protocols::loops::Loops Class Reference

#include <Loops.hh>

Inheritance diagram for protocols::loops::Loops:

Collaboration diagram for protocols::loops::Loops:

Public Types
typedef utility::vector1< Loop >	LoopList
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 &	operator= (Loops const &src)
virtual	~Loops ()
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
LoopsFileIOOP	get_loop_file_reader () 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 Loop &	operator[] (core::Size const i) const
Loop &	operator[] (core::Size const i)
bool	operator== (Loops const &other) const
bool	operator!= (Loops const &other) const

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_
LoopsFileIOOP	loop_file_reader_
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)

Detailed Description

Definition at line 50 of file Loops.hh.

Member Typedef Documentation

typedef LoopList::const_iterator protocols::loops::Loops::const_iterator

Definition at line 56 of file Loops.hh.

typedef LoopList::iterator protocols::loops::Loops::iterator

Definition at line 55 of file Loops.hh.

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

Definition at line 53 of file Loops.hh.

typedef utility::vector1< SerializedLoop > protocols::loops::Loops::SerializedLoopList

Definition at line 54 of file Loops.hh.

Constructor & Destructor Documentation

protocols::loops::Loops::Loops

(

)

Definition at line 55 of file Loops.cc.

References init().

protocols::loops::Loops::Loops

(

const Loops &

src)

Definition at line 60 of file Loops.cc.

References init(), and loops().

protocols::loops::Loops::Loops

(

SerializedLoopList const &

src)

Definition at line 65 of file Loops.cc.

References init(), and setup_loops_from_data().

protocols::loops::Loops::Loops

(

std::string const &

loop_file_name)

Definition at line 70 of file Loops.cc.

References init().

protocols::loops::Loops::Loops

(

bool

setup_loops_from_options_system)

Definition at line 75 of file Loops.cc.

References init().

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

virtual

Definition at line 81 of file Loops.cc.

Member Function Documentation

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

Definition at line 210 of file Loops.cc.

References protocols::loops::Loop::cut(), loops_, 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::loops::addScoresForLoopParts(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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::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::loops::loop_mover::refine::LoopRefineInnerCycle::get_one_random_loop(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::forge::methods::intervals_to_confirmation_loops(), protocols::forge::methods::intervals_to_loops(), invert(), protocols::loops::loopfinder(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), 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::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::parse_seeds(), protocols::antibody::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::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::hybridization::FoldTreeHybridize::setup_foldtree(), 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(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors().

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
	)

Definition at line 247 of file Loops.cc.

References add_loop().

void protocols::loops::Loops::add_loop

(

const const_iterator &

it)

Definition at line 259 of file Loops.cc.

References add_loop().

void protocols::loops::Loops::add_loop

(

const iterator &

it)

Definition at line 265 of file Loops.cc.

References add_loop().

void protocols::loops::Loops::add_overlap_loop

(

Loops

loops)

Definition at line 286 of file Loops.cc.

References begin(), and end().

void protocols::loops::Loops::add_overlap_loop

(

const Loop

loop)

Definition at line 294 of file Loops.cc.

References protocols::loops::Loop::cut(), delete_loop(), protocols::loops::Loop::is_extended(), loops_, protocols::loops::Loop::skip_rate(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), and protocols::loops::stop.

void protocols::loops::Loops::auto_choose_cutpoints

(

core::pose::Pose const &

pose)

Definition at line 540 of file Loops.cc.

References v_begin(), and v_end().

Referenced by protocols::rbsegment_relax::guess_rbsegs_from_pose().

Loops::const_iterator protocols::loops::Loops::begin

(

)

const

Definition at line 124 of file Loops.cc.

References loops_.

