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protocols::loops::Loops Class Reference

#include <Loops.hh>

Inheritance diagram for protocols::loops::Loops:
Inheritance graph
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Public Types

typedef utility::vector1< LoopLoopList
 
typedef utility::vector1
< SerializedLoop
SerializedLoopList
 
typedef LoopList::iterator iterator
 
typedef LoopList::const_iterator const_iterator
 

Public Member Functions

bool empty () const
 
core::Size num_loop () const
 
const_iterator begin () const
 
const_iterator end () const
 
iterator v_begin ()
 
iterator v_end ()
 
 Loops ()
 
 Loops (const Loops &src)
 
 Loops (SerializedLoopList const &src)
 
 Loops (std::string const &loop_file_name)
 
 Loops (bool setup_loops_from_options_system)
 
 Loops (utility::vector1< bool > const &selection, bool randomize_cutpoint=true)
 
Loopsoperator= (Loops const &src)
 
 ~Loops () override
 
LoopsOP clone () const
 
void read_loops_options ()
 
void write_loops_to_file (std::string const &filename, std::string token="LOOP") const
 
void write_loops_to_stream (std::ostream &data, std::string token) const
 
void add_loop (Loop loop, core::Size minimal_gap=0)
 
void add_loop (core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false)
 
void add_loop (const const_iterator &it)
 
void add_loop (const iterator &it)
 
void push_back (Loop loop)
 
void push_back (core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false)
 
void add_overlap_loop (Loops loops)
 
void add_overlap_loop (const Loop &loop)
 
void delete_loop (core::Size const start, core::Size const stop)
 
const_iterator one_random_loop () const
 
core::Size loop_size (core::Size const loop_num) const
 
core::Size loop_size () const
 return number of residues in all loops of this definition – sum_i( loop_size( i ) ) More...
 
core::Size size () const
 
core::Size nr_residues () const
 
void sequential_order ()
 
void clear ()
 
LoopList const & loops () const
 
bool is_loop_residue (core::Size const seqpos, int const offset=0) const
 Is seqpos contained in any of my loops? More...
 
bool has (core::Size const seqpos, int const offset=0) const
 is seqpos a residue in this Loops container ? More...
 
void set_extended (bool input)
 
void make_sequence_shift (int shift)
 
bool loop_of_residue (core::Size const seqpos, Loop &loop) const
 yield the Loop which contains the residue seqpos, returns false if seqpos is not in any residue. More...
 
Loops invert (core::Size num_residues) const
 Given the total number of residues, returns the inverse of this selection. More...
 
void switch_movemap (core::kinematics::MoveMap &movemap, core::id::TorsionType, bool allow_moves=true) const
 switch DOF_Type for residues in loop. id::CHI, id::BB — don't use with id::JUMP More...
 
core::Size loop_index_of_residue (core::Size const seqpos) const
 
void auto_choose_cutpoints (core::pose::Pose const &pose)
 
void choose_cutpoints (core::pose::Pose const &pose)
 
void verify_against (core::pose::Pose const &pose) const
 
void remove_terminal_loops (core::pose::Pose const &pose)
 
void grow_all_loops (core::Size nres, core::Real magnitude)
 Extend a loop. More...
 
void grow_all_loops (core::pose::Pose const &pose, core::Real magnitude)
 Extend a loop (don't extend across cutpoints) More...
 
void grow_loop (core::pose::Pose const &pose, Loop &loop, core::Real magnitude)
 Extend a loop (don't extend across cutpoints) More...
 
void grow_loop_away_from_sheets (core::pose::Pose const &pose, Loop &loop, core::Real magnitude)
 if possible grows loop will not cross cutpoints or if possible into sheets More...
 
void grow_loop (core::Size nres, Loop &loop, core::Real magnitude)
 Extend a loop. More...
 
void grow_loop (core::Size nres, Loop &loop, core::Real mag_left, core::Real mag_right)
 Extend a loop unequally in both dirs. More...
 
std::string const & loop_file_name ()
 
void set_loop_file_name_and_reset (std::string const &loop_filename)
 
bool strict_looprelax_checks ()
 
void set_strict_looprelax_checks (bool const check)
 
std::string const & file_reading_token ()
 
void set_file_reading_token (std::string const &token)
 
void center_of_mass (const core::pose::Pose &pose, numeric::xyzVector< core::Real > *center) const
 Computes the center of mass of the Ca atoms specified by this instance, writing the result to

. Assumes there is no missing backbone density.
More...
 
template<class T >
void transfer_to_residue_vector (utility::vector1< T > &, T val) const
 set each loop-residue in the vector to val. input vector of nres length ( if shorter last residues of loop are ignored ) More...
 
void get_residues (utility::vector1< Size > &selection) const
 add all residues within this loop definition into selection More...
 
const Loopoperator[] (core::Size const i) const
 
Loopoperator[] (core::Size const i)
 
bool operator== (Loops const &other) const
 
bool operator!= (Loops const &other) const
 

Static Public Member Functions

static LoopsFileIOOP get_loop_file_reader ()
 Convenience function for creating a (stateless!) class that is able to read in loops files in several different formats. More...
 

