Module _protocols_loops_

addScoresForLoopParts( (Pose)pose, (Loops)loops, (ScoreFunction)scorefxn, (Pose)native_pose, (int)nloops) -> None :
    protocols/loops/util.hh:57

    C++ signature :
        void addScoresForLoopParts(core::pose::Pose {lvalue},protocols::loops::Loops,core::scoring::ScoreFunction,core::pose::Pose {lvalue},unsigned long)

add_coordinate_constraints_to_pose( (Pose)pose, (Pose)constraint_target_pose, (Loops)exclude_regions) -> None :
    protocols/loops/util.hh:72

    C++ signature :
        void add_coordinate_constraints_to_pose(core::pose::Pose {lvalue},core::pose::Pose,protocols::loops::Loops {lvalue})

add_cutpoint_variants( (Pose)pose) -> None :
    ///////////////////////////////////////////////////////////////////////////////
     Add cutpoint variants to all the cutpoints in a Pose.
    

    C++ signature :
        void add_cutpoint_variants(core::pose::Pose {lvalue})

add_loop_flank_residues_bb_to_movemap( (Loops)loops, (MoveMap)mm [, (int)flank_size=2]) -> None :
    add flank stem residues to the loop movemap
    

    C++ signature :
        void add_loop_flank_residues_bb_to_movemap(protocols::loops::Loops,core::kinematics::MoveMap {lvalue} [,unsigned long=2])

add_single_cutpoint_variant( (Pose)pose, (int)cutpoint) -> None :
    Add cutpoint variants around a single cutpoint (defined by residue number).
    

    C++ signature :
        void add_single_cutpoint_variant(core::pose::Pose {lvalue},unsigned long)

add_single_cutpoint_variant( (Pose)pose, (Loop)loop) -> None :
    Add cutpoint variants around a single cutpoint (defined by a Loop).
    

    C++ signature :
        void add_single_cutpoint_variant(core::pose::Pose {lvalue},protocols::loops::Loop)

apply_sequence_mapping( (Pose)pose, (str)target_seq, (SequenceMapping)start_mapping) -> None :
    protocols/loops/loops_main.hh:325

    C++ signature :
        void apply_sequence_mapping(core::pose::Pose {lvalue},std::string,core::id::SequenceMapping)

ccd_close_loops( (Pose)pose, (Loops)loops, (MoveMap)mm) -> None :
    close loops by the CCD mechanism
    

    C++ signature :
        void ccd_close_loops(core::pose::Pose {lvalue},protocols::loops::Loops,core::kinematics::MoveMap)

compute_ss_regions( (float)max_loop_frac, (int)min_length, (SecondaryStructure)ss) -> Loops :
    protocols/loops/util.hh:64

    C++ signature :
        protocols::loops::Loops compute_ss_regions(double,unsigned long,core::fragment::SecondaryStructure)

define_scorable_core_from_secondary_structure( (SecondaryStructure), (Loops)score_core) -> None :
    protocols/loops/util.hh:81

    C++ signature :
        void define_scorable_core_from_secondary_structure(core::fragment::SecondaryStructure,protocols::loops::Loops {lvalue})

extend_sequence_mapping( (Pose)pose, (SequenceMapping)mapping, (str)source_seq, (str)target_seq) -> None :
    protocols/loops/loops_main.hh:310

    C++ signature :
        void extend_sequence_mapping(core::pose::Pose,core::id::SequenceMapping {lvalue},std::string {lvalue},std::string {lvalue})

extract_continuous_chunks( (Pose)pose [, (int)minimum_size=3 [, (float)CA_CA_distance_cutoff=4]]) -> Loops :
    protocols/loops/util.hh:128

    C++ signature :
        protocols::loops::Loops extract_continuous_chunks(core::pose::Pose [,unsigned long=3 [,double=4]])

extract_secondary_structure_chunks( (Pose)pose, (str)extracted_ss_type) -> Loops :
    Extract secondary structure chunks from the pose, using a given secondary structure type
    

    C++ signature :
        protocols::loops::Loops extract_secondary_structure_chunks(core::pose::Pose,char)

extract_secondary_structure_chunks( (Pose)pose [, (str)extracted_ss_types='HE' [, (int)gap_size=1 [, (int)minimum_length_of_chunk_helix=5 [, (int)minimum_length_of_chunk_strand=3 [, (float)CA_CA_distance_cutoff=4]]]]]) -> 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);
    

