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- addScoresForLoopParts(...) method of builtins.PyCapsule instance
- addScoresForLoopParts(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction, native_pose : rosetta.core.pose.Pose, nloops : int) -> NoneType
- add_coordinate_constraints_to_pose(...) method of builtins.PyCapsule instance
- add_coordinate_constraints_to_pose(pose : rosetta.core.pose.Pose, constraint_target_pose : rosetta.core.pose.Pose, exclude_regions : rosetta.protocols.loops.Loops) -> NoneType
- add_cutpoint_variants(...) method of builtins.PyCapsule instance
- add_cutpoint_variants(pose : rosetta.core.pose.Pose) -> NoneType
///////////////////////////////////////////////////////////////////////////////
Add cutpoint variants to all the cutpoints in a Pose.
- add_loop_flank_residues_bb_to_movemap(...) method of builtins.PyCapsule instance
- add_loop_flank_residues_bb_to_movemap(*args, **kwargs)
Overloaded function.
1. add_loop_flank_residues_bb_to_movemap(loops : rosetta.protocols.loops.Loops, mm : rosetta.core.kinematics.MoveMap) -> NoneType
add flank stem residues to the loop movemap
2. add_loop_flank_residues_bb_to_movemap(loops : rosetta.protocols.loops.Loops, mm : rosetta.core.kinematics.MoveMap, flank_size : int) -> NoneType
add flank stem residues to the loop movemap
- add_single_cutpoint_variant(...) method of builtins.PyCapsule instance
- add_single_cutpoint_variant(*args, **kwargs)
Overloaded function.
1. add_single_cutpoint_variant(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
Add cutpoint variants around a single cutpoint (defined by a Loop).
2. add_single_cutpoint_variant(pose : rosetta.core.pose.Pose, cutpoint : int) -> NoneType
Add cutpoint variants around a single cutpoint (defined by residue number).
- apply_sequence_mapping(...) method of builtins.PyCapsule instance
- apply_sequence_mapping(pose : rosetta.core.pose.Pose, target_seq : str, start_mapping : rosetta.core.id.SequenceMapping) -> NoneType
- ccd_close_loops(...) method of builtins.PyCapsule instance
- ccd_close_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, mm : rosetta.core.kinematics.MoveMap) -> NoneType
close loops by the CCD mechanism
- compute_ss_regions(...) method of builtins.PyCapsule instance
- compute_ss_regions(max_loop_frac : float, min_length : int, ss : rosetta.core.fragment.SecondaryStructure) -> rosetta.protocols.loops.Loops
- define_scorable_core_from_secondary_structure(...) method of builtins.PyCapsule instance
- define_scorable_core_from_secondary_structure( : rosetta.core.fragment.SecondaryStructure, score_core : rosetta.protocols.loops.Loops) -> NoneType
- extend_sequence_mapping(...) method of builtins.PyCapsule instance
- extend_sequence_mapping(pose : rosetta.core.pose.Pose, mapping : rosetta.core.id.SequenceMapping, source_seq : str, target_seq : str) -> NoneType
- extract_continuous_chunks(...) method of builtins.PyCapsule instance
- extract_continuous_chunks(*args, **kwargs)
Overloaded function.
1. extract_continuous_chunks(pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops
2. extract_continuous_chunks(pose : rosetta.core.pose.Pose, minimum_size : int) -> rosetta.protocols.loops.Loops
3. extract_continuous_chunks(pose : rosetta.core.pose.Pose, minimum_size : int, CA_CA_distance_cutoff : float) -> rosetta.protocols.loops.Loops
- extract_secondary_structure_chunks(...) method of builtins.PyCapsule instance
- extract_secondary_structure_chunks(*args, **kwargs)
Overloaded function.
1. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
2. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_types : str) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
3. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_types : str, gap_size : int) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
4. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_types : str, gap_size : int, minimum_length_of_chunk_helix : int) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
5. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_types : str, gap_size : int, minimum_length_of_chunk_helix : int, minimum_length_of_chunk_strand : int) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
6. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_types : str, gap_size : int, minimum_length_of_chunk_helix : int, minimum_length_of_chunk_strand : int, CA_CA_distance_cutoff : float) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
7. extract_secondary_structure_chunks(pose : rosetta.core.pose.Pose, extracted_ss_type : str) -> rosetta.protocols.loops.Loops
Extract secondary structure chunks from the pose, using a given secondary structure type
- filter_loop_neighbors_by_distance(...) method of builtins.PyCapsule instance
- filter_loop_neighbors_by_distance(pose : rosetta.core.pose.Pose, map : rosetta.utility.vector1_bool, loops : rosetta.protocols.loops.Loops, dist_cutoff : float) -> NoneType
filter set of loop neighbors to a certain CB distance
Takes distance from selection to neighbors to trim neighbors.
- find_non_protein_chunks(...) method of builtins.PyCapsule instance
- find_non_protein_chunks(pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops
- fix_with_coord_cst(...) method of builtins.PyCapsule instance
- fix_with_coord_cst(rigid : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose, bCstAllAtom : bool, : rosetta.utility.vector1_double) -> NoneType
- fold_tree_from_loops(...) method of builtins.PyCapsule instance
- fold_tree_from_loops(*args, **kwargs)
Overloaded function.
1. fold_tree_from_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, f : rosetta.core.kinematics.FoldTree) -> NoneType
construct a fold tree from loop definition
2. fold_tree_from_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, f : rosetta.core.kinematics.FoldTree, terminal_cutpoint : bool) -> NoneType
construct a fold tree from loop definition
- get_cen_scorefxn(...) method of builtins.PyCapsule instance
- get_cen_scorefxn() -> rosetta.core.scoring.ScoreFunction
- get_fa_scorefxn(...) method of builtins.PyCapsule instance
- get_fa_scorefxn() -> rosetta.core.scoring.ScoreFunction
- has_severe_pep_bond_geom_issues(...) method of builtins.PyCapsule instance
- has_severe_pep_bond_geom_issues(*args, **kwargs)
Overloaded function.
1. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
2. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, check_bonds : bool) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
3. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, check_bonds : bool, check_angles : bool) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
4. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, check_bonds : bool, check_angles : bool, max_c_n_dis : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
5. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, check_bonds : bool, check_angles : bool, max_c_n_dis : float, allowed_ca_c_n_deviation : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
6. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, check_bonds : bool, check_angles : bool, max_c_n_dis : float, allowed_ca_c_n_deviation : float, allowed_c_n_ca_deviation : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
7. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
8. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int, check_bonds : bool) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
9. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int, check_bonds : bool, check_angles : bool) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
10. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int, check_bonds : bool, check_angles : bool, max_c_n_dis : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
11. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int, check_bonds : bool, check_angles : bool, max_c_n_dis : float, allowed_ca_c_n_deviation : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
12. has_severe_pep_bond_geom_issues(pose : rosetta.core.pose.Pose, resnum : int, check_bonds : bool, check_angles : bool, max_c_n_dis : float, allowed_ca_c_n_deviation : float, allowed_c_n_ca_deviation : float) -> (bool, int)
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
cutoffs are: 1.5, 15, 15
Jared Adolf-Bryfogle (jadolfbr.com)
- idealize_loop(...) method of builtins.PyCapsule instance
- idealize_loop(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
set ideal BB geometry; this must occur so that loops with missing density work.
- loop_local_rmsd(...) method of builtins.PyCapsule instance
- loop_local_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> float
calculate rmsd of loop residues with repect to native (loop fit)
- loop_rmsd(...) method of builtins.PyCapsule instance
- loop_rmsd(*args, **kwargs)
Overloaded function.
1. loop_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> float
calculate rmsd of loop residues with repect to native (template aligned)
2. loop_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, CA_only : bool) -> float
calculate rmsd of loop residues with repect to native (template aligned)
3. loop_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, CA_only : bool, bb_only : bool) -> float
calculate rmsd of loop residues with repect to native (template aligned)
- loop_rmsd_with_superimpose(...) method of builtins.PyCapsule instance
- loop_rmsd_with_superimpose(*args, **kwargs)
Overloaded function.
