movers

Bindings for protocols::motif_grafting::movers namespace

class pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator, : pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator) → pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator

C++: protocols::motif_grafting::movers::MotifGraftCreator::operator=(const class protocols::motif_grafting::movers::MotifGraftCreator &) –> class protocols::motif_grafting::movers::MotifGraftCreator &

create_mover(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::motif_grafting::movers::MotifGraftCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator) → str

C++: protocols::motif_grafting::movers::MotifGraftCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::motif_grafting::movers::MotifGraftCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, : pyrosetta.rosetta.core.pose.Pose) → None

Apply mover function*

C++: protocols::motif_grafting::movers::MotifGraftMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, : pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover) → pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover

C++: protocols::motif_grafting::movers::MotifGraftMover::operator=(const class protocols::motif_grafting::movers::MotifGraftMover &) –> class protocols::motif_grafting::movers::MotifGraftMover &

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.motif_grafting.movers.MotifGraftMover) → pyrosetta.rosetta.protocols.moves.Mover

Function used by roseta to create clones of movers*

C++: protocols::motif_grafting::movers::MotifGraftMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

count_clashes_between_two_poses(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_A: pyrosetta.rosetta.core.pose.Pose, p_B: pyrosetta.rosetta.core.pose.Pose, clash_cutoff: int, clash_atom_scale: float) → int

Count the Number of Clashes between two poses

C++: protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, double) –> unsigned long

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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

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

generate_combinations_of_motif_fragments_by_delta_variation(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_motif_: pyrosetta.rosetta.core.pose.Pose, combinatory_fragment_size_delta: pyrosetta.rosetta.utility.vector1_std_pair_long_long_t, min_fragment_size: int, vv_resulting_permutations: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t) → None

Generate all the combination of different legths of the motif fragment as requested in combinatory_fragment_size_delta * Uses permutate_n_vv_of_pairs to generate the permutations*

C++: protocols::motif_grafting::movers::MotifGraftMover::generate_combinations_of_motif_fragments_by_delta_variation(const class std::shared_ptr<class core::pose::Pose> &, const class utility::vector1<struct std::pair<long, long>, class std::allocator<struct std::pair<long, long> > > &, unsigned long, class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > > &) –> void

generate_match_pose(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, target_pose: pyrosetta.rosetta.core.pose.Pose, contextStructure: pyrosetta.rosetta.core.pose.Pose, b_revert_graft_to_native_sequence: bool, motif_match: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → None

Generate pose corresponding to the given match *

C++: protocols::motif_grafting::movers::MotifGraftMover::generate_match_pose(class core::pose::Pose &, const class core::pose::Pose &, bool, class protocols::motif_grafting::movers::MotifMatch) –> void

generate_scaffold_matches(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, target_scaffold: pyrosetta.rosetta.core.pose.Pose, target_motif_: pyrosetta.rosetta.core.pose.Pose, target_contextStructure_: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t

Identify all potential matches for the given target scaffold (this is where the motif grafting code is called)*

C++: protocols::motif_grafting::movers::MotifGraftMover::generate_scaffold_matches(class core::pose::Pose &, class std::shared_ptr<class core::pose::Pose> &, class std::shared_ptr<class core::pose::Pose> &) –> class std::priority_queue<class protocols::motif_grafting::movers::MotifMatch, class std::vector<class protocols::motif_grafting::movers::MotifMatch, class std::allocator<class protocols::motif_grafting::movers::MotifMatch> >, struct std::less<class protocols::motif_grafting::movers::MotifMatch> >

get_additional_output(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover) → pyrosetta.rosetta.core.pose.Pose

Iterate over the results to get additional matches in the queue*

C++: protocols::motif_grafting::movers::MotifGraftMover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_bb_alignment_and_transformation(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, poseA: pyrosetta.rosetta.core.pose.Pose, positions_to_alignA: pyrosetta.rosetta.utility.vector1_unsigned_long, poseB: pyrosetta.rosetta.core.pose.Pose, positions_to_alignB: pyrosetta.rosetta.utility.vector1_unsigned_long, RotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, TvecA: pyrosetta.rosetta.numeric.xyzVector_double_t, TvecB: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Performs alignment of the protein BB on the selected aminoacids. *Returns the RMSD, *Returns by reference the rotation Matrix and Translation Vector, *Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. *Will fail if the number of residues to align is not the same in the two poses. *