    C++ signature :
        protocols::loops::Loops extract_secondary_structure_chunks(core::pose::Pose [,std::string='HE' [,unsigned long=1 [,unsigned long=5 [,unsigned long=3 [,double=4]]]]])

filter_loop_neighbors_by_distance( (Pose)pose, (vector1_bool)map, (Loops)loops, (float)dist_cutoff) -> None :
    filter set of loop neighbors to a certain CB distance
    

    C++ signature :
        void filter_loop_neighbors_by_distance(core::pose::Pose,utility::vector1<bool, std::allocator<bool> > {lvalue},protocols::loops::Loops,double {lvalue})

find_non_protein_chunks( (Pose)pose) -> Loops :
    protocols/loops/util.hh:108

    C++ signature :
        protocols::loops::Loops find_non_protein_chunks(core::pose::Pose)

fix_with_coord_cst( (Loops)rigid, (Pose)pose, (bool)bCstAllAtom, (vector1_Real)) -> None :
    protocols/loops/util.hh:31

    C++ signature :
        void fix_with_coord_cst(protocols::loops::Loops,core::pose::Pose {lvalue},bool,utility::vector1<double, std::allocator<double> > {lvalue})

fold_tree_from_loops( (Pose)pose, (Loops)loops, (FoldTree)f [, (bool)terminal_cutpoint=False]) -> None :
    the main function for perform loop modeling
    /voi/d
    loops_main( core::pose::Pose & pose );
    construct a fold tree from loop definition
    

    C++ signature :
        void fold_tree_from_loops(core::pose::Pose,protocols::loops::Loops,core::kinematics::FoldTree {lvalue} [,bool=False])

    protocols/loops/util.hh:69

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_cen_scorefxn()

Returns: ScoreFunction :

    protocols/loops/util.hh:67

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_fa_scorefxn()

Returns: ScoreFunction :

get_tenA_neighbor_residues( (Pose)pose, (vector1_bool)residue_positions) -> None :
    get neighbor residues within 10 A CB distance cutoff
    

    C++ signature :
        void get_tenA_neighbor_residues(core::pose::Pose,utility::vector1<bool, std::allocator<bool> > {lvalue})

has_severe_pep_bond_geom_issues( (Pose)pose, (int)resnum [, (bool)check_bonds=True [, (bool)check_angles=True [, (float)max_c_n_dis=2.0 [, (float)allowed_ca_c_n_deviation=25.0 [, (float)allowed_c_n_ca_deviation=25.0]]]]]) -> object :
    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.
    Stringent cutoffs are: 1.5, 15, 15
    

    C++ signature :
        std::pair<bool, unsigned long> has_severe_pep_bond_geom_issues(core::pose::Pose,unsigned long [,bool=True [,bool=True [,double=2.0 [,double=25.0 [,double=25.0]]]]])

has_severe_pep_bond_geom_issues( (Pose)pose, (Loop)loop [, (bool)check_bonds=True [, (bool)check_angles=True [, (float)max_c_n_dis=2.0 [, (float)allowed_ca_c_n_deviation=25.0 [, (float)allowed_c_n_ca_deviation=25.0]]]]]) -> object :
    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.
    Stringent cutoffs are: 1.5, 15, 15
    

    C++ signature :
        std::pair<bool, unsigned long> has_severe_pep_bond_geom_issues(core::pose::Pose,protocols::loops::Loop [,bool=True [,bool=True [,double=2.0 [,double=25.0 [,double=25.0]]]]])

idealize_loop( (Pose)pose, (Loop)loop) -> None :
    set ideal BB geometry; this must occur so that loops with missing density work.
    

