit &

build_rotamer(*args, **kwargs)

Overloaded function.

1. build_rotamer(self: pyrosetta.rosetta.protocols.motifs.MotifHit, build_rotamer: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::motifs::MotifHit::build_rotamer(const class core::conformation::Residue &) –> void

2. build_rotamer(self: pyrosetta.rosetta.protocols.motifs.MotifHit) -> pyrosetta.rosetta.core.conformation.Residue

C++: protocols::motifs::MotifHit::build_rotamer() const –> const class std::shared_ptr<class core::conformation::Residue> &

clone(self: pyrosetta.rosetta.protocols.motifs.MotifHit) → pyrosetta.rosetta.protocols.motifs.MotifHit

C++: protocols::motifs::MotifHit::clone() const –> class std::shared_ptr<class protocols::motifs::MotifHit>

dump_motif_hit(self: pyrosetta.rosetta.protocols.motifs.MotifHit) → None

C++: protocols::motifs::MotifHit::dump_motif_hit() –> void

final_test(*args, **kwargs)

Overloaded function.

1. final_test(self: pyrosetta.rosetta.protocols.motifs.MotifHit, final_test: float) -> None

C++: protocols::motifs::MotifHit::final_test(const double &) –> void

2. final_test(self: pyrosetta.rosetta.protocols.motifs.MotifHit) -> float

C++: protocols::motifs::MotifHit::final_test() const –> const double &

motifcop(self: pyrosetta.rosetta.protocols.motifs.MotifHit) → pyrosetta.rosetta.protocols.motifs.Motif

C++: protocols::motifs::MotifHit::motifcop() const –> const class std::shared_ptr<const class protocols::motifs::Motif> &

passed_automorphism(self: pyrosetta.rosetta.protocols.motifs.MotifHit) → bool

C++: protocols::motifs::MotifHit::passed_automorphism() const –> const bool &

target_conformer(*args, **kwargs)

Overloaded function.

1. target_conformer(self: pyrosetta.rosetta.protocols.motifs.MotifHit, target_conformer: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::motifs::MotifHit::target_conformer(const class core::conformation::Residue &) –> void

2. target_conformer(self: pyrosetta.rosetta.protocols.motifs.MotifHit) -> pyrosetta.rosetta.core.conformation.Residue

C++: protocols::motifs::MotifHit::target_conformer() const –> const class std::shared_ptr<class core::conformation::Residue> &

vbpos(self: pyrosetta.rosetta.protocols.motifs.MotifHit) → int

C++: protocols::motifs::MotifHit::vbpos() const –> const unsigned long &

class pyrosetta.rosetta.protocols.motifs.MotifLibrary

Bases: pybind11_object

add_from_file(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary, motif_filename: str) → None

C++: protocols::motifs::MotifLibrary::add_from_file(const std::string &) –> void

add_ligand_from_file(*args, **kwargs)

Overloaded function.

1. add_ligand_from_file(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary, motif_filename: str) -> None

C++: protocols::motifs::MotifLibrary::add_ligand_from_file(const std::string &) –> void

2. add_ligand_from_file(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary, motif_filename: str, check_for_bad_motifs: bool, ligand_atom_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::motifs::MotifLibrary::add_ligand_from_file(const std::string &, bool, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

add_to_library(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary, new_motif: protocols::motifs::Motif) → None

C++: protocols::motifs::MotifLibrary::add_to_library(const class protocols::motifs::Motif &) –> void

assign(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary, : pyrosetta.rosetta.protocols.motifs.MotifLibrary) → pyrosetta.rosetta.protocols.motifs.MotifLibrary

C++: protocols::motifs::MotifLibrary::operator=(const class protocols::motifs::MotifLibrary &) –> class protocols::motifs::MotifLibrary &

library(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_Motif_t

C++: protocols::motifs::MotifLibrary::library() const –> const class utility::vector1<class std::shared_ptr<const class protocols::motifs::Motif>, class std::allocator<class std::shared_ptr<const class protocols::motifs::Motif> > > &

nmotifs(self: pyrosetta.rosetta.protocols.motifs.MotifLibrary) → int

C++: protocols::motifs::MotifLibrary::nmotifs() –> unsigned long

class pyrosetta.rosetta.protocols.motifs.MotifSearch

Bases: pybind11_object

BuildPosition_from_Size(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BP: int) → None