Referenced by protocols::loops::add_loop_flank_residues_bb_to_movemap(), add_overlap_loop(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::LoopRefine::apply(), protocols::LoopRebuild::build_random_loops(), protocols::loops::ccd_close_loops(), protocols::simple_moves::WobbleMover::ccd_closure(), center_of_mass(), protocols::medal::chunk_probabilities(), protocols::topology_broker::copy_internal_coords(), protocols::antibody::CDRH3Modeler::cutpoints_separation(), protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score(), protocols::loops::extract_secondary_structure_chunks(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::loops::fix_with_coord_cst(), protocols::forge::methods::fold_tree_from_loops(), protocols::topology_broker::RigidChunkClaimer::generate_claims(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::anchored_design::AnchorMoversData::input_loops_into_tuples(), protocols::toolbox::KClusterData::KClusterData(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::comparative_modeling::ThreadingJob::loops(), protocols::loops::loops_set_move_map(), protocols::loops::operator<<(), OPT_1GRP_KEY(), protocols::topology_broker::RigidChunkClaimer::receive_message(), protocols::loops::remove_short_chunks(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::loops::select_loop_residues(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fibril::superimpose_pose_on_subset_bb(), switch_movemap(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), transfer_to_residue_vector(), verify_against(), and write_loops_to_stream().

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).

Definition at line 129 of file Loops.cc.

References begin(), end(), and 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)

Definition at line 546 of file Loops.cc.

References v_begin(), and v_end().

void protocols::loops::Loops::clear

(

)

Definition at line 450 of file Loops.cc.

References loops_.

Referenced by protocols::abinitio::get_core(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), read_loop_file(), protocols::rbsegment_relax::read_RBSegment_file(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::seeded_abinitio::SeedFoldTree::SeedFoldTree(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::rbsegment_relax::select_RBsegments(), protocols::topology_broker::CoordConstraintClaimer::set_defaults(), protocols::rbsegment_relax::AutoRBMover::setup_topology(), and protocols::rigid::RigidBodyMotionMover::update_chunks().

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

Definition at line 347 of file Loops.cc.

References loops_.

Referenced by add_overlap_loop().

bool protocols::loops::Loops::empty

(

)

const

Definition at line 122 of file Loops.cc.

References num_loop().

Referenced by protocols::loops::safe_set_extended_torsions_and_idealize_loops(), and protocols::loops::set_extended_torsions_and_idealize_loops().

Loops::const_iterator protocols::loops::Loops::end

(

)

const

Definition at line 125 of file Loops.cc.

References loops_.

Referenced by protocols::loops::add_loop_flank_residues_bb_to_movemap(), add_overlap_loop(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::LoopRefine::apply(), protocols::LoopRebuild::build_random_loops(), protocols::loops::ccd_close_loops(), center_of_mass(), protocols::medal::chunk_probabilities(), protocols::topology_broker::copy_internal_coords(), protocols::antibody::CDRH3Modeler::cutpoints_separation(), protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score(), protocols::loops::extract_secondary_structure_chunks(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::loops::fix_with_coord_cst(), protocols::forge::methods::fold_tree_from_loops(), protocols::topology_broker::RigidChunkClaimer::generate_claims(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::anchored_design::AnchorMoversData::input_loops_into_tuples(), protocols::toolbox::KClusterData::KClusterData(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::comparative_modeling::ThreadingJob::loops(), protocols::loops::loops_set_move_map(), one_random_loop(), protocols::loops::operator<<(), OPT_1GRP_KEY(), protocols::loops::remove_short_chunks(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::loops::select_loop_residues(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fibril::superimpose_pose_on_subset_bb(), switch_movemap(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), transfer_to_residue_vector(), verify_against(), and write_loops_to_stream().

std::string const & protocols::loops::Loops::file_reading_token

(

)

Definition at line 767 of file Loops.cc.

References file_reading_token_.

LoopsFileIOOP protocols::loops::Loops::get_loop_file_reader

(

)

const

Definition at line 456 of file Loops.cc.

References loop_file_reader_.

void protocols::loops::Loops::get_residues

(

utility::vector1< Size > &

selection)

const

add all residues within this loop definition into selection

Definition at line 741 of file Loops.cc.

References loops_.

Referenced by protocols::abinitio::IterativeBase::add_core_evaluator(), protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), and protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators().

void protocols::loops::Loops::grow_all_loops	(	core::Size	nres,
		core::Real	magnitude
	)

Extend a loop.

Definition at line 585 of file Loops.cc.

