Rosetta 3.4
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protocols::loops Namespace Reference

Namespaces

namespace  loop_closure
namespace  loop_mover

Classes

class  EXCN_Loop_not_closed
class  FoldTreeFromLoops
class  FoldTreeFromLoopsCreator
struct  SerializedLoop
class  Loop
 single loop definition More...
class  RationalLoopComparator
 Orders loops by start position. More...
class  Loop_lt
 used to sort Loops by start-res More...
class  LoopMoverFactory
 Create LoopMover Reporters. More...
class  Loops
class  LoopsFileIO

Typedefs

typedef
utility::pointer::owning_ptr
< FoldTreeFromLoops
FoldTreeFromLoopsOP
typedef
utility::pointer::owning_ptr
< FoldTreeFromLoops const > 
FoldTreeFromLoopsCOP
typedef
utility::pointer::owning_ptr
< Loop
LoopOP
typedef
utility::pointer::owning_ptr
< Loop const > 
LoopCOP
typedef
utility::pointer::owning_ptr
< Loops
LoopsOP
typedef
utility::pointer::owning_ptr
< Loops const > 
LoopsCOP
typedef
utility::pointer::owning_ptr
< LoopsFileIO
LoopsFileIOOP
typedef
utility::pointer::owning_ptr
< LoopsFileIO const > 
LoopsFileIOCOP