Private Member Functions

void init (LoopList const &loops_in, bool const read_loop_file_from_options=false, std::string const &passed_in_filename="")
 
LoopList setup_loops_from_data (SerializedLoopList const &loop_data)
 
void read_loop_file ()
 

Private Attributes

LoopList loops_
 
bool strict_looprelax_checks_on_file_reads_
 
std::string loop_filename_
 
std::string file_reading_token_
 

Friends

std::ostream & operator<< (std::ostream &os, const Loops &loops)
 

Member Typedef Documentation

typedef LoopList::const_iterator protocols::loops::Loops::const_iterator
typedef LoopList::iterator protocols::loops::Loops::iterator
typedef utility::vector1< Loop > protocols::loops::Loops::LoopList

Constructor & Destructor Documentation

protocols::loops::Loops::Loops ( )

References init().

Referenced by clone().

protocols::loops::Loops::Loops ( const Loops src)

References init(), and loops().

protocols::loops::Loops::Loops ( SerializedLoopList const &  src)

References init(), and setup_loops_from_data().

protocols::loops::Loops::Loops ( std::string const &  loop_file_name)

References init().

protocols::loops::Loops::Loops ( bool  setup_loops_from_options_system)

References init().

protocols::loops::Loops::Loops ( utility::vector1< bool > const &  selection,
bool  randomize_cutpoint = true 
)
protocols::loops::Loops::~Loops ( )
overridedefault

Member Function Documentation

void protocols::loops::Loops::add_loop ( loops::Loop  loop,
core::Size  minimal_gap = 0 
)

References protocols::loops::Loop::cut(), loops_, protocols::mean_field::max(), protocols::mean_field::min(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, and protocols::loops::tr().

Referenced by protocols::loops::add_loop(), add_loop(), protocols::antibody::design::add_loops_from_bool_vector(), protocols::loops::addScoresForLoopParts(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::loops::compute_ss_regions(), protocols::nonlocal::SheetTranslate::decompose_structure(), protocols::nonlocal::HelixRotate::decompose_structure(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::hybridization::HybridizeProtocol::domain_parse_templates(), protocols::antibody::design::GeneralAntibodyModeler::extend_CDR(), protocols::loops::extract_secondary_structure_chunks(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::loops::find_non_protein_chunks(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::loophash::LoopHashLibrary::get_all(), protocols::abinitio::get_core(), protocols::pose_length_moves::FixAllLoopsMover::get_loops(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::get_one_random_loop(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::forge::methods::intervals_to_confirmation_loops(), protocols::forge::methods::intervals_to_loops(), invert(), protocols::loops::loopfinder(), Loops(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::loops::move_map_from_loop(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::parse_seeds(), protocols::antibody_legacy::Antibody::populate_all_cdrs(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), push_back(), protocols::loops::remove_short_chunks(), protocols::loops::remove_small_gaps(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::select_loop_residues(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::antibody::AntibodyInfo::setup_simple_fold_tree(), protocols::hybridization::DDomainParse::split(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors(), protocols::rigid::RigidBodyMotionMover::update_chunks(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

void protocols::loops::Loops::add_loop ( core::Size const  start,
core::Size const  stop,
core::Size const  cut = 0,
core::Real  skip_rate = 0.0,
bool const  extended = false 
)

References add_loop().

void protocols::loops::Loops::add_loop ( const const_iterator it)

References add_loop().

void protocols::loops::Loops::add_loop ( const iterator it)

References add_loop().

void protocols::loops::Loops::add_overlap_loop ( Loops  loops)
void protocols::loops::Loops::add_overlap_loop ( const Loop loop)
void protocols::loops::Loops::auto_choose_cutpoints ( core::pose::Pose const &  pose)
Loops::const_iterator protocols::loops::Loops::begin ( ) const
void protocols::loops::Loops::center_of_mass ( const core::pose::Pose pose,
numeric::xyzVector< core::Real > *  center 
) const

Computes the center of mass of the Ca atoms specified by this instance, writing the result to

. Assumes there is no missing backbone density.

