#include <Loops.hh>

Inheritance 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 (utility::vector1< bool > const &selection, bool randomize_cutpoint=true)

Loops &	operator= (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 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

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

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

Constructor & Destructor Documentation

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

References init().

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`
	)

References add_loop(), end(), init(), core::scoring::rg, and protocols::loops::start.

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().

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 )

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 )

References v_begin(), and v_end().

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

Loops::const_iterator protocols::loops::Loops::begin ( ) const

References loops_.

Referenced by protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::WobbleMover::ccd_closure(), protocols::loops::extract_secondary_structure_chunks(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel(), protocols::topology_broker::RigidChunkClaimer::receive_message(), protocols::loops::remove_short_chunks(), protocols::loops::split_by_ca_ca_dist(), and protocols::loops::split_by_resSeq().

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 ( )

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().

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

Referenced by protocols::loops::deep_copy().

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

References num_loop().

Referenced by protocols::denovo_design::movers::BuildDeNovoBackboneMover::fold_attempt(), 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

References loops_.

Referenced by protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::loops::extract_secondary_structure_chunks(), Loops(), one_random_loop(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel(), protocols::loops::remove_short_chunks(), protocols::rbsegment_relax::select_RBsegments(), protocols::loops::split_by_ca_ca_dist(), and protocols::loops::split_by_resSeq().

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

add all residues within this loop definition into selection

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.

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

Referenced by protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::abscript::RigidChunkCM::select_parts(), 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)

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
	)

Extend a loop unequally in both dirs.

Extend a loop.

References loops(), protocols::mean_field::max(), protocols::mean_field::min(), 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

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

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

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.

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::abinitio::abscript::RigidChunkCM::select_parts(), 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?

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 ( )

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

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.

References loops_.

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

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 ) )

References loops_, and size().

Referenced by nr_residues().

Loops::LoopList const & protocols::loops::Loops::loops ( ) const

References loops_.

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

void protocols::loops::Loops::make_sequence_shift ( int shift )

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

References loop_size().

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

References loops_.

Loops::const_iterator protocols::loops::Loops::one_random_loop ( ) const

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

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

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 )

References add_loop().

Referenced by protocols::hybridization::HybridizeFoldtreeDynamic::add_overlapping_pair_chunks(), protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::nonlocal::combine_and_trim(), protocols::electron_density::findLoopFromDensity(), protocols::topology_broker::RigidChunkClaimer::generate_claims(), protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::fibril::make_symmetric_fibril(), protocols::rbsegment_relax::read_RBSegment_file(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), protocols::abinitio::abscript::RigidChunkCM::select_parts(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::rbsegment_relax::select_RBsegments(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

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`
	)