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protocols::loops::Loop Class Reference

single loop definition More...

#include <Loop.hh>

Inheritance diagram for protocols::loops::Loop:
Inheritance graph
[legend]

Public Member Functions

 ~Loop () override
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 Loop ()
 default constructor More...
 
 Loop (SerializedLoop loop)
 
 Loop (core::Size const start_in, core::Size const stop_in, core::Size const cut_in=0, core::Real skip_rate=0.0, bool const extended_in=false)
 input constructor More...
 
bool is_extended () const
 
core::Size start () const
 
core::Size stop () const
 
core::Size cut () const
 
core::Size size () const
 
core::Real skip_rate () const
 
void set_extended (bool input)
 
void set_start (core::Size input)
 
void set_stop (core::Size input)
 
void set_cut (core::Size input)
 
core::Size length () const
 Assuming that the loop represents a contiguous stretch of residues, returns the length. Makes no assumptions about directionality. That is, Loop(3,8).length() == Loop(8,3).length(). Constant time procedure. More...
 
bool increasing () const
 Returns true if the loop's elements are increasing. More...
 
bool decreasing () const
 Returns true if the loop's elements are decreasing. More...
 
core::Size midpoint () const
 Returns the midpoint of the loop. More...
 
bool operator< (Loop const &larger) const
 
bool operator== (Loop const &other) const
 
bool operator!= (Loop const &other) const
 
void get_residues (utility::vector1< Size > &selection) const
 add all residues within this loop definition into 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...
 
void choose_cutpoint (core::pose::Pose const &pose)
 
void auto_choose_cutpoint (core::pose::Pose const &pose)
 Autochoose a cutpoint using the secondary structure of the pose unless cutpoint is already set. More...
 
bool is_terminal (core::pose::Pose const &pose) const
 
virtual void show (std::ostream &output=std::cout) const
 Generate a string representation of Loop. More...
 

Private Attributes

core::Size start_
 
core::Size stop_
 
core::Size cut_
 
core::Real skip_rate_
 
bool extended_
 

Detailed Description

single loop definition

Constructor & Destructor Documentation

protocols::loops::Loop::~Loop ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::loops::Loop::Loop ( )
inline

default constructor

protocols::loops::Loop::Loop ( SerializedLoop  loop)
inline
protocols::loops::Loop::Loop ( core::Size const  start_in,
core::Size const  stop_in,
core::Size const  cut_in = 0,
core::Real  skip_rate = 0.0,
bool const  extended_in = false 
)
inline

input constructor

Member Function Documentation

void protocols::loops::Loop::auto_choose_cutpoint ( core::pose::Pose const &  pose)
inline

Autochoose a cutpoint using the secondary structure of the pose unless cutpoint is already set.

References choose_cutpoint(), and cut_.

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply().

void protocols::loops::Loop::choose_cutpoint ( core::pose::Pose const &  pose)
core::Size protocols::loops::Loop::cut ( ) const
inline

References cut_.

Referenced by protocols::loops::Loops::add_loop(), protocols::loops::Loops::add_overlap_loop(), protocols::loops::add_single_cutpoint_variant(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::kinematic_closure::ClosureProblem::cut_residue(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::antibody::H3RefineCCD::init(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), operator<(), operator==(), protocols::kinematic_closure::pivot_pickers::LoopPivots::pick(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), and protocols::loops::loop_mover::LoopCM::yield_claims().

bool protocols::loops::Loop::decreasing ( ) const
inline

Returns true if the loop's elements are decreasing.

References increasing().

void protocols::loops::Loop::get_residues ( utility::vector1< Size > &  selection) const

add all residues within this loop definition into selection

References start_, and stop_.

bool protocols::loops::Loop::increasing ( ) const
inline

Returns true if the loop's elements are increasing.

References start(), and stop().

Referenced by decreasing(), and midpoint().

bool protocols::loops::Loop::is_extended ( ) const
inline
bool protocols::loops::Loop::is_terminal ( core::pose::Pose const &  pose) const
core::Size protocols::loops::Loop::length ( ) const
inline
core::Size protocols::loops::Loop::midpoint ( ) const
inline
bool protocols::loops::Loop::operator!= ( Loop const &  other) const
inline
bool protocols::loops::Loop::operator< ( Loop const &  larger) const
inline

References cut(), size(), and start().

bool protocols::loops::Loop::operator== ( Loop const &  other) const
inline

References cut(), size(), and start().

void protocols::loops::Loop::set_cut ( core::Size  input)
inline
void protocols::loops::Loop::set_extended ( bool  input)
inline

References extended_.

void protocols::loops::Loop::set_start ( core::Size  input)
inline
void protocols::loops::Loop::set_stop ( core::Size  input)
inline
void protocols::loops::Loop::show ( std::ostream &  output = std::cout) const
virtual

Generate a string representation of Loop.

Print the start, stop and cut residues along with the skip rate and the whether or not the loop will be extended.

References cut_, extended_, size(), skip_rate_, start_, and stop_.