1. loop_rmsd_with_superimpose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> float
As above but actuall superimposes the non-loop part
2. loop_rmsd_with_superimpose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, CA_only : bool) -> float
As above but actuall superimposes the non-loop part
3. loop_rmsd_with_superimpose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, CA_only : bool, bb_only : bool) -> float
As above but actuall superimposes the non-loop part
- loop_rmsd_with_superimpose_core(...) method of builtins.PyCapsule instance
- loop_rmsd_with_superimpose_core(*args, **kwargs)
Overloaded function.
1. loop_rmsd_with_superimpose_core(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, core : rosetta.protocols.loops.Loops) -> float
As above but actually superimposes only the core part (in case there are multiple loops...)
2. loop_rmsd_with_superimpose_core(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, core : rosetta.protocols.loops.Loops, CA_only : bool) -> float
As above but actually superimposes only the core part (in case there are multiple loops...)
3. loop_rmsd_with_superimpose_core(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, core : rosetta.protocols.loops.Loops, CA_only : bool, bb_only : bool) -> float
As above but actually superimposes only the core part (in case there are multiple loops...)
- loopfinder(...) method of builtins.PyCapsule instance
- loopfinder(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> NoneType
- loops_around_residues(...) method of builtins.PyCapsule instance
- loops_around_residues(*args, **kwargs)
Overloaded function.
1. loops_around_residues(loops : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose, residue_indices : rosetta.utility.vector1_unsigned_long) -> NoneType
2. loops_around_residues(loops : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose, residue_indices : rosetta.utility.vector1_unsigned_long, gapsize : int) -> NoneType
3. loops_around_residues(loops : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose, residue_indices : rosetta.utility.vector1_unsigned_long, gapsize : int, extend : int) -> NoneType
- loops_from_string(...) method of builtins.PyCapsule instance
- loops_from_string(loop_str : str, pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops
loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop
- loops_set_move_map(...) method of builtins.PyCapsule instance
- loops_set_move_map(*args, **kwargs)
Overloaded function.
1. loops_set_move_map(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool, mm : rosetta.core.kinematics.MoveMap, neighbor_dist : float, allow_omega_move : bool, allow_takeoff_torsion_move : bool) -> NoneType
create a MoveMap for use of minimization based on loop definition (wrapper)
2. loops_set_move_map(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool, mm : rosetta.core.kinematics.MoveMap) -> NoneType
3. loops_set_move_map(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool, mm : rosetta.core.kinematics.MoveMap, neighbor_dist : float) -> NoneType
4. loops_set_move_map(loops : rosetta.protocols.loops.Loops, allow_sc_move : rosetta.utility.vector1_bool, mm : rosetta.core.kinematics.MoveMap) -> NoneType
create a MoveMap for use of minimization based on loop definition
5. loops_set_move_map(loops : rosetta.protocols.loops.Loops, allow_sc_move : rosetta.utility.vector1_bool, mm : rosetta.core.kinematics.MoveMap, allow_omega_move : bool, allow_takeoff_torsion_move : bool) -> NoneType
- move_map_from_loop(...) method of builtins.PyCapsule instance
- move_map_from_loop(*args, **kwargs)
Overloaded function.
1. move_map_from_loop(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, fix_template_sc : bool) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
2. move_map_from_loop(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, fix_template_sc : bool, neighbor_dist : float) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
3. move_map_from_loop(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, fix_template_sc : bool, neighbor_dist : float, flanking_residues : bool) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
- move_map_from_loops(...) method of builtins.PyCapsule instance
- move_map_from_loops(*args, **kwargs)
Overloaded function.
1. move_map_from_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
2. move_map_from_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool, neighbor_dist : float) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
3. move_map_from_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, fix_template_sc : bool, neighbor_dist : float, flanking_residues : bool) -> rosetta.core.kinematics.MoveMap
Create a new MoveMapOP for use in minimizing the given loop.