Functions

static basic::Tracer TR ("protocols.loops.FoldTreeFromLoopsWrapper")
static basic::Tracer tr ("protocols.loops.Loop")
static
numeric::random::RandomGenerator 
RG (429)
std::ostream & operator<< (std::ostream &os, const Loop &loop)
void loopfinder (core::pose::Pose &pose, loops::Loops &loops)
static basic::Tracer tr ("protocols.loops.LoopMoverFactory")
static basic::Tracer tr ("loops")
static
numeric::random::RandomGenerator 
RG (430)
std::ostream & operator<< (std::ostream &os, const Loops &loops)
basic::Tracer tt ("protocols.loops.loops_main")
static
numeric::random::RandomGenerator 
RG (31413)
void read_loop_fragments (std::vector< core::fragment::FragSetOP > &frag_libs)
void read_loop_fragments (utility::vector1< core::fragment::FragSetOP > &frag_libs)
void fold_tree_from_loops (core::pose::Pose const &pose, Loops const &loops, core::kinematics::FoldTree &f, bool terminal_cutpoint=false)
 the main function for perform loop modeling
void set_single_loop_fold_tree (core::pose::Pose &pose, Loop const &loop)
void set_loop_cutpoint_in_pose_fold_tree (Size const new_cutpoint, pose::Pose &pose, Size const loop_begin, Size const loop_end)
void remove_cutpoint_variants (core::pose::Pose &pose, bool force)
void add_cutpoint_variants (core::pose::Pose &pose)
void add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)
void loops_set_move_map (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, core::Real neighbor_dist=10.0)
 create a MoveMap for use of minimization based on loop definition (wrapper)
void loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm)
 create a MoveMap for use of minimization based on loop definition
void set_move_map_for_centroid_loop (Loop const &loop, core::kinematics::MoveMap &mm)
void ccd_close_loops (core::pose::Pose &pose, Loops const &loops, core::kinematics::MoveMap const &mm)
 close loops by the CCD mechanism
void get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions)
 get neighbor residues within 10 A CB distance cutoff
void select_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary in a sequence map.
void select_loop_residues (pose::Pose const &pose, Loop const &loop, bool const include_neighbors, utility::vector1< bool > &map, Real neighbor_dist)
void filter_loop_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > &map, Loops const &loops, core::Real &dist_cutoff)
 filter set of loop neighbors to a certain CB distance
void extend_sequence_mapping (pose::Pose const &pose, id::SequenceMapping &mapping, std::string &source_seq, std::string &target_seq)
void apply_sequence_mapping (pose::Pose &pose, std::string const &target_seq, id::SequenceMapping const &start_mapping)
void trim_back_sequence_mapping (core::id::SequenceMapping &mapping, std::string const &source_seq, std::string const &target_seq, core::Size const min_loop_size)
bool set_secstruct_from_psipred_ss2 (core::pose::Pose &pose)
 helper function to set secondary structure of a Pose from an external file.
bool set_secstruct_from_dssp (core::pose::Pose &pose, std::string const &filename)
 another helper function to set secondary structure of a Pose from an external file.
void idealize_loop (core::pose::Pose &pose, Loop const &loop)
void set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
void remove_missing_density (core::pose::Pose &pose, Loop const &loop)
core::Real native_loop_core_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose, loops::Loops loops, int &corelength)
Real loop_rmsd_with_superimpose (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 As above but actuall superimposes the non-loop part.
Real loop_rmsd_with_superimpose_core (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, Loops const &core, bool CA_only=false, bool bb_only=true)
 As above but actually superimposes only the core part (in case there are multiple loops...)
Real loop_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 calculate rmsd of loop residues with repect to native (template aligned)
Real loop_local_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops)
 calculate rmsd of loop residues with repect to native (loop fit)
static basic::Tracer tr ("protocols.loops.LoopsFileIO")
std::ostream & operator<< (std::ostream &os, const LoopsFileIO &loops)
static basic::Tracer TR ("protocols.loops.make_loops", t_info)
void add_loop (Size seg_begin, Size seg_end, pose::Pose const &pose, loops::Loops &loops)
void loops_around_residues (loops::Loops &loops, pose::Pose const &pose, vector1< Size > const &residue_indices, Size gapsize, Size extend)
 add a set of loops 'built' around the provided residue indices
void fix_with_coord_cst (Loops const &rigid, core::pose::Pose &pose, bool bCstAllAtom, utility::vector1< core::Real > &weights)
void select_loop_frags (loops::Loops const &loops, core::fragment::FragSet &source, core::fragment::FragSet &loop_frags, Size shorten)
 get frags that are fully within the Loop --- shorten(=true/false) frags that are close to the end of loops.
void safe_set_extended_torsions_and_idealize_loops (const protocols::loops::Loops &loops, core::pose::Pose *pose)
 Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops.
void set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops)
void addScoresForLoopParts (core::pose::Pose &pose, loops::Loops loops, const core::scoring::ScoreFunction &scorefxn, core::pose::Pose &native_pose, core::Size nloops)
loops::Loops compute_ss_regions (core::Real max_loop_frac, core::Size min_length, core::fragment::SecondaryStructure const &ss)
core::scoring::ScoreFunctionOP get_cen_scorefxn ()
core::scoring::ScoreFunctionOP get_fa_scorefxn ()
void add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)
LoopsOP loops_from_string (std::string const loop_str, core::pose::Pose const &pose)
 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
void define_scorable_core_from_secondary_structure (core::fragment::SecondaryStructure const &ss_def, protocols::loops::Loops &scored_core)
protocols::loops::Loops extract_secondary_structure_chunks (core::pose::Pose const &pose, char const extracted_ss_type)
 Extract secondary structure chunks from the secondary structure.
protocols::loops::Loops split_by_resSeq (core::pose::Pose const &pose)
protocols::loops::Loops split_by_resSeq (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks)
protocols::loops::Loops split_by_ca_ca_dist (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks, core::Real const CA_CA_distance_cutoff=4)
 Split into separate chunks if CA-CA distance is over the cutoff.
protocols::loops::Loops remove_small_gaps (protocols::loops::Loops const &input_chunks, core::Size gap_size=1)
 If two chunks are separated by a small gap of size <= <gap_size>, combine them.
protocols::loops::Loops remove_short_chunks (protocols::loops::Loops const &input_chunks, core::Size min_length=3)
 Remove small chunks.
protocols::loops::Loops extract_secondary_structure_chunks (core::pose::Pose const &pose, std::string extracted_ss_types="HE", core::Size gap_size=1, core::Size minimum_length_of_chunk_helix=5, core::Size minimum_length_of_chunk_strand=3, core::Real CA_CA_distance_cutoff=4)
 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);.
protocols::loops::Loops extract_continuous_chunks (core::pose::Pose const &pose, core::Size const minimum_size, core::Real const CA_CA_distance_cutoff)

Variables

static const double EXT_PHI = -150
static const double EXT_PSI = +150
static const double EXT_OMG = 180