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

Referenced by protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::topology_broker::RigidChunkClaimer::select_parts(), and protocols::abinitio::AbrelaxApplication::setup_fold().

void protocols::loops::Loops::grow_all_loops	(	core::pose::Pose const &	pose,
		core::Real	magnitude
	)

Extend a loop (don't extend across cutpoints)

Definition at line 577 of file Loops.cc.

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.

Definition at line 593 of file Loops.cc.

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

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.

Definition at line 649 of file Loops.cc.

References grow_loop().

void protocols::loops::Loops::grow_loop	(	core::Size	nres,
		Loop &	loop,
		core::Real	mag_left,
		core::Real	mag_right
	)

Extend a loop unequally in both dirs.

Extend a loop.

Definition at line 658 of file Loops.cc.

References loops_, protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::stop, protocols::loops::tr(), v_begin(), and v_end().

void protocols::loops::Loops::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

Definition at line 613 of file Loops.cc.

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

bool protocols::loops::Loops::has	(	core::Size const	seqpos,
		int const	offset = 0
	)		const

is seqpos a residue in this Loops container ?

Definition at line 530 of file Loops.cc.

References is_loop_residue().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), and protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags().

void protocols::loops::Loops::init ( LoopList const &  loops_in, bool const  read_loop_file_from_options = false, std::string const &  passed_in_filename = ""  )

private

Definition at line 83 of file Loops.cc.

References loop_filename_, loops_, read_loops_options(), and set_loop_file_name_and_reset().

Referenced by Loops().

Loops protocols::loops::Loops::invert

(

core::Size

num_residues)

const

Given the total number of residues, returns the inverse of this selection.

Given the total number of residues, inverts this set of loops. Note: the inline comments are geared toward comparative modeling, but are not specific to it. Think of "unaligned" as this, "aligned" as its inverse.

Definition at line 496 of file Loops.cc.

References add_loop(), num_loop(), sequential_order(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::select_parts(), and protocols::abinitio::AbrelaxApplication::setup_fold().

bool protocols::loops::Loops::is_loop_residue	(	core::Size const	seqpos,
		int const	offset = 0
	)		const

Is seqpos contained in any of my loops?

Definition at line 401 of file Loops.cc.

References loops_.

Referenced by protocols::seeded_abinitio::add_dist_constraints(), protocols::loops::addScoresForLoopParts(), protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::seeded_abinitio::SwapSegment::copying_side_chains(), protocols::seeded_abinitio::define_movemap_chains(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), has(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::motifs::mutate_loops_for_search(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

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

(

)

Definition at line 747 of file Loops.cc.

References loop_filename_.

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), and read_loop_file().

Size protocols::loops::Loops::loop_index_of_residue

(

core::Size const

seqpos)

const

Definition at line 421 of file Loops.cc.

References loops_.

Referenced by protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::topology_broker::connects_rigid_regions(), and protocols::topology_broker::is_not_neighbor_to_rigid().

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.

Definition at line 410 of file Loops.cc.

References loops_.

Size protocols::loops::Loops::loop_size

(

core::Size const

loop_num)

const

Definition at line 375 of file Loops.cc.

References loops_.

Referenced by protocols::seeded_abinitio::SwapSegment::apply(), and protocols::toolbox::KClusterData::KClusterData().

Size protocols::loops::Loops::loop_size

(

)

const

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

Definition at line 383 of file Loops.cc.

References loops_, and size().

Referenced by nr_residues().

Loops::LoopList const & protocols::loops::Loops::loops

(

)

const

Definition at line 454 of file Loops.cc.

References loops_.

Referenced by protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), Loops(), and protocols::electron_density::SetupForDensityScoringMover::mask().

void protocols::loops::Loops::make_sequence_shift

(

int

shift)

Definition at line 809 of file Loops.cc.

References v_begin(), and v_end().

Referenced by protocols::seeded_abinitio::SwapSegment::apply(), protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer(), and protocols::topology_broker::FibrilModelingClaimer::read_tag().

core::Size protocols::loops::Loops::nr_residues

(

)

const

Definition at line 396 of file Loops.cc.

References loop_size().

core::Size protocols::loops::Loops::num_loop

(

)

const

Definition at line 123 of file Loops.cc.