Referenced by protocols::loops::operator<<(), and protocols::loops::loop_closure::ccd::CCDLoopClosureMover::show().

core::Size protocols::loops::Loop::size ( ) const
inline
core::Real protocols::loops::Loop::skip_rate ( ) const
inline
core::Size protocols::loops::Loop::start ( ) const
inline

References start_.

Referenced by protocols::loops::Loops::add_loop(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::loops::Loops::add_overlap_loop(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::RefineOneCDRLoopCentroid::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::nonlocal::avg_ca_position(), protocols::loops::loop_closure::ccd::ShortLoopClosure::catch_fragment(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchor_position(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction(), protocols::rigid::RigidBodyMotionMover::compute_bias(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::nonlocal::decompose(), protocols::nonlocal::SheetTranslate::decompose_structure(), protocols::nonlocal::HelixRotate::decompose_structure(), protocols::loop_modeling::samplers::LegacyKicSampler::do_apply(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::star::Extender::extend_unaligned(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap(), protocols::kinematic_closure::ClosureProblem::first_residue(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries(), protocols::abinitio::AbrelaxApplication::fold(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::antibody::AntibodyInfo::get_CDR_length(), protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem(), protocols::antibody::design::GeneralAntibodyModeler::get_cdrs_movemap_with_overhang(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::loops::idealize_loop(), increasing(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::antibody::H3RefineCCD::init(), protocols::loops::loop_closure::ccd::LoopClosure::init(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::loops::Loops::invert(), is_terminal(), protocols::nonlocal::SheetTranslate::is_valid(), protocols::nonlocal::HelixRotate::is_valid(), protocols::nonlocal::HelixRotate::jump_containing_helix(), protocols::nonlocal::SheetTranslate::jump_containing_sheet(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), protocols::antibody::AntibodyInfo::kink_cation_residue(), length(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), midpoint(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), protocols::loops::RationalLoopComparator::operator()(), protocols::loops::Loop_lt::operator()(), operator<(), operator==(), protocols::kinematic_closure::pivot_pickers::EndToEndPivots::pick(), protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots::pick(), protocols::kinematic_closure::pivot_pickers::LoopPivots::pick(), protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots::pick(), protocols::kinematic_closure::pivot_pickers::StandardPivots::pick(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop(), protocols::loops::set_move_map_for_centroid_loop(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::setup_torsions(), protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), switch_movemap(), and protocols::loops::loop_mover::LoopCM::yield_claims().

core::Size protocols::loops::Loop::stop ( ) const
inline

References stop_.

Referenced by protocols::loops::Loops::add_loop(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::loops::Loops::add_overlap_loop(), protocols::nonlocal::SheetTranslate::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody::RefineOneCDRLoopCentroid::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::nonlocal::avg_ca_position(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchor_position(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction(), protocols::rigid::RigidBodyMotionMover::compute_bias(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::nonlocal::decompose(), protocols::nonlocal::SheetTranslate::decompose_structure(), protocols::nonlocal::HelixRotate::decompose_structure(), protocols::antibody::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::loop_modeling::samplers::LegacyKicSampler::do_apply(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::star::Extender::extend_unaligned(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::antibody::AntibodyInfo::get_CDR_length(), protocols::antibody::AntibodyInfo::get_CDR_sequence_with_stem(), protocols::antibody::design::GeneralAntibodyModeler::get_cdrs_movemap_with_overhang(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::loops::idealize_loop(), increasing(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::antibody::H3RefineCCD::init(), protocols::loops::loop_closure::ccd::LoopClosure::init(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::loops::Loops::invert(), is_terminal(), protocols::nonlocal::SheetTranslate::is_valid(), protocols::nonlocal::HelixRotate::is_valid(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_anion_residue(), protocols::antibody::AntibodyInfo::kink_begin(), protocols::antibody::AntibodyInfo::kink_end(), protocols::antibody::AntibodyInfo::kink_trp(), protocols::kinematic_closure::ClosureProblem::last_residue(), length(), protocols::abinitio::abscript::loop_stop_comp(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), midpoint(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), protocols::loops::Loop_lt::operator()(), protocols::kinematic_closure::pivot_pickers::EndToEndPivots::pick(), protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots::pick(), protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots::pick(), protocols::kinematic_closure::pivot_pickers::LoopPivots::pick(), protocols::kinematic_closure::pivot_pickers::StandardPivots::pick(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions(), protocols::loops::set_move_map_for_centroid_loop(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::setup_torsions(), protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), switch_movemap(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and protocols::loops::loop_mover::LoopCM::yield_claims().

void protocols::loops::Loop::switch_movemap ( core::kinematics::MoveMap movemap,
core::id::TorsionType  id,
bool  allow_moves = true 
) const

switch DOF_Type for residues in loop. id::CHI, id::BB — don't use with id::JUMP

References core::kinematics::MoveMap::set(), start(), and stop().

Member Data Documentation

core::Size protocols::loops::Loop::cut_
private
bool protocols::loops::Loop::extended_
private

Referenced by is_extended(), set_extended(), and show().

core::Real protocols::loops::Loop::skip_rate_
private

Referenced by show(), and skip_rate().

core::Size protocols::loops::Loop::start_
private
core::Size protocols::loops::Loop::stop_
private

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