Typedef Documentation


Function Documentation

void protocols::loops::add_coordinate_constraints_to_pose ( core::pose::Pose pose,
const core::pose::Pose constraint_target_pose,
protocols::loops::Loops exclude_regions 
)
void protocols::loops::add_cutpoint_variants ( core::pose::Pose pose)
void protocols::loops::add_loop ( Size  seg_begin,
Size  seg_end,
pose::Pose const &  pose,
loops::Loops &  loops 
)
void protocols::loops::add_single_cutpoint_variant ( core::pose::Pose pose,
const Loop &  loop 
)
void protocols::loops::addScoresForLoopParts ( core::pose::Pose pose,
loops::Loops  loops,
const core::scoring::ScoreFunction scorefxn,
core::pose::Pose native_pose,
core::Size  nloops 
)
void protocols::loops::apply_sequence_mapping ( pose::Pose pose,
std::string const &  target_seq,
id::SequenceMapping const &  start_mapping 
)
void protocols::loops::ccd_close_loops ( pose::Pose pose,
Loops const &  loops,
kinematics::MoveMap const &  mm 
)

close loops by the CCD mechanism

take a pose and loop defintions, close each loop separately by the CCD algorithm. Currently hard-code all parameters related to CCD and then call fast_ccd_loop_closure for closing this single loop

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), and protocols::loops::loop_closure::ccd::fast_ccd_loop_closure().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop().

loops::Loops protocols::loops::compute_ss_regions ( core::Real  max_loop_frac,
core::Size  min_length,
core::fragment::SecondaryStructure const &  ss 
)
void protocols::loops::define_scorable_core_from_secondary_structure ( core::fragment::SecondaryStructure const &  ss_def,
protocols::loops::Loops scored_core 
)
void protocols::loops::extend_sequence_mapping ( pose::Pose const &  pose,
id::SequenceMapping mapping,
std::string &  source_seq,
std::string &  target_seq 
)
protocols::loops::Loops protocols::loops::extract_continuous_chunks ( core::pose::Pose const &  pose,
core::Size const  minimum_size,
core::Real const  CA_CA_distance_cutoff 
)
protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks ( core::pose::Pose const &  pose,
char const  extracted_ss_type 
)

Extract secondary structure chunks from the secondary structure.

Extract secondary structure chunks from the pose, using a given secondary structure type.

References core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::comparative_modeling::hybridize::HybridizeProtocol::add_template(), and extract_secondary_structure_chunks().

protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks ( core::pose::Pose const &  pose,
std::string  extracted_ss_types,
core::Size  gap_size,
core::Size  minimum_length_of_chunk_helix,
core::Size  minimum_length_of_chunk_strand,
core::Real  CA_CA_distance_cutoff 
)

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);.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), extract_secondary_structure_chunks(), remove_short_chunks(), remove_small_gaps(), split_by_ca_ca_dist(), and split_by_resSeq().

void protocols::loops::filter_loop_neighbors_by_distance ( pose::Pose const &  pose,
utility::vector1< bool > &  map,
Loops const &  loops,
Real dist_cutoff 
)

filter set of loop neighbors to a certain CB distance

neighbors contains the set of potential neighbors to the loop residues given in loops. This set is reduced to only contain neighbors within dist_cutoff of any residue in loops.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by select_loop_residues().

void protocols::loops::fix_with_coord_cst ( Loops const &  rigid,
core::pose::Pose pose,
bool  bCstAllAtom,
utility::vector1< core::Real > &  weights 
)
void protocols::loops::fold_tree_from_loops ( core::pose::Pose const &  pose,
Loops const &  loops,
kinematics::FoldTree f,
bool  terminal_cutpoint 
)
core::scoring::ScoreFunctionOP protocols::loops::get_cen_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::loops::get_fa_scorefxn ( )
void protocols::loops::get_tenA_neighbor_residues ( pose::Pose const &  pose,
utility::vector1< bool > &  residue_positions 
)

get neighbor residues within 10 A CB distance cutoff

use TenANeighborGraph. As input, residue_positions[i] is true for residues to be counted. As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.

References core::pose::Pose::energies(), core::chemical::ResidueType::name(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::type().

Referenced by select_loop_residues().

void protocols::loops::idealize_loop ( core::pose::Pose pose,
Loop const &  loop 
)
core::Real protocols::loops::loop_local_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops 
)

calculate rmsd of loop residues with repect to native (loop fit)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of each loop after fitting it onto the reference loop and when there are multiple loops, return the mean value.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), protocols::loops::Loops::num_loop(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

core::Real protocols::loops::loop_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
bool  CA_only,
bool  bb_only 
)
core::Real protocols::loops::loop_rmsd_with_superimpose ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
bool  CA_only,
bool  bb_only 
)

As above but actuall superimposes the non-loop part.