References loops_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchors(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score(), empty(), protocols::antibody2::LHRepulsiveRampLegacy::finalize_setup(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::hybridization::HybridizeFoldtreeDynamic::get_core_chunk_index_from_position(), protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops(), protocols::antibody2::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::loops::loops_set_move_map(), protocols::antibody::AntibodyModeler::relax_cdrs(), protocols::loops::remove_small_gaps(), protocols::hybridization::renumber_with_pdb_info(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::hybridization::FoldTreeHybridize::revert_loops_to_original(), protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::star::StarAbinitio::setup_kinematics(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

Loops::const_iterator protocols::loops::Loops::one_random_loop

(

)

const

Definition at line 364 of file Loops.cc.

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

Referenced by protocols::rbsegment_relax::AutoRBMover::apply().

bool protocols::loops::Loops::operator!=

(

Loops const &

other)

const

Definition at line 803 of file Loops.cc.

Loops & protocols::loops::Loops::operator=

(

Loops const &

src)

Definition at line 787 of file Loops.cc.

References loops_.

bool protocols::loops::Loops::operator==

(

Loops const &

other)

const

Definition at line 793 of file Loops.cc.

References loops_, and size().

const Loop & protocols::loops::Loops::operator[]

(

core::Size const

i)

const

Definition at line 777 of file Loops.cc.

References loops_.

Loop & protocols::loops::Loops::operator[]

(

core::Size const

i)

Definition at line 782 of file Loops.cc.

References loops_.

void protocols::loops::Loops::push_back

(

Loop

loop)

Definition at line 271 of file Loops.cc.

References add_loop().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::LoopRebuild::build_random_loops(), protocols::nonlocal::combine_and_trim(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::fibril::make_symmetric_fibril(), protocols::rbsegment_relax::read_RBSegment_file(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), protocols::topology_broker::RigidChunkClaimer::select_parts(), and protocols::rbsegment_relax::select_RBsegments().

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
	)

Definition at line 276 of file Loops.cc.

References add_loop().

void protocols::loops::Loops::read_loop_file ( )

private

Soon to be deprecated.

Definition at line 477 of file Loops.cc.

References clear(), loop_file_name(), loops_, protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), setup_loops_from_data(), and protocols::loops::tr().

Referenced by set_loop_file_name_and_reset().

void protocols::loops::Loops::read_loops_options

(

)

Definition at line 103 of file Loops.cc.

References loop_filename_, protocols::loops::RG(), set_loop_file_name_and_reset(), and protocols::loops::tr().

Referenced by init().

void protocols::loops::Loops::remove_terminal_loops

(

core::pose::Pose const &

pose)

Definition at line 432 of file Loops.cc.

References loops_.

void protocols::loops::Loops::sequential_order

(

)

Definition at line 445 of file Loops.cc.

References loops_.

Referenced by protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::nonlocal::SheetTranslate::decompose_structure(), protocols::nonlocal::HelixRotate::decompose_structure(), protocols::loops::fold_tree_from_loops(), invert(), protocols::antibody::Antibody::populate_all_cdrs(), protocols::anchored_design::AnchorMoversData::set_loops_and_anchor(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), and protocols::rigid::RigidBodyMotionMover::update_chunks().

void protocols::loops::Loops::set_extended

(

bool

input)

Definition at line 534 of file Loops.cc.

References v_begin(), and v_end().

void protocols::loops::Loops::set_file_reading_token

(

std::string const &

token)

Definition at line 772 of file Loops.cc.

References file_reading_token_.

void protocols::loops::Loops::set_loop_file_name_and_reset

(

std::string const &

loop_filename)

Definition at line 751 of file Loops.cc.

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)

Definition at line 762 of file Loops.cc.

References strict_looprelax_checks_on_file_reads_.

Loops::LoopList protocols::loops::Loops::setup_loops_from_data ( SerializedLoopList const &  loop_data)

private

Definition at line 465 of file Loops.cc.

Referenced by Loops(), and read_loop_file().

core::Size protocols::loops::Loops::size

(

)

const

Definition at line 392 of file Loops.cc.