C++: protocols::motifs::MotifSearch::BuildPosition_from_Size(const class core::pose::Pose &, const unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, src: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.protocols.motifs.MotifSearch

C++: protocols::motifs::MotifSearch::operator=(const class protocols::motifs::MotifSearch &) –> class protocols::motifs::MotifSearch &

bp_motifhits(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, seqpos: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_MotifHit_t

C++: protocols::motifs::MotifSearch::bp_motifhits(const unsigned long) –> class utility::vector1<class std::shared_ptr<const class protocols::motifs::MotifHit>, class std::allocator<class std::shared_ptr<const class protocols::motifs::MotifHit> > >

bp_rotamers(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, seqpos: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

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

build_positionOPs(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_motifs_BuildPosition_t

C++: protocols::motifs::MotifSearch::build_positionOPs() const –> const class utility::vector1<class std::shared_ptr<class protocols::motifs::BuildPosition>, class std::allocator<class std::shared_ptr<class protocols::motifs::BuildPosition> > > &

defs2BuildPositions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → None

C++: protocols::motifs::MotifSearch::defs2BuildPositions(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> > > &) –> void

defs2BuildPositions_findts(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, defs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) → None

C++: protocols::motifs::MotifSearch::defs2BuildPositions_findts(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> > > &) –> void

dna_positions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

dtest_cutoff(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → float

C++: protocols::motifs::MotifSearch::dtest_cutoff() const –> const double &

identify_motif_BuildPositions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::MotifSearch::identify_motif_BuildPositions(const class core::pose::Pose &) –> void

identify_motif_build_positions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

incorporate_motifs(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::MotifSearch::incorporate_motifs(const class core::pose::Pose &) –> void

initialize(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BPs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

map2keyvector(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, mappositions: pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::motifs::MotifSearch::map2keyvector(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 > > > > >) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

minimize(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → bool

C++: protocols::motifs::MotifSearch::minimize() const –> const bool &

motif_library(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_Motif_t

C++: protocols::motifs::MotifSearch::motif_library() const –> const class utility::vector1<class std::shared_ptr<const class protocols::motifs::Motif>, class std::allocator<class std::shared_ptr<const class protocols::motifs::Motif> > > &

override_option_input(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, r1: float, z1: float, r2: float, z2: float, d1: float, rlevel: int, bpdata: bool, bump_check: bool) → None

C++: protocols::motifs::MotifSearch::override_option_input(const double &, const double &, const double &, const double &, const double &, const unsigned long &, const bool, const bool) –> void

position_vector_setup(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::motifs::MotifSearch::position_vector_setup(const class core::pose::Pose &) –> void

protein_DNA_motif_build_positions_JA(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, target_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

protein_DNA_motif_target_positions_JA(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, build_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, target_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, short_tl: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

protein_dna_motif(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → bool

C++: protocols::motifs::MotifSearch::protein_dna_motif() –> bool

protein_positions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

reset_option_input(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → None

C++: protocols::motifs::MotifSearch::reset_option_input() –> void

rmsd_cutoff_1(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → float

C++: protocols::motifs::MotifSearch::rmsd_cutoff_1() const –> const double &

rmsd_cutoff_2(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → float

C++: protocols::motifs::MotifSearch::rmsd_cutoff_2() const –> const double &

rot_level(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → int

C++: protocols::motifs::MotifSearch::rot_level() const –> const unsigned long &

run(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, input_BPs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

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

set_motif_library(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, motiflibrary: pyrosetta.rosetta.protocols.motifs.MotifLibrary) → None

C++: protocols::motifs::MotifSearch::set_motif_library(class protocols::motifs::MotifLibrary &) –> void

shorten_target_list(self: pyrosetta.rosetta.protocols.motifs.MotifSearch, pose: pyrosetta.rosetta.core.pose.Pose, bp: int, full_tl: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

target_conformers_map(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t

C++: protocols::motifs::MotifSearch::target_conformers_map() const –> 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> > > > > > &

target_positions(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t

C++: protocols::motifs::MotifSearch::target_positions() const –> const 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 > > > > > &

ztest_cutoff_1(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → float

C++: protocols::motifs::MotifSearch::ztest_cutoff_1() const –> const double &

ztest_cutoff_2(self: pyrosetta.rosetta.protocols.motifs.MotifSearch) → float

C++: protocols::motifs::MotifSearch::ztest_cutoff_2() const –> const double &

class pyrosetta.rosetta.protocols.motifs.SingleMotif

Bases: Motif

apply_check(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, pos: int) → bool

C++: protocols::motifs::Motif::apply_check(const class core::pose::Pose &, const unsigned long) const –> bool

assign(self: pyrosetta.rosetta.protocols.motifs.SingleMotif, : pyrosetta.rosetta.protocols.motifs.SingleMotif) → pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::SingleMotif::operator=(const class protocols::motifs::SingleMotif &) –> class protocols::motifs::SingleMotif &

backward_check(self: pyrosetta.rosetta.protocols.motifs.Motif, check_res: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: protocols::motifs::Motif::backward_check(const class core::conformation::Residue &) const –> bool

backward_jump(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::motifs::Motif::backward_jump() const –> const class core::kinematics::Jump &

build_inverted_rotamers(*args, **kwargs)

Overloaded function.

1. build_inverted_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, motif_anchor_position: int, use_forward: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

2. build_inverted_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, motif_anchor_position: int, use_forward: bool, rotamer_build_position: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

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

build_rotamers(*args, **kwargs)

Overloaded function.

1. build_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, ex_: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

2. build_rotamers(self: pyrosetta.rosetta.protocols.motifs.Motif, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_build_position: int, ex_: int, res2: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

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

clone(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.protocols.motifs.Motif

C++: protocols::motifs::Motif::clone() const –> class std::shared_ptr<class protocols::motifs::Motif>

forward_check(self: pyrosetta.rosetta.protocols.motifs.Motif, check_res: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: protocols::motifs::Motif::forward_check(const class core::conformation::Residue &) const –> bool

forward_jump(self: pyrosetta.rosetta.protocols.motifs.Motif) → pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::motifs::Motif::forward_jump() const –> const class core::kinematics::Jump &

has_path(self: pyrosetta.rosetta.protocols.motifs.Motif) → bool

C++: protocols::motifs::Motif::has_path() const –> bool

has_remark(self: pyrosetta.rosetta.protocols.motifs.Motif) → bool

C++: protocols::motifs::Motif::has_remark() const –> bool

path(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::path() const –> const std::string &

place_atom(*args, **kwargs)

Overloaded function.

1. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom) -> None

2. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool) -> None

3. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool, atomtype: str) -> None

C++: protocols::motifs::Motif::place_atom(const class core::conformation::Residue &, class core::conformation::Residue &, class core::conformation::Atom &, bool, const std::string &) const –> void

4. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int) -> None

5. place_atom(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atom(const class core::conformation::Residue &, class core::conformation::Residue &, class core::conformation::Atom &, const unsigned long &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atom_(*args, **kwargs)

Overloaded function.

1. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom) -> None

2. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool) -> None

3. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, one_three: bool, atomtype: str) -> None

C++: protocols::motifs::Motif::place_atom_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, class core::conformation::Atom &, bool, const std::string &) const –> void

4. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int) -> None

5. place_atom_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atm: pyrosetta.rosetta.core.conformation.Atom, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, atomtype: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atom_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, class core::conformation::Atom &, const unsigned long &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atoms(*args, **kwargs)

Overloaded function.

1. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_std_string, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool) const –> void

3. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_atoms(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_atoms_(*args, **kwargs)

Overloaded function.

1. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_std_string, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool) const –> void

3. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_atoms_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, atoms: pyrosetta.rosetta.utility.vector1_unsigned_long, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_atoms_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_residue(*args, **kwargs)

Overloaded function.

1. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue) -> None

2. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue(const class core::conformation::Residue &, class core::conformation::Residue &, bool) const –> void

3. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_residue(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue(const class core::conformation::Residue &, class core::conformation::Residue &, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

place_residue_(*args, **kwargs)

Overloaded function.

1. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool) -> None

2. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, bool) const –> void

3. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int) -> None

4. place_residue_(self: pyrosetta.rosetta.protocols.motifs.Motif, fixed: pyrosetta.rosetta.core.conformation.Residue, mobile: pyrosetta.rosetta.core.conformation.Residue, forward: bool, res2_atom1_index_in: int, res2_atom2_index_in: int, res2_atom3_index_in: int, one_three: bool) -> None

C++: protocols::motifs::Motif::place_residue_(const class core::conformation::Residue &, class core::conformation::Residue &, bool, const unsigned long &, const unsigned long &, const unsigned long &, bool) const –> void

print(*args, **kwargs)

Overloaded function.