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

References loop_rmsd_with_superimpose_core().

Referenced by protocols::cluster::ClusterPhilStyle_Loop::get_distance_measure().

core::Real protocols::loops::loop_rmsd_with_superimpose_core ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
Loops const &  core,
bool  CA_only,
bool  bb_only 
)

As above but actually superimposes only the core part (in case there are multiple loops...)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), protocols::loops::Loops::is_loop_residue(), loop_rmsd(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), protocols::loops::Loops::size(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_filters::LoopRmsdEvaluator::apply(), and loop_rmsd_with_superimpose().

void protocols::loops::loopfinder ( core::pose::Pose pose,
loops::Loops &  loops 
)
void protocols::loops::loops_around_residues ( loops::Loops &  loops,
pose::Pose const &  pose,
vector1< Size > const &  residue_indices,
Size  gapsize,
Size  extend 
)

add a set of loops 'built' around the provided residue indices

A maximum of gapsize residues are allowed between specified residues for any given loop, loop ends are extended by extend residues, and chain discontinuity starts a new loop

Author:
ashworth

References add_loop(), make_table_of_pilot_apps::begin, core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, protocols::loops::Loops::num_loop(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::apply().

LoopsOP protocols::loops::loops_from_string ( std::string const  loop_str,
core::pose::Pose const &  pose 
)

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

References protocols::rosetta_scripts::parse_resnum(), and core::pose::Pose::total_residue().

Referenced by protocols::loops::FoldTreeFromLoops::apply(), and protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag().

void protocols::loops::loops_set_move_map ( Loops const &  loops,
utility::vector1< bool > const &  allow_sc_move,
core::kinematics::MoveMap mm 
)

create a MoveMap for use of minimization based on loop definition

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable.

References core::id::BB, protocols::loops::Loops::begin(), protocols::loops::Loops::end(), protocols::loops::Loops::num_loop(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

void protocols::loops::loops_set_move_map ( pose::Pose pose,
Loops const &  loops,
bool const  fix_template_sc,
core::kinematics::MoveMap mm,
Real  neighbor_dist 
)

create a MoveMap for use of minimization based on loop definition (wrapper)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable. Default neighbors are 10A CB dist from loop residues; neighbor_dist can be used to further filter the neighbors. This is a wrapper function which determine moveable sidechains and then call actual loop_set_move_map function to set up move map properly

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), select_loop_residues(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors().

core::Real protocols::loops::native_loop_core_CA_rmsd ( const core::pose::Pose native_pose,
const core::pose::Pose pose,
loops::Loops  loops,
int corelength 
)
std::ostream& protocols::loops::operator<< ( std::ostream &  os,
const Loop &  loop 
) [inline]
std::ostream& protocols::loops::operator<< ( std::ostream &  os,
const Loops &  loops 
)
std::ostream& protocols::loops::operator<< ( std::ostream &  os,
const LoopsFileIO &  loops 
)
void protocols::loops::read_loop_fragments ( utility::vector1< core::fragment::FragSetOP > &  frag_libs)

References read_loop_fragments().

void protocols::loops::read_loop_fragments ( std::vector< core::fragment::FragSetOP > &  frag_libs)
void protocols::loops::remove_cutpoint_variants ( core::pose::Pose pose,
bool  force 
)
void protocols::loops::remove_missing_density ( core::pose::Pose pose,
Loop const &  loop 
)
protocols::loops::Loops protocols::loops::remove_short_chunks ( protocols::loops::Loops const &  input_chunks,
core::Size  minimum_length_of_chunk 
)
protocols::loops::Loops protocols::loops::remove_small_gaps ( protocols::loops::Loops const &  input_chunks,
core::Size  gap_size 
)

If two chunks are separated by a small gap of size <= <gap_size>, combine them.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::num_loop(), and protocols::loops::Loop::set_stop().