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::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::LoopRebuild::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::LoopRebuild::barcode_extend_stems(), protocols::LoopRebuild::build_random_loops(), protocols::nonlocal::combine_and_trim(), 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::hybridization::ChunkTrialMover::get_alignment_from_chunk_mapping(), grow_all_loops(), protocols::rbsegment_relax::AutoRBMover::grow_flexible(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), 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::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(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

bool protocols::loops::Loops::strict_looprelax_checks

(

)

Definition at line 757 of file Loops.cc.

References strict_looprelax_checks_on_file_reads_.

void protocols::loops::Loops::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

Definition at line 152 of file Loops.cc.

References begin(), and end().

Referenced by protocols::topology_broker::RigidChunkClaimer::adjust_relax_movemap(), protocols::forge::methods::fold_tree_from_loops(), protocols::topology_broker::FragmentClaimer::generate_claims(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), and protocols::loops::select_loop_frags().

template<class T >

void protocols::loops::Loops::transfer_to_residue_vector	(	utility::vector1< T > &	vector,
		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 )

Definition at line 32 of file Loops.tmpl.hh.

References begin(), and end().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), and protocols::topology_broker::RigidChunkClaimer::manipulate_cut_bias().

Loops::iterator protocols::loops::Loops::v_begin

(

)

Definition at line 126 of file Loops.cc.

References loops_.

Referenced by auto_choose_cutpoints(), choose_cutpoints(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), grow_loop(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), make_sequence_shift(), protocols::rbsegment_relax::read_RBSegment_file(), and set_extended().

Loops::iterator protocols::loops::Loops::v_end

(

)

Definition at line 127 of file Loops.cc.

References loops_.

Referenced by auto_choose_cutpoints(), choose_cutpoints(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), grow_loop(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), make_sequence_shift(), protocols::rbsegment_relax::read_RBSegment_file(), and set_extended().

void protocols::loops::Loops::verify_against

(

core::pose::Pose const &

pose)

const

Definition at line 553 of file Loops.cc.

References begin(), end(), core::pose::Pose::total_residue(), and protocols::loops::tr().

Referenced by protocols::LoopRebuild::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), and protocols::abinitio::AbrelaxApplication::setup_fold().

void protocols::loops::Loops::write_loops_to_file	(	std::string const &	filename,
		std::string	token = "LOOP"
	)		const

Definition at line 175 of file Loops.cc.

References write_loops_to_stream().

Referenced by protocols::abinitio::IterativeBase::add_core_evaluator(), and protocols::abinitio::IterativeFullatom::gen_resample_core().

void protocols::loops::Loops::write_loops_to_stream	(	std::ostream &	data,
		std::string	token
	)		const

Definition at line 194 of file Loops.cc.

References begin(), and end().

Referenced by write_loops_to_file().

Friends And Related Function Documentation

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

friend

Definition at line 164 of file Loops.cc.

Member Data Documentation

std::string protocols::loops::Loops::file_reading_token_

private

Definition at line 297 of file Loops.hh.

Referenced by file_reading_token(), and set_file_reading_token().

LoopsFileIOOP protocols::loops::Loops::loop_file_reader_

mutableprivate

Definition at line 292 of file Loops.hh.

Referenced by get_loop_file_reader().

std::string protocols::loops::Loops::loop_filename_

private

Definition at line 296 of file Loops.hh.

Referenced by init(), loop_file_name(), read_loops_options(), and set_loop_file_name_and_reset().

LoopList protocols::loops::Loops::loops_

private

Definition at line 291 of file Loops.hh.

Referenced by add_loop(), add_overlap_loop(), begin(), clear(), delete_loop(), end(), get_residues(), grow_all_loops(), grow_loop(), init(), is_loop_residue(), loop_index_of_residue(), loop_of_residue(), loop_size(), loops(), num_loop(), one_random_loop(), operator=(), operator==(), operator[](), read_loop_file(), remove_terminal_loops(), sequential_order(), size(), v_begin(), and v_end().

bool protocols::loops::Loops::strict_looprelax_checks_on_file_reads_

private

Definition at line 294 of file Loops.hh.

Referenced by set_strict_looprelax_checks(), and strict_looprelax_checks().

---

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

• src/protocols/loops/Loops.hh
• src/protocols/loops/Loops.cc
• src/protocols/loops/Loops.tmpl.hh