C++: protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> double

get_bb_alignment_and_transformation_wTipsExtraInfo(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, v_isNorC: pyrosetta.rosetta.utility.vector1_bool, poseA: pyrosetta.rosetta.core.pose.Pose, positions_to_alignA: pyrosetta.rosetta.utility.vector1_unsigned_long, poseB: pyrosetta.rosetta.core.pose.Pose, positions_to_alignB: pyrosetta.rosetta.utility.vector1_unsigned_long, RotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, TvecA: pyrosetta.rosetta.numeric.xyzVector_double_t, TvecB: pyrosetta.rosetta.numeric.xyzVector_double_t, RMSD_tip_elements: pyrosetta.rosetta.utility.vector1_double) → float

Performs alignment of the protein BB on the selected aminoacids. *Returns the RMSD, *Returns by reference the rotation Matrix and Translation Vector, *Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. *Will fail if the number of residues to align is not the same in the two poses. *

C++: protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation_wTipsExtraInfo(const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class utility::vector1<double, class std::allocator<double> > &) –> double

get_bb_distance(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, poseA: pyrosetta.rosetta.core.pose.Pose, positions_to_alignA: pyrosetta.rosetta.utility.vector1_unsigned_long, poseB: pyrosetta.rosetta.core.pose.Pose, positions_to_alignB: pyrosetta.rosetta.utility.vector1_unsigned_long) → float

Returns the BB distance of two poses respect to indexes*

C++: protocols::motif_grafting::movers::MotifGraftMover::get_bb_distance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> double

get_clash_score_from_pose(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_input: pyrosetta.rosetta.core.pose.Pose, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → float

Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure*

C++: protocols::motif_grafting::movers::MotifGraftMover::get_clash_score_from_pose(class core::pose::Pose &, const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> double

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_fragments_by_CA_distances_and_NCpoints_restrains(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_scaffold: pyrosetta.rosetta.core.pose.Pose, p_motif_: pyrosetta.rosetta.core.pose.Pose, vv_scaffold_fragments_indexes: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t, v_motif_fragments_indexes: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, RMSD_tol: float, max_fragment_replacement_size_delta: pyrosetta.rosetta.utility.vector1_std_pair_long_long_t, v_motif_fragments_permutation: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, b_only_allow_if_N_point_match_aa_identity: bool, b_only_allow_if_C_point_match_aa_identity: bool, b_N_point_can_replace_proline: bool, b_C_point_can_replace_proline: bool) → bool

returns by reference two vectors of indexes (vv_scaffold_fragments_indexes, v_motif_fragments_indexes) * that hold the lower and upper bounds of the fragments. Indeed the corresponding to the scaffold one is a vector of vectors, since each pose_scaffold can have many matches

C++: protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(const class core::pose::Pose &, const class std::shared_ptr<class core::pose::Pose> &, class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > > &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const double &, const class utility::vector1<struct std::pair<long, long>, class std::allocator<struct std::pair<long, long> > > &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const bool &, const bool &, const bool &, const bool &) –> bool

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_matching_fragments(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, target_scaffold: pyrosetta.rosetta.core.pose.Pose, target_motif_: pyrosetta.rosetta.core.pose.Pose, target_contextStructure_: pyrosetta.rosetta.core.pose.Pose, RMSD_tol: float, NC_points_RMSD_tol: float, clash_atom_scale: float, clash_cutoff: int, min_fragment_size: int, clash_test_residue: str, max_fragment_replacement_size_delta_: pyrosetta.rosetta.utility.vector1_std_pair_long_long_t, combinatory_fragment_size_delta: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, vvr_hotspots: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, b_full_motif_bb_alignment: bool, b_allow_independent_alignment_per_fragment: bool, b_graft_only_hotspots_by_sidechain_replacement: bool, b_only_allow_if_N_point_match_aa_identity: bool, b_only_allow_if_C_point_match_aa_identity: bool, pq: pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t) → None

Return a priority queue with the sucessful epigrafts *

C++: protocols::motif_grafting::movers::MotifGraftMover::get_matching_fragments(const class core::pose::Pose &, const class std::shared_ptr<class core::pose::Pose> &, const class std::shared_ptr<class core::pose::Pose> &, const double &, const double &, const double &, const unsigned long &, const unsigned long &, const std::string &, const class utility::vector1<struct std::pair<long, long>, class std::allocator<struct std::pair<long, long> > > &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const bool &, const bool &, const bool &, const bool &, const bool &, class std::priority_queue<class protocols::motif_grafting::movers::MotifMatch, class std::vector<class protocols::motif_grafting::movers::MotifMatch, class std::allocator<class protocols::motif_grafting::movers::MotifMatch> >, struct std::less<class protocols::motif_grafting::movers::MotifMatch> > &) –> void

get_mono_aa_pose_copy(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_input: pyrosetta.rosetta.core.pose.Pose, aminoacid_code: str) → pyrosetta.rosetta.core.pose.Pose

returns a copy of the pose that replaces all the aminoacids for a single selected aminoacid*