Note: if this method is called on an instance without any Loop's, returns (0,0,0).

References core::pose::Pose::xyz().

Referenced by protocols::nonlocal::StarTreeBuilder::set_up(), and protocols::star::StarAbinitio::setup_kinematics().

void protocols::loops::Loops::choose_cutpoints ( core::pose::Pose const &  pose)

References v_begin(), and v_end().

void protocols::loops::Loops::clear ( )
LoopsOP protocols::loops::Loops::clone ( ) const

References Loops().

void protocols::loops::Loops::delete_loop ( core::Size const  start,
core::Size const  stop 
)

References loops_.

Referenced by add_overlap_loop().

bool protocols::loops::Loops::empty ( ) const
Loops::const_iterator protocols::loops::Loops::end ( ) const
std::string const & protocols::loops::Loops::file_reading_token ( )

References file_reading_token_.

LoopsFileIOOP protocols::loops::Loops::get_loop_file_reader ( )
static

Convenience function for creating a (stateless!) class that is able to read in loops files in several different formats.

void protocols::loops::Loops::get_residues ( utility::vector1< Size > &  selection) const
void protocols::loops::Loops::grow_all_loops ( core::Size  nres,
core::Real  magnitude 
)
void protocols::loops::Loops::grow_all_loops ( core::pose::Pose const &  pose,
core::Real  magnitude 
)

Extend a loop (don't extend across cutpoints)

References grow_loop(), loops_, and size().

void protocols::loops::Loops::grow_loop ( core::pose::Pose const &  pose,
Loop loop,
core::Real  magnitude 
)

Extend a loop (don't extend across cutpoints)

Extend a loop .. don't extend across cutpoints in the pose.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by grow_all_loops(), grow_loop(), and grow_loop_away_from_sheets().

void protocols::loops::Loops::grow_loop ( core::Size  nres,
Loop loop,
core::Real  magnitude 
)

Extend a loop.

References grow_loop().

void protocols::loops::Loops::grow_loop ( core::Size  nres,
Loop loop,
core::Real  mag_left,
core::Real  mag_right 
)
void protocols::loops::Loops::grow_loop_away_from_sheets ( core::pose::Pose const &  pose,
Loop loop,
core::Real  magnitude 
)
bool protocols::loops::Loops::has ( core::Size const  seqpos,
int const  offset = 0 
) const

is seqpos a residue in this Loops container ?

References is_loop_residue().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings().

void protocols::loops::Loops::init ( LoopList const &  loops_in,
bool const  read_loop_file_from_options = false,
std::string const &  passed_in_filename = "" 
)
private
Loops protocols::loops::Loops::invert ( core::Size  num_residues) const
bool protocols::loops::Loops::is_loop_residue ( core::Size const  seqpos,
int const  offset = 0 
) const
std::string const & protocols::loops::Loops::loop_file_name ( )
Size protocols::loops::Loops::loop_index_of_residue ( core::Size const  seqpos) const
bool protocols::loops::Loops::loop_of_residue ( core::Size const  seqpos,
Loop loop 
) const

yield the Loop which contains the residue seqpos, returns false if seqpos is not in any residue.

References loops_.

Size protocols::loops::Loops::loop_size ( core::Size const  loop_num) const
Size protocols::loops::Loops::loop_size ( ) const

return number of residues in all loops of this definition – sum_i( loop_size( i ) )

References loops_, and size().

Referenced by nr_residues().

Loops::LoopList const & protocols::loops::Loops::loops ( ) const
void protocols::loops::Loops::make_sequence_shift ( int  shift)
core::Size protocols::loops::Loops::nr_residues ( ) const

References loop_size().

core::Size protocols::loops::Loops::num_loop ( ) const

References loops_.

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::pose_length_moves::AnalyzeLoopModeling::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchors(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), protocols::hybridization::HybridizeProtocol::domain_parse_templates(), protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score(), empty(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::hybridization::HybridizeFoldtreeDynamic::get_core_chunk_index_from_position(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops(), protocols::antibody::AntibodyInfo::get_MoveMap_for_LoopsandDock(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), invert(), protocols::nonlocal::HelixRotate::jump_containing_helix(), protocols::nonlocal::SheetTranslate::jump_containing_sheet(), protocols::loops::loop_local_rmsd(), protocols::loops::loops_around_residues(), protocols::antibody_legacy::AntibodyModeler::relax_cdrs(), protocols::loops::remove_small_gaps(), protocols::hybridization::renumber_with_pdb_info(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::star::StarAbinitio::setup_kinematics(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and protocols::hybridization::HybridizeProtocol::update_last_template().