    C++ signature :
        void idealize_loop(core::pose::Pose {lvalue},protocols::loops::Loop)

loop_local_rmsd( (Pose)pose1, (Pose)pose2, (Loops)loops) -> float :
    calculate rmsd of loop residues with repect to native (loop fit)
    

    C++ signature :
        double loop_local_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops)

loop_rmsd( (Pose)pose1, (Pose)pose2, (Loops)loops [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
    calculate rmsd of loop residues with repect to native (template aligned)
    

    C++ signature :
        double loop_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops [,bool=False [,bool=True]])

loop_rmsd_with_superimpose( (Pose)pose1, (Pose)pose2, (Loops)loops [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
    As above but actuall superimposes the non-loop part
    

    C++ signature :
        double loop_rmsd_with_superimpose(core::pose::Pose,core::pose::Pose,protocols::loops::Loops [,bool=False [,bool=True]])

loop_rmsd_with_superimpose_core( (Pose)pose1, (Pose)pose2, (Loops)loops, (Loops)core [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
    As above but actually superimposes only the core part (in case there are multiple loops...)
    

    C++ signature :
        double loop_rmsd_with_superimpose_core(core::pose::Pose,core::pose::Pose,protocols::loops::Loops,protocols::loops::Loops [,bool=False [,bool=True]])

loopfinder( (Pose)pose, (Loops)loops) -> None :
    protocols/loops/loopfinder.hh:29

    C++ signature :
        void loopfinder(core::pose::Pose {lvalue},protocols::loops::Loops {lvalue})

loops_around_residues( (Loops)loops, (Pose)pose, (vector1_Size)residue_indices [, (int)gapsize=6 [, (int)extend=2]]) -> None :
    protocols/loops/make_loops.hh:35

    C++ signature :
        void loops_around_residues(protocols::loops::Loops {lvalue},core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> > [,unsigned long=6 [,unsigned long=2]])

loops_from_string( (str)loop_str, (Pose)pose) -> 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
    

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> loops_from_string(std::string,core::pose::Pose)

loops_set_move_map( (Loops)loops, (vector1_bool)allow_sc_move, (MoveMap)mm, (bool)allow_omega_move, (bool)allow_takeoff_torsion_move) -> None :
    protocols/loops/loops_main.hh:110

    C++ signature :
        void loops_set_move_map(protocols::loops::Loops,utility::vector1<bool, std::allocator<bool> >,core::kinematics::MoveMap {lvalue},bool,bool)

loops_set_move_map( (Loops)loops, (vector1_bool)allow_sc_move, (MoveMap)mm) -> None :
    create a MoveMap for use of minimization based on loop definition
    

    C++ signature :
        void loops_set_move_map(protocols::loops::Loops,utility::vector1<bool, std::allocator<bool> >,core::kinematics::MoveMap {lvalue})

loops_set_move_map( (Pose)pose, (Loops)loops, (bool)fix_template_sc, (MoveMap)mm [, (float)neighbor_dist=10.0]) -> None :
    protocols/loops/loops_main.hh:93

    C++ signature :
        void loops_set_move_map(core::pose::Pose {lvalue},protocols::loops::Loops,bool,core::kinematics::MoveMap {lvalue} [,double=10.0])

loops_set_move_map( (Pose)pose, (Loops)loops, (bool)fix_template_sc, (MoveMap)mm, (float)neighbor_dist, (bool)allow_omega_move, (bool)allow_takeoff_torsion_move) -> None :
    create a MoveMap for use of minimization based on loop definition (wrapper)
    

    C++ signature :
        void loops_set_move_map(core::pose::Pose {lvalue},protocols::loops::Loops,bool,core::kinematics::MoveMap {lvalue},double,bool,bool)

move_map_from_loop( (Pose)pose, (Loop)loop, (bool)fix_template_sc [, (float)neighbor_dist=10.0 [, (bool)flanking_residues=False]]) -> MoveMap :
    Create a new MoveMapOP for use in minimizing the given loop.
    

    C++ signature :
        boost::shared_ptr<core::kinematics::MoveMap> move_map_from_loop(core::pose::Pose {lvalue},protocols::loops::Loop,bool [,double=10.0 [,bool=False]])

move_map_from_loops( (Pose)pose, (Loops)loops, (bool)fix_template_sc [, (float)neighbor_dist=10.0 [, (bool)flanking_residues=False]]) -> MoveMap :
    Create a new MoveMapOP for use in minimizing the given loop.
    