C++: protocols::motif_grafting::movers::MotifGraftMover::get_mono_aa_pose_copy(const class core::pose::Pose &, const std::string &) –> class core::pose::Pose

get_name(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover) → str

C++: protocols::motif_grafting::movers::MotifGraftMover::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_next_nonredundant_motifmatch(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, match: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch, match_xform: pyrosetta.rosetta.numeric.HomogeneousTransform_double_t) → bool

Used during output to discard redundant results *

C++: protocols::motif_grafting::movers::MotifGraftMover::get_next_nonredundant_motifmatch(class protocols::motif_grafting::movers::MotifMatch &, class numeric::HomogeneousTransform<double> &) –> bool

get_next_output(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, work_pose: pyrosetta.rosetta.core.pose.Pose) → bool

Used during output to discard redundant results and apply filter *

C++: protocols::motif_grafting::movers::MotifGraftMover::get_next_output(class core::pose::Pose &) –> bool

get_rotated_and_translated_pose(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_scaffold: pyrosetta.rosetta.core.pose.Pose, RotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, TvecA: pyrosetta.rosetta.numeric.xyzVector_double_t, TvecB: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.core.pose.Pose

Function that returns by reference a rotated copy of the pose

C++: protocols::motif_grafting::movers::MotifGraftMover::get_rotated_and_translated_pose(const class core::pose::Pose &, const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> 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 > > &

init_parameters(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, s_contextStructure: str, s_motif: str, r_RMSD_tolerance: float, r_NC_points_RMSD_tolerance: float, gp_r_clash_atom_scale: float, i_clash_score_cutoff: int, i_min_fragment_size: int, s_combinatory_fragment_size_delta: str, s_max_fragment_replacement_size_delta: str, s_clash_test_residue: str, s_hotspots: str, b_full_motif_bb_alignment: bool, b_allow_independent_alignment_per_fragment: bool, b_graft_only_hotspots_by_sidechain_replacement: bool, b_only_allow_if_N_point_match_aa_identity: bool, b_only_allow_if_C_point_match_aa_identity: bool, b_revert_graft_to_native_sequence: bool, b_allow_repeat_same_graft_output: bool, b_reinit_every_apply: bool, r_output_cluster_tolerance: float, f_output_filter: pyrosetta.rosetta.protocols.filters.Filter) → None

MotifGraftMover parameters and options initializer*

C++: protocols::motif_grafting::movers::MotifGraftMover::init_parameters(const std::string &, const std::string &, const double &, const double &, const double &, const unsigned long &, const unsigned long &, const std::string &, const std::string &, const std::string &, const std::string &, bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const double &, const class std::shared_ptr<const class protocols::filters::Filter> &) –> void

join_two_poses_by_jump(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_A: pyrosetta.rosetta.core.pose.Pose, p_B: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose

returns a pose with two input poses merged (with a jump in-between) and with the PDB info corrected

C++: protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(const class core::pose::Pose &, const class core::pose::Pose &) –> class core::pose::Pose

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::motif_grafting::movers::MotifGraftMover::mover_name() –> std::string

static name() → str

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

parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, s_contextStructure: str, s_motif: str, r_RMSD_tolerance: float, r_NC_points_RMSD_tolerance: float, r_clash_atom_scale: float, i_clash_score_cutoff: int, i_min_fragment_size: int, s_combinatory_fragment_size_delta: str, s_max_fragment_replacement_size_delta: str, s_clash_test_residue: str, s_hotspots: str, b_full_motif_bb_alignment: bool, b_allow_independent_alignment_per_fragment: bool, b_graft_only_hotspots_by_sidechain_replacement: bool, b_only_allow_if_N_point_match_aa_identity: bool, b_only_allow_if_C_point_match_aa_identity: bool, b_revert_graft_to_native_sequence: bool, b_allow_repeat_same_graft_output: bool, b_reinit_every_apply: bool, r_output_cluster_tolerance: float, f_output_filter: pyrosetta.rosetta.protocols.filters.Filter) → None

C++: protocols::motif_grafting::movers::MotifGraftMover::parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(const std::string &, const std::string &, const double &, const double &, const double &, const unsigned long &, const unsigned long &, const std::string &, const std::string &, const std::string &, const std::string &, bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const bool &, const double &, const class std::shared_ptr<const class protocols::filters::Filter> &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Fuction to parse RosettaScripts XML options*

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

permutate_n_vv_of_pairs(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, vv_of_pairs: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t, buff_combVec: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, start_index: int, vv_resulting_permutations: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t) → None

As the name suggests in generates all the permutations of a vector of vectors of pairs (Alex: we should templatize this! Maybe alrready there?)*