- native_loop_core_CA_rmsd(...) method of builtins.PyCapsule instance
- native_loop_core_CA_rmsd(native_pose : rosetta.core.pose.Pose, pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, corelength : int) -> float
- read_loop_fragments(...) method of builtins.PyCapsule instance
- read_loop_fragments(*args, **kwargs)
Overloaded function.
1. read_loop_fragments(frag_libs : rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
2. read_loop_fragments(frag_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
- remove_cutpoint_variants(...) method of builtins.PyCapsule instance
- remove_cutpoint_variants(*args, **kwargs)
Overloaded function.
1. remove_cutpoint_variants(pose : rosetta.core.pose.Pose) -> NoneType
Remove cutpoint variants
2. remove_cutpoint_variants(pose : rosetta.core.pose.Pose, force : bool) -> NoneType
Remove cutpoint variants
- remove_missing_density(...) method of builtins.PyCapsule instance
- remove_missing_density(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
///////////////////////////////////////////////////////////////////////////////
Rebuild a loop via fragment insertion + ccd closure + minimization
- remove_short_chunks(...) method of builtins.PyCapsule instance
- remove_short_chunks(*args, **kwargs)
Overloaded function.
1. remove_short_chunks(input_chunks : rosetta.protocols.loops.Loops) -> rosetta.protocols.loops.Loops
Remove small chunks
2. remove_short_chunks(input_chunks : rosetta.protocols.loops.Loops, min_length : int) -> rosetta.protocols.loops.Loops
Remove small chunks
- remove_small_gaps(...) method of builtins.PyCapsule instance
- remove_small_gaps(*args, **kwargs)
Overloaded function.
1. remove_small_gaps(input_chunks : rosetta.protocols.loops.Loops) -> rosetta.protocols.loops.Loops
If two chunks are separated by a small gap of size <= <gap_size>, combine them
2. remove_small_gaps(input_chunks : rosetta.protocols.loops.Loops, gap_size : int) -> rosetta.protocols.loops.Loops
If two chunks are separated by a small gap of size <= <gap_size>, combine them
- safe_set_extended_torsions_and_idealize_loops(...) method of builtins.PyCapsule instance
- safe_set_extended_torsions_and_idealize_loops(loops : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose) -> NoneType
Identical to set_extended_torsions_and_idealize_loops() without the irrational
behavior surrounding empty loops.
- select_loop_frags(...) method of builtins.PyCapsule instance
- select_loop_frags(*args, **kwargs)
Overloaded function.
1. select_loop_frags(loops : rosetta.protocols.loops.Loops, source : rosetta.core.fragment.FragSet, loop_frags : rosetta.core.fragment.FragSet) -> NoneType
get frags that are fully within the Loop --- shorten(=true/false) frags that are close to the end of loops.
2. select_loop_frags(loops : rosetta.protocols.loops.Loops, source : rosetta.core.fragment.FragSet, loop_frags : rosetta.core.fragment.FragSet, min_size : int) -> NoneType
get frags that are fully within the Loop --- shorten(=true/false) frags that are close to the end of loops.
- select_loop_residues(...) method of builtins.PyCapsule instance
- select_loop_residues(*args, **kwargs)
Overloaded function.