    C++ signature :
        boost::shared_ptr<core::kinematics::MoveMap> move_map_from_loops(core::pose::Pose {lvalue},protocols::loops::Loops,bool [,double=10.0 [,bool=False]])

native_loop_core_CA_rmsd( (Pose)native_pose, (Pose)pose, (Loops)loops, (int)corelength) -> float :
    protocols/loops/loops_main.hh:251

    C++ signature :
        double native_loop_core_CA_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops,int {lvalue})

read_loop_fragments( (object)frag_libs) -> None :
    protocols/loops/loops_main.hh:236

    C++ signature :
        void read_loop_fragments(utility::vector1<boost::shared_ptr<core::fragment::FragSet>, std::allocator<boost::shared_ptr<core::fragment::FragSet> > > {lvalue})

read_loop_fragments( (object)frag_libs) -> None :
    protocols/loops/loops_main.hh:232

    C++ signature :
        void read_loop_fragments(std::vector<boost::shared_ptr<core::fragment::FragSet>, std::allocator<boost::shared_ptr<core::fragment::FragSet> > > {lvalue})

remove_cutpoint_variants( (Pose)pose [, (bool)force=False]) -> None :
    Remove cutpoint variants
    

    C++ signature :
        void remove_cutpoint_variants(core::pose::Pose {lvalue} [,bool=False])

remove_missing_density( (Pose)pose, (Loop)loop) -> None :
    ///////////////////////////////////////////////////////////////////////////////
     Rebuild a loop via fragment insertion + ccd closure + minimization
    

    C++ signature :
        void remove_missing_density(core::pose::Pose {lvalue},protocols::loops::Loop)

remove_short_chunks( (Loops)input_chunks [, (int)min_length=3]) -> Loops :
    Remove small chunks
    

    C++ signature :
        protocols::loops::Loops remove_short_chunks(protocols::loops::Loops [,unsigned long=3])

remove_small_gaps( (Loops)input_chunks [, (int)gap_size=1]) -> Loops :
    If two chunks are separated by a small gap of size <= <gap_size>, combine them
    

    C++ signature :
        protocols::loops::Loops remove_small_gaps(protocols::loops::Loops [,unsigned long=1])

safe_set_extended_torsions_and_idealize_loops( (Loops)loops, (Pose)pose) -> None :
    Identical to set_extended_torsions_and_idealize_loops() without the irrational
    behavior surrounding empty loops.
    

    C++ signature :
        void safe_set_extended_torsions_and_idealize_loops(protocols::loops::Loops,core::pose::Pose*)

select_loop_frags( (Loops)loops, (FragSet)source, (FragSet)loop_frags [, (int)min_size=1]) -> None :
    get frags that are fully within the Loop --- shorten(=true/false) frags that are close to the end of loops.
    

    C++ signature :
        void select_loop_frags(protocols::loops::Loops,core::fragment::FragSet {lvalue},core::fragment::FragSet {lvalue} [,unsigned long=1])

select_loop_residues( (Pose)pose, (Loop)loop, (bool)include_neighbors [, (float)neighbor_dist=10.0]) -> vector1_bool :
    protocols/loops/loops_main.hh:192

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > select_loop_residues(core::pose::Pose,protocols::loops::Loop,bool [,double=10.0])

select_loop_residues( (Pose)pose, (Loop)loop, (bool)include_neighbors, (vector1_bool)map [, (float)neighbor_dist=10.0]) -> None :
    protocols/loops/loops_main.hh:184

    C++ signature :
        void select_loop_residues(core::pose::Pose,protocols::loops::Loop,bool,utility::vector1<bool, std::allocator<bool> > {lvalue} [,double=10.0])

select_loop_residues( (Pose)pose, (Loops)loops, (bool)include_neighbors [, (float)neighbor_dist=10.0]) -> vector1_bool :
    mark loop residues and its neighbors as necessary in a sequence map.
    

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > select_loop_residues(core::pose::Pose,protocols::loops::Loops,bool [,double=10.0])

select_loop_residues( (Pose)pose, (Loops)loops, (bool)include_neighbors, (vector1_bool)map [, (float)neighbor_dist=10.0]) -> None :
    mark loop residues and its neighbors as necessary in a sequence map.
    

    C++ signature :
        void select_loop_residues(core::pose::Pose,protocols::loops::Loops,bool,utility::vector1<bool, std::allocator<bool> > {lvalue} [,double=10.0])

set_extended_torsions( (Pose)pose, (Loop)loop) -> None :
    Set a loop to extended torsion angles.
    