C++: protocols::motif_grafting::movers::MotifGraftMover::permutate_n_vv_of_pairs(const class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > > &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, unsigned long, class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > > &) –> 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::motif_grafting::movers::MotifGraftMover::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

stich_motif_in_scaffold_by_indexes_rotation_and_translation(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, p_scaffold: pyrosetta.rosetta.core.pose.Pose, p_motif_: pyrosetta.rosetta.core.pose.Pose, m2s_dat: pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data, skip_motif_extremes: bool) → pyrosetta.rosetta.core.pose.Pose

Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure*

C++: protocols::motif_grafting::movers::MotifGraftMover::stich_motif_in_scaffold_by_indexes_rotation_and_translation(const class core::pose::Pose &, const class core::pose::Pose &, struct protocols::motif_grafting::movers::motif2scaffold_data &, const bool &) –> class core::pose::Pose

superposition_transform(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover, natoms: int, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, ref_coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, RotM: pyrosetta.rosetta.numeric.xyzMatrix_double_t, TvecA: pyrosetta.rosetta.numeric.xyzVector_double_t, TvecB: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Helper Fortran wrapper to get the aligment of two matrixes as well as the corresponding transform*

C++: protocols::motif_grafting::movers::MotifGraftMover::superposition_transform(unsigned long, const class ObjexxFCL::FArray1<double> &, class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> 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.motif_grafting.movers.MotifMatch

Bases: pybind11_object

b_is_full_motif_bb_alignment(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → bool

C++: protocols::motif_grafting::movers::MotifMatch::b_is_full_motif_bb_alignment() const –> bool

get_RMSD(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → float

C++: protocols::motif_grafting::movers::MotifMatch::get_RMSD() const –> double

get_allow_independent_alignment_per_fragment_mode(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → str

C++: protocols::motif_grafting::movers::MotifMatch::get_allow_independent_alignment_per_fragment_mode() const –> std::string

get_clash_score(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → float

C++: protocols::motif_grafting::movers::MotifMatch::get_clash_score() const –> double

get_full_motif_bb_alignment_mode(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → str

C++: protocols::motif_grafting::movers::MotifMatch::get_full_motif_bb_alignment_mode() const –> std::string

get_homogeneous_transform_com_from_orig(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch, com: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

C++: protocols::motif_grafting::movers::MotifMatch::get_homogeneous_transform_com_from_orig(class numeric::xyzVector<double>) const –> class numeric::HomogeneousTransform<double>

get_motif_fragments_RMSD(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → float

C++: protocols::motif_grafting::movers::MotifMatch::get_motif_fragments_RMSD() const –> double

get_motif_ranges(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch, ndx_shift: int) → str

C++: protocols::motif_grafting::movers::MotifMatch::get_motif_ranges(const unsigned long &) const –> std::string

get_scaffold2motif_size_change(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → str

C++: protocols::motif_grafting::movers::MotifMatch::get_scaffold2motif_size_change() const –> std::string

get_scaffold_fragment_data(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch) → pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data

C++: protocols::motif_grafting::movers::MotifMatch::get_scaffold_fragment_data() const –> struct protocols::motif_grafting::movers::motif2scaffold_data

get_scaffold_ranges(self: pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch, ndx_shift: int) → str

C++: protocols::motif_grafting::movers::MotifMatch::get_scaffold_ranges(const unsigned long &) const –> std::string

pyrosetta.rosetta.protocols.motif_grafting.movers.compare_motif2scaffold_data_by_scaffold_low2high(a: pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes, b: pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes) → bool

C++: protocols::motif_grafting::movers::compare_motif2scaffold_data_by_scaffold_low2high(const struct protocols::motif_grafting::movers::motif2scaffold_indexes &, const struct protocols::motif_grafting::movers::motif2scaffold_indexes &) –> bool

class pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data

Bases: pybind11_object

structure that contains the motif2scaffold_indexes data in a vector and adds fields for fragment matching information*

property RMSD

property RotM

property TvecA

property TvecB

assign(self: pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data, : pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data) → pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data

C++: protocols::motif_grafting::movers::motif2scaffold_data::operator=(const struct protocols::motif_grafting::movers::motif2scaffold_data &) –> struct protocols::motif_grafting::movers::motif2scaffold_data &

property b_allow_independent_alignment_per_fragment

property b_full_motif_bb_alignment

property b_graft_only_hotspots_by_sidechain_replacement

property clash_score

property motif_fragments_RMSD

property v_indexes

property vvr_hotspots

class pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes

Bases: pybind11_object

structure that contains the data of corresponding fragments in the motif and scaffold*

property motifHigh

property motifLow

property scaffoldHigh

property scaffoldLow