Referenced by extract_secondary_structure_chunks().

static numeric::random::RandomGenerator protocols::loops::RG ( 430  ) [static]
static numeric::random::RandomGenerator protocols::loops::RG ( 429  ) [static]
static numeric::random::RandomGenerator protocols::loops::RG ( 31413  ) [static]
void protocols::loops::safe_set_extended_torsions_and_idealize_loops ( const protocols::loops::Loops loops,
core::pose::Pose pose 
)

Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops.

References protocols::loops::Loops::empty(), and set_extended_torsions_and_idealize_loops().

void protocols::loops::select_loop_frags ( loops::Loops const &  loops,
core::fragment::FragSet source,
core::fragment::FragSet loop_frags,
Size  shorten 
)
void protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loops const &  loops,
bool const  include_neighbors,
utility::vector1< bool > &  map,
Real  neighbor_dist 
)
void protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loop const &  loop,
bool const  include_neighbors,
utility::vector1< bool > &  map,
Real  neighbor_dist 
)

for one loop only

References protocols::loops::Loops::add_loop(), and select_loop_residues().

void protocols::loops::set_extended_torsions ( core::pose::Pose pose,
Loop const &  loop 
)
void protocols::loops::set_extended_torsions_and_idealize_loops ( core::pose::Pose pose,
loops::Loops  loops 
)
void protocols::loops::set_loop_cutpoint_in_pose_fold_tree ( Size const  new_cutpoint,
pose::Pose pose,
Size const  loop_begin,
Size const  loop_end 
)

Slide a loop cutpoint to a (potentially) new position

Note:
Updates the pose's foldtree, either moving or adding a loop cutpoint
Updates CUTPOINT_UPPER and CUTPOINT_LOWER variant status of residues in loop to match new cutpoint location

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), core::pose::remove_variant_type_from_pose_residue(), and core::pack::tt().

void protocols::loops::set_move_map_for_centroid_loop ( Loop const &  loop,
core::kinematics::MoveMap mm 
)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable.

References core::id::BB, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), and protocols::loop_build::LoopMover_SlidingWindow::model_loop().

bool protocols::loops::set_secstruct_from_dssp ( pose::Pose pose,
std::string const &  filename 
)

another helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a DSSP file and set that to a Pose. (Rhiju's copy of Chu's psipred reader). Chu, should these functions be moved somewhere to core, along with pdb readers, etc?

References core::pose::Pose::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::total_residue(), and core::pack::tt().

Referenced by protocols::comparative_modeling::initialize_ss(), and protocols::loop_build::LoopBuild_main().

bool protocols::loops::set_secstruct_from_psipred_ss2 ( pose::Pose pose)

helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a psipred_ss2 file and set that to a Pose. A temporary setup since there is very limited ss support in Pose right now.

References core::pose::read_psipred_ss2_file(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::set_ss_from_phipsi(), and core::pack::tt().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::LoopRebuild::apply(), protocols::comparative_modeling::initialize_ss(), and protocols::loop_build::LoopBuild_main().

void protocols::loops::set_single_loop_fold_tree ( core::pose::Pose pose,
Loop const &  loop 
)
protocols::loops::Loops protocols::loops::split_by_ca_ca_dist ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  input_chunks,
core::Real const  CA_CA_distance_cutoff 
)
protocols::loops::Loops protocols::loops::split_by_resSeq ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  input_chunks 
)
protocols::loops::Loops protocols::loops::split_by_resSeq ( core::pose::Pose const &  pose)
static basic::Tracer protocols::loops::tr ( "loops"  ) [static]
static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopsFileIO"  ) [static]
static basic::Tracer protocols::loops::tr ( "protocols.loops.Loop"  ) [static]
static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopMoverFactory"  ) [static]
static basic::Tracer protocols::loops::TR ( "protocols.loops.make_loops"  ,
t_info   
) [static]
static basic::Tracer protocols::loops::TR ( "protocols.loops.FoldTreeFromLoopsWrapper"  ) [static]
void protocols::loops::trim_back_sequence_mapping ( id::SequenceMapping mapping,
std::string const &  source_seq,
std::string const &  target_seq,
Size const  min_loop_size 
)

Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.

References core::id::SequenceMapping::reverse(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and core::pack::tt().

basic::Tracer protocols::loops::tt ( "protocols.loops.loops_main"  )

Variable Documentation

const double protocols::loops::EXT_OMG = 180 [static]
const double protocols::loops::EXT_PHI = -150 [static]
const double protocols::loops::EXT_PSI = +150 [static]
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