    C++ signature :
        void set_extended_torsions(core::pose::Pose {lvalue},protocols::loops::Loop)

set_extended_torsions_and_idealize_loops( (Pose)pose, (Loops)loops) -> None :
    protocols/loops/util.hh:43

    C++ signature :
        void set_extended_torsions_and_idealize_loops(core::pose::Pose {lvalue},protocols::loops::Loops)

set_loop_cutpoint_in_pose_fold_tree( (int)new_cutpoint, (Pose)pose, (int)loop_begin, (int)loop_end) -> None :
    protocols/loops/loops_main.hh:318

    C++ signature :
        void set_loop_cutpoint_in_pose_fold_tree(unsigned long,core::pose::Pose {lvalue},unsigned long,unsigned long)

set_move_map_for_centroid_loop( (Loop)loop, (MoveMap)mm) -> None :
    protocols/loops/loops_main.hh:136

    C++ signature :
        void set_move_map_for_centroid_loop(protocols::loops::Loop,core::kinematics::MoveMap {lvalue})

set_secstruct_from_dssp( (Pose)pose, (str)filename) -> bool :
    another helper function to set secondary structure of a Pose from an external file.
    

    C++ signature :
        bool set_secstruct_from_dssp(core::pose::Pose {lvalue},std::string)

set_secstruct_from_psipred_ss2( (Pose)pose) -> bool :
    helper function to set secondary structure of a Pose from an external
    file.
    

    C++ signature :
        bool set_secstruct_from_psipred_ss2(core::pose::Pose {lvalue})

set_single_loop_fold_tree( (Pose)pose, (Loop)loop) -> None :
    ///////////////////////////////////////////////////////////////////////////////
     Set the fold tree to contain a single chain break at the loops' position
    

    C++ signature :
        void set_single_loop_fold_tree(core::pose::Pose {lvalue},protocols::loops::Loop)

split_by_ca_ca_dist( (Pose)pose, (Loops)input_chunks [, (float)CA_CA_distance_cutoff=4]) -> Loops :
    Split into separate chunks if CA-CA distance is over the cutoff
    

    C++ signature :
        protocols::loops::Loops split_by_ca_ca_dist(core::pose::Pose,protocols::loops::Loops [,double=4])

split_by_resSeq( (Pose)pose, (Loops)input_chunks) -> Loops :
    protocols/loops/util.hh:105

    C++ signature :
        protocols::loops::Loops split_by_resSeq(core::pose::Pose,protocols::loops::Loops)

split_by_resSeq( (Pose)pose) -> Loops :
    protocols/loops/util.hh:103

    C++ signature :
        protocols::loops::Loops split_by_resSeq(core::pose::Pose)

trim_back_sequence_mapping( (SequenceMapping)mapping, (str)source_seq, (str)target_seq, (int)min_loop_size) -> None :
    Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.
    

    C++ signature :
        void trim_back_sequence_mapping(core::id::SequenceMapping {lvalue},std::string,std::string,unsigned long)

validate_loop_start_stop( (bool)prohibit_single_residue_loops, (int)start, (int)stop, (str)filename, (int)linecount) -> None :
    Checks if there is a problem with the beginning and ending residues defined
    in a loops file.
    

    C++ signature :
        void validate_loop_start_stop(bool,unsigned long,unsigned long,std::string,unsigned long)

chainID

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.chainID

cut_point

Value:

rosetta.protocols.loops._protocols_loops_.ResidueIdentifier.cut_point

extend

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.extend

extras

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.extras

iCode

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.iCode

number_of_configuration_keywords

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.number_of_ configuration_keywords

number_of_residue_identifiers

Value:

rosetta.protocols.loops._protocols_loops_.ResidueIdentifier.number_of_ residue_identifiers

resSeq

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.resSeq

skip_rate

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.skip_rate

start

Value:

rosetta.protocols.loops._protocols_loops_.ResidueIdentifier.start

stop

Value:

rosetta.protocols.loops._protocols_loops_.ResidueIdentifier.stop

use_pose_numbering

Value:

rosetta.protocols.loops._protocols_loops_.LoopConfiguration.use_pose_n umbering