Rosetta 3.4
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protocols::loops::Loop Class Reference

single loop definition More...

#include <Loop.hh>

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List of all members.

Public Member Functions

 Loop ()
 default constructor
 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
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.
bool increasing () const
 Returns true if the loop's elements are increasing.
bool decreasing () const
 Returns true if the loop's elements are decreasing.
core::Size midpoint () const
 Returns the midpoint of the loop.
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
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
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.
bool is_terminal (core::pose::Pose const &pose) const

Friends

std::ostream & operator<< (std::ostream &os, const Loop &loop)

Detailed Description

single loop definition


Constructor & Destructor Documentation

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().

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]
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

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]

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.

References start(), and stop().

Referenced by protocols::nonlocal::avg_ca_position(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::medal::chunk_probabilities(), protocols::nonlocal::decompose(), and midpoint().

core::Size protocols::loops::Loop::midpoint ( ) const [inline]

Returns the midpoint of the loop.

References increasing(), length(), start(), and stop().

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]
void protocols::loops::Loop::set_start ( core::Size  input) [inline]
void protocols::loops::Loop::set_stop ( core::Size  input) [inline]
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]

Referenced by protocols::loops::Loops::add_loop(), protocols::loops::Loops::add_overlap_loop(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::CcdMover::apply(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), protocols::nonlocal::avg_ca_position(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::comparative_modeling::bounded_loops_from_alignment(), protocols::loops::loop_closure::ccd::ShortLoopClosure::catch_fragment(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::medal::chunk_probabilities(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::nonlocal::decompose(), protocols::star::Extender::extend_unaligned(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::abinitio::AbrelaxApplication::fold(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::loops::idealize_loop(), increasing(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::loops::loop_closure::ccd::LoopClosure::init(), protocols::loops::Loops::invert(), is_terminal(), length(), 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_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::Loop_lt::operator()(), protocols::loops::RationalLoopComparator::operator()(), operator<(), operator==(), protocols::loops::remove_missing_density(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::set_extended_torsions(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::loops::set_move_map_for_centroid_loop(), protocols::loops::set_single_loop_fold_tree(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), setup_pert_foldtree(), protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure(), protocols::antibody2::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), and switch_movemap().

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

Referenced by protocols::loops::Loops::add_loop(), protocols::loops::Loops::add_overlap_loop(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::CcdMover::apply(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), protocols::nonlocal::avg_ca_position(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::comparative_modeling::bounded_loops_from_alignment(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::medal::chunk_probabilities(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::nonlocal::decompose(), protocols::star::Extender::extend_unaligned(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::loops::idealize_loop(), increasing(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::loops::loop_closure::ccd::LoopClosure::init(), protocols::loops::Loops::invert(), is_terminal(), length(), 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_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::Loop_lt::operator()(), protocols::loops::remove_missing_density(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::loops::set_extended_torsions(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::loops::set_move_map_for_centroid_loop(), protocols::loops::set_single_loop_fold_tree(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), setup_pert_foldtree(), protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure(), protocols::antibody2::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), and switch_movemap().

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().


Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
const Loop loop 
) [friend]

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