1. print(self: pyrosetta.rosetta.protocols.motifs.Motif, os: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::motifs::Motif::print(std::ostream &) const –> void

2. print(self: pyrosetta.rosetta.protocols.motifs.Motif) -> str

C++: protocols::motifs::Motif::print() const –> std::string

remark(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::remark() const –> const std::string &

res1_atom1_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom1_index() const –> const unsigned long &

res1_atom1_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

WARNING res*_atom*_int() values are not consistently initialized in constructors

C++: protocols::motifs::Motif::res1_atom1_int() const –> const int &

res1_atom1_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom1_name() const –> const std::string &

res1_atom2_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom2_index() const –> const unsigned long &

res1_atom2_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom2_int() const –> const int &

res1_atom2_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom2_name() const –> const std::string &

res1_atom3_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom3_index() const –> const unsigned long &

res1_atom3_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res1_atom3_int() const –> const int &

res1_atom3_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res1_atom3_name() const –> const std::string &

res2_atom1_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom1_index() const –> const unsigned long &

res2_atom1_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

WARNING res*_atom*_int() values are not consistently initialized in constructors

C++: protocols::motifs::Motif::res2_atom1_int() const –> const int &

res2_atom1_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom1_name() const –> const std::string &

res2_atom2_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom2_index() const –> const unsigned long &

res2_atom2_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom2_int() const –> const int &

res2_atom2_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom2_name() const –> const std::string &

res2_atom3_index(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom3_index() const –> const unsigned long &

res2_atom3_int(self: pyrosetta.rosetta.protocols.motifs.Motif) → int

C++: protocols::motifs::Motif::res2_atom3_int() const –> const int &

res2_atom3_name(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::res2_atom3_name() const –> const std::string &

restype_name1(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::restype_name1() const –> const std::string &

restype_name2(self: pyrosetta.rosetta.protocols.motifs.Motif) → str

C++: protocols::motifs::Motif::restype_name2() const –> const std::string &

store_path(self: pyrosetta.rosetta.protocols.motifs.Motif, path_in: str) → None

C++: protocols::motifs::Motif::store_path(const std::string &) –> void

store_remark(self: pyrosetta.rosetta.protocols.motifs.Motif, remark_in: str) → None

C++: protocols::motifs::Motif::store_remark(const std::string &) –> void

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<std::string, class std::allocator<std::string > > &) –> 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_t_std_allocator_std_pair_const_unsigned_long_std_set_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_t_std_allocator_std_pair_const_unsigned_long_std_set_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(*args, **kwargs)

Overloaded function.

1. get_LigandMotifLibrary_user() -> pyrosetta.rosetta.protocols.motifs.MotifLibrary

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

2. get_LigandMotifLibrary_user(check_for_bad_motifs: bool, ligand_atom_names: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.protocols.motifs.MotifLibrary

C++: protocols::motifs::get_LigandMotifLibrary_user(bool, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> 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_t_std_allocator_std_pair_const_unsigned_long_std_set_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 std::string &, 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 std::string &) –> 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_std_allocator_std_pair_const_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(*args, **kwargs)

Overloaded function.

1. single_ligand_motif_from_stream(motif_info: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.protocols.motifs.SingleMotif

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

2. single_ligand_motif_from_stream(motif_info: pyrosetta.rosetta.std.istream, check_for_bad_motifs: bool) -> pyrosetta.rosetta.protocols.motifs.SingleMotif

C++: protocols::motifs::single_ligand_motif_from_stream(std::istream &, bool) –> 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(std::istream &) –> 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>

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

Overloaded function.

1. write_motifs_to_disk(ml: pyrosetta.rosetta.protocols.motifs.MotifLibrary, filename: str) -> None

C++: protocols::motifs::write_motifs_to_disk(class protocols::motifs::MotifLibrary, std::string) –> void

2. write_motifs_to_disk(motifcops: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_motifs_Motif_t, filename: str) -> None

C++: protocols::motifs::write_motifs_to_disk(class utility::vector1<class std::shared_ptr<const class protocols::motifs::Motif>, class std::allocator<class std::shared_ptr<const class protocols::motifs::Motif> > >, std::string) –> void