1. select_loop_residues(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, include_neighbors : bool, map : rosetta.utility.vector1_bool) -> NoneType
mark loop residues and its neighbors as necessary in a sequence map.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
2. select_loop_residues(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, include_neighbors : bool, map : rosetta.utility.vector1_bool, neighbor_dist : float) -> NoneType
mark loop residues and its neighbors as necessary in a sequence map.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
3. select_loop_residues(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, include_neighbors : bool) -> rosetta.utility.vector1_bool
mark loop residues and its neighbors as necessary in a sequence map.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
4. select_loop_residues(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, include_neighbors : bool, neighbor_dist : float) -> rosetta.utility.vector1_bool
mark loop residues and its neighbors as necessary in a sequence map.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
5. select_loop_residues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, include_neighbors : bool, map : rosetta.utility.vector1_bool) -> NoneType
mark loop residues and its neighbors as necessary for one loop.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
6. select_loop_residues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, include_neighbors : bool, map : rosetta.utility.vector1_bool, neighbor_dist : float) -> NoneType
mark loop residues and its neighbors as necessary for one loop.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
7. select_loop_residues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, include_neighbors : bool) -> rosetta.utility.vector1_bool
mark loop residues and its neighbors as necessary for one loop.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
8. select_loop_residues(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, include_neighbors : bool, neighbor_dist : float) -> rosetta.utility.vector1_bool
mark loop residues and its neighbors as necessary for one loop.
Uses 10A neighbor graph for neighbors
THEN takes distance from selection to neighbors to trim neighbors.
Excludes disulfide residues.
- set_extended_torsions(...) method of builtins.PyCapsule instance
- set_extended_torsions(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
Set a loop to extended torsion angles.
- set_extended_torsions_and_idealize_loops(...) method of builtins.PyCapsule instance
- set_extended_torsions_and_idealize_loops(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> NoneType
- set_loop_cutpoint_in_pose_fold_tree(...) method of builtins.PyCapsule instance
- set_loop_cutpoint_in_pose_fold_tree(new_cutpoint : int, pose : rosetta.core.pose.Pose, loop_begin : int, loop_end : int) -> NoneType
- set_move_map_for_centroid_loop(...) method of builtins.PyCapsule instance
- set_move_map_for_centroid_loop(loop : rosetta.protocols.loops.Loop, mm : rosetta.core.kinematics.MoveMap) -> NoneType
- set_secstruct_from_dssp(...) method of builtins.PyCapsule instance
- set_secstruct_from_dssp(pose : rosetta.core.pose.Pose, filename : str) -> bool
another helper function to set secondary structure of a Pose from an external file.
- set_secstruct_from_psipred_ss2(...) method of builtins.PyCapsule instance
- set_secstruct_from_psipred_ss2(pose : rosetta.core.pose.Pose) -> bool
helper function to set secondary structure of a Pose from an external
file.
- set_single_loop_fold_tree(...) method of builtins.PyCapsule instance
- set_single_loop_fold_tree(pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
///////////////////////////////////////////////////////////////////////////////
Set the fold tree to contain a single chain break at the loops' position
- split_by_ca_ca_dist(...) method of builtins.PyCapsule instance
- split_by_ca_ca_dist(*args, **kwargs)
Overloaded function.
1. split_by_ca_ca_dist(pose : rosetta.core.pose.Pose, input_chunks : rosetta.protocols.loops.Loops) -> rosetta.protocols.loops.Loops
Split into separate chunks if CA-CA distance is over the cutoff
2. split_by_ca_ca_dist(pose : rosetta.core.pose.Pose, input_chunks : rosetta.protocols.loops.Loops, CA_CA_distance_cutoff : float) -> rosetta.protocols.loops.Loops
Split into separate chunks if CA-CA distance is over the cutoff
- split_by_resSeq(...) method of builtins.PyCapsule instance
- split_by_resSeq(*args, **kwargs)
Overloaded function.
1. split_by_resSeq(pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops
2. split_by_resSeq(pose : rosetta.core.pose.Pose, input_chunks : rosetta.protocols.loops.Loops) -> rosetta.protocols.loops.Loops
- trim_back_sequence_mapping(...) method of builtins.PyCapsule instance
- trim_back_sequence_mapping(mapping : rosetta.core.id.SequenceMapping, source_seq : str, target_seq : str, min_loop_size : int) -> NoneType
Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.
- validate_loop_start_stop(...) method of builtins.PyCapsule instance
- validate_loop_start_stop(prohibit_single_residue_loops : bool, start : int, stop : int, filename : str, linecount : int) -> NoneType
Checks if there is a problem with the beginning and ending residues defined
in a loops file.
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