Loops::const_iterator protocols::loops::Loops::one_random_loop ( ) const
bool protocols::loops::Loops::operator!= ( Loops const &  other) const
Loops & protocols::loops::Loops::operator= ( Loops const &  src)

References loops_.

bool protocols::loops::Loops::operator== ( Loops const &  other) const

References loops_, and size().

const Loop & protocols::loops::Loops::operator[] ( core::Size const  i) const

References loops_.

Loop & protocols::loops::Loops::operator[] ( core::Size const  i)

References loops_.

void protocols::loops::Loops::push_back ( Loop  loop)
void protocols::loops::Loops::push_back ( core::Size const  start,
core::Size const  stop,
core::Size const  cut = 0,
core::Real  skip_rate = 0.0,
bool const  extended = false 
)

References add_loop().

void protocols::loops::Loops::read_loop_file ( )
private
void protocols::loops::Loops::read_loops_options ( )
void protocols::loops::Loops::remove_terminal_loops ( core::pose::Pose const &  pose)

References loops_.

void protocols::loops::Loops::sequential_order ( )
void protocols::loops::Loops::set_extended ( bool  input)

References v_begin(), and v_end().

void protocols::loops::Loops::set_file_reading_token ( std::string const &  token)

References file_reading_token_.

void protocols::loops::Loops::set_loop_file_name_and_reset ( std::string const &  loop_filename)

References loop_filename_, and read_loop_file().

Referenced by init(), and read_loops_options().

void protocols::loops::Loops::set_strict_looprelax_checks ( bool const  check)
Loops::LoopList protocols::loops::Loops::setup_loops_from_data ( SerializedLoopList const &  loop_data)
private

Referenced by Loops(), and read_loop_file().

core::Size protocols::loops::Loops::size ( ) const

References loops_.

Referenced by protocols::seeded_abinitio::add_dist_constraints(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::loops::addScoresForLoopParts(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::rigid::RigidBodyMotionMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::LoopRebuild::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::LoopRebuild::barcode_extend_stems(), protocols::nonlocal::combine_and_trim(), protocols::simple_ddg::SSElementBisectddGFilter::compute(), protocols::simple_filters::SSElementMotifContactFilter::compute(), protocols::rigid::RigidBodyMotionMover::compute_bias(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::topology_broker::FragmentClaimer::generate_claims(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), grow_all_loops(), protocols::rbsegment_relax::AutoRBMover::grow_flexible(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::loops::loop_rmsd_with_superimpose_core(), loop_size(), protocols::hybridization::HybridizeFoldtreeDynamic::make_complete_chunks(), protocols::forge::methods::make_star_foldtree(), protocols::loops::native_loop_core_CA_rmsd(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), one_random_loop(), operator==(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::rbsegment_relax::read_RBSegment_file(), protocols::topology_broker::RigidChunkClaimer::receive_message(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), protocols::LoopRebuild::select_one_loop(), protocols::abinitio::abscript::RigidChunkCM::select_parts(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::rbsegment_relax::select_RBsegments(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::star::setup_constraints(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), protocols::hybridization::MRMover::trim_target_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and protocols::simple_filters::SSElementMotifContactFilter::which_ssElement().

bool protocols::loops::Loops::strict_looprelax_checks ( )
void protocols::loops::Loops::switch_movemap ( core::kinematics::MoveMap movemap,
core::id::TorsionType  id,
bool  allow_moves = true 
) const
template<class T >
void protocols::loops::Loops::transfer_to_residue_vector ( utility::vector1< T > &  vector,
val 
) const
Loops::iterator protocols::loops::Loops::v_begin ( )
Loops::iterator protocols::loops::Loops::v_end ( )
void protocols::loops::Loops::verify_against ( core::pose::Pose const &  pose) const
void protocols::loops::Loops::write_loops_to_file ( std::string const &  filename,
std::string  token = "LOOP" 
) const
void protocols::loops::Loops::write_loops_to_stream ( std::ostream &  data,
std::string  token 
) const

Referenced by write_loops_to_file().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
const Loops loops 
)
friend

Member Data Documentation

std::string protocols::loops::Loops::file_reading_token_
private
std::string protocols::loops::Loops::loop_filename_
private
LoopList protocols::loops::Loops::loops_
private
bool protocols::loops::Loops::strict_looprelax_checks_on_file_reads_
private

The documentation for this class was generated from the following files: