Namespaces
	loop_closure

	loop_mover

	loops_definers

Classes
class	EXCN_Loop_not_closed

class	FoldTreeFromLoops

class	FoldTreeFromLoopsCreator

struct	SerializedLoop
	Bare-bones representation of a loop. More...

class	Loop
	single loop definition More...

class	RationalLoopComparator
	Orders loops by start position. More...

class	Loop_lt
	used to sort Loops by start-res More...

class	LoopMoverFactory
	Create LoopMover Reporters. More...

class	Loops

class	LoopsFileFallbackConfiguration

class	LoopsFileFallbackConfigurationCreator

class	ResidueIndexDescription
	a class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another. More...

class	ResidueIndexDescriptionFromFile

class	LoopFromFileData

class	LoopsFileData

class	GuardedLoopsFromFile
	This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure. More...

class	LoopsFileIO

class	PoseNumberedLoopFileReader

class	JSONFormattedLoopsFileReader

class	LoopsFileLoader

class	LoopsFileLoaderCreator

class	LoopsFileOptions

class	LoopsFileOptionsCreator

Typedefs
typedef utility::pointer::owning_ptr < FoldTreeFromLoops >	FoldTreeFromLoopsOP

typedef utility::pointer::owning_ptr < FoldTreeFromLoops const >	FoldTreeFromLoopsCOP

typedef utility::pointer::owning_ptr < Loop >	LoopOP

typedef utility::pointer::owning_ptr < Loop const >	LoopCOP

typedef utility::vector1 < SerializedLoop >	SerializedLoopList

typedef utility::pointer::owning_ptr < Loops >	LoopsOP

typedef utility::pointer::owning_ptr < Loops const >	LoopsCOP

typedef utility::pointer::owning_ptr < LoopsFileFallbackConfiguration >	LoopsFileFallbackConfigurationOP

typedef utility::pointer::owning_ptr < LoopsFileFallbackConfiguration const >	LoopsFileFallbackConfigurationCOP

typedef utility::pointer::owning_ptr < LoopsFileData >	LoopsFileDataOP

typedef utility::pointer::owning_ptr < LoopsFileData const >	LoopsFileDataCOP

typedef utility::pointer::owning_ptr < LoopsFileIO >	LoopsFileIOOP

typedef utility::pointer::owning_ptr < LoopsFileIO const >	LoopsFileIOCOP

typedef utility::pointer::owning_ptr < GuardedLoopsFromFile >	GuardedLoopsFromFileOP

typedef utility::pointer::owning_ptr < GuardedLoopsFromFile const >	GuardedLoopsFromFileCOP

typedef utility::pointer::owning_ptr < LoopsFileLoader >	LoopsFileLoaderOP

typedef utility::pointer::owning_ptr < LoopsFileLoader const >	LoopsFileLoaderCOP

typedef utility::pointer::owning_ptr < LoopsFileOptions >	LoopsFileOptionsOP

typedef utility::pointer::owning_ptr < LoopsFileOptions const >	LoopsFileOptionsCOP

Enumerations
enum	ResidueIdentifier { start =1, stop, cut_point, number_of_residue_identifiers =cut_point }
	The following enumerators are used for parsing JSON formatted loop files. More...

enum	LoopConfiguration { extras =number_of_residue_identifiers + 1, resSeq, iCode, chainID, skip_rate, extend, use_pose_numbering, number_of_configuration_keywords =use_pose_numbering }

Functions
static basic::Tracer	TR ("protocols.loops.FoldTreeFromLoopsWrapper")

static basic::Tracer	tr ("protocols.loops.Loop")

static numeric::random::RandomGenerator	RG (429)

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

void	loopfinder (core::pose::Pose &pose, loops::Loops &loops)

static basic::Tracer	tr ("protocols.loops.LoopMoverFactory")

static basic::Tracer	tr ("loops")

static numeric::random::RandomGenerator	RG (430)

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

basic::Tracer	tt ("protocols.loops.loops_main")

static numeric::random::RandomGenerator	RG (31413)

void	read_loop_fragments (std::vector< core::fragment::FragSetOP > &frag_libs)

void	read_loop_fragments (utility::vector1< core::fragment::FragSetOP > &frag_libs)

void	fold_tree_from_loops (core::pose::Pose const &pose, Loops const &loops, core::kinematics::FoldTree &f, bool terminal_cutpoint=false)
	the main function for perform loop modeling More...

void	set_single_loop_fold_tree (core::pose::Pose &pose, Loop const &loop)

void	set_loop_cutpoint_in_pose_fold_tree (Size const new_cutpoint, pose::Pose &pose, Size const loop_begin, Size const loop_end)

void	remove_cutpoint_variants (core::pose::Pose &pose, bool force)

void	add_cutpoint_variants (core::pose::Pose &pose)

void	add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)

void	loops_set_move_map (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, core::Real neighbor_dist=10.0)
	create a MoveMap for use of minimization based on loop definition (wrapper) More...

void	loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm)
	create a MoveMap for use of minimization based on loop definition More...

void	set_move_map_for_centroid_loop (Loop const &loop, core::kinematics::MoveMap &mm)

void	add_loop_flank_residues_bb_to_movemap (Loops const &loops, core::kinematics::MoveMap &mm, core::Size flank_size=2)
	add flank stem residues to the loop movemap More...

void	ccd_close_loops (core::pose::Pose &pose, Loops const &loops, core::kinematics::MoveMap const &mm)
	close loops by the CCD mechanism More...

void	get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions)
	get neighbor residues within 10 A CB distance cutoff More...

void	select_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
	mark loop residues and its neighbors as necessary in a sequence map. More...

void	select_loop_residues (pose::Pose const &pose, Loop const &loop, bool const include_neighbors, utility::vector1< bool > &map, Real neighbor_dist)

void	filter_loop_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > &map, Loops const &loops, core::Real &dist_cutoff)
	filter set of loop neighbors to a certain CB distance More...

void	extend_sequence_mapping (pose::Pose const &pose, id::SequenceMapping &mapping, std::string &source_seq, std::string &target_seq)

void	apply_sequence_mapping (pose::Pose &pose, std::string const &target_seq, id::SequenceMapping const &start_mapping)

void	trim_back_sequence_mapping (core::id::SequenceMapping &mapping, std::string const &source_seq, std::string const &target_seq, core::Size const min_loop_size)

bool	set_secstruct_from_psipred_ss2 (core::pose::Pose &pose)
	helper function to set secondary structure of a Pose from an external file. More...

bool	set_secstruct_from_dssp (core::pose::Pose &pose, std::string const &filename)
	another helper function to set secondary structure of a Pose from an external file. More...

void	idealize_loop (core::pose::Pose &pose, Loop const &loop)

void	set_extended_torsions (core::pose::Pose &pose, Loop const &loop)

void	remove_missing_density (core::pose::Pose &pose, Loop const &loop)

core::Real	native_loop_core_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose, loops::Loops loops, int &corelength)

Real	loop_rmsd_with_superimpose (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
	As above but actuall superimposes the non-loop part. More...

Real	loop_rmsd_with_superimpose_core (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, Loops const &core, bool CA_only=false, bool bb_only=true)
	As above but actually superimposes only the core part (in case there are multiple loops...) More...

Real	loop_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
	calculate rmsd of loop residues with repect to native (template aligned) More...

Real	loop_local_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops)
	calculate rmsd of loop residues with repect to native (loop fit) More...

static numeric::random::RandomGenerator	RG (1337)

static basic::Tracer	tr ("protocols.loops.LoopsFileIO")

void	validate_loop_start_stop (bool prohibit_single_residue_loops, core::Size start, core::Size stop, std::string const &filename, core::Size linecount)
	Checks if there is a problem with the beginning and ending residues defined in a loops file. More...

std::ostream &	operator<< (std::ostream &os, const LoopsFileIO &)

static basic::Tracer	TR ("protocols.loops.make_loops", t_info)

void	add_loop (Size seg_begin, Size seg_end, pose::Pose const &pose, loops::Loops &loops)

void	loops_around_residues (loops::Loops &loops, pose::Pose const &pose, vector1< Size > const &residue_indices, Size gapsize, Size extend)
	add a set of loops 'built' around the provided residue indices More...

void	fix_with_coord_cst (Loops const &rigid, core::pose::Pose &pose, bool bCstAllAtom, utility::vector1< core::Real > &weights)

void	select_loop_frags (loops::Loops const &loops, core::fragment::FragSet &source, core::fragment::FragSet &loop_frags, Size shorten)
	get frags that are fully within the Loop — shorten(=true/false) frags that are close to the end of loops. More...

void	safe_set_extended_torsions_and_idealize_loops (const protocols::loops::Loops &loops, core::pose::Pose *pose)
	Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops. More...

void	set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops)

void	addScoresForLoopParts (core::pose::Pose &pose, loops::Loops loops, const core::scoring::ScoreFunction &scorefxn, core::pose::Pose &native_pose, core::Size nloops)

loops::Loops	compute_ss_regions (core::Real max_loop_frac, core::Size min_length, core::fragment::SecondaryStructure const &ss)

core::scoring::ScoreFunctionOP	get_cen_scorefxn ()

core::scoring::ScoreFunctionOP	get_fa_scorefxn ()

void	add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)

LoopsOP	loops_from_string (std::string const loop_str, core::pose::Pose const &pose)
	loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop More...

void	define_scorable_core_from_secondary_structure (core::fragment::SecondaryStructure const &ss_def, protocols::loops::Loops &scored_core)

protocols::loops::Loops	extract_secondary_structure_chunks (core::pose::Pose const &pose, char const extracted_ss_type)
	Extract secondary structure chunks from the secondary structure. More...

protocols::loops::Loops	split_by_resSeq (core::pose::Pose const &pose)

protocols::loops::Loops	find_non_protein_chunks (core::pose::Pose const &pose)

protocols::loops::Loops	split_by_resSeq (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks)

protocols::loops::Loops	split_by_ca_ca_dist (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks, core::Real const CA_CA_distance_cutoff=4)
	Split into separate chunks if CA-CA distance is over the cutoff. More...

protocols::loops::Loops	remove_small_gaps (protocols::loops::Loops const &input_chunks, core::Size gap_size=1)
	If two chunks are separated by a small gap of size <= <gap_size>, combine them. More...

protocols::loops::Loops	remove_short_chunks (protocols::loops::Loops const &input_chunks, core::Size min_length=3)
	Remove small chunks. More...

protocols::loops::Loops	extract_secondary_structure_chunks (core::pose::Pose const &pose, std::string extracted_ss_types="HE", core::Size gap_size=1, core::Size minimum_length_of_chunk_helix=5, core::Size minimum_length_of_chunk_strand=3, core::Real CA_CA_distance_cutoff=4)
	Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( pose ); dssp_obj.insert_ss_into_pose( pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);. More...

protocols::loops::Loops	extract_continuous_chunks (core::pose::Pose const &pose, core::Size const minimum_size, core::Real const CA_CA_distance_cutoff)

Variables
static const double	EXT_PHI = -150

static const double	EXT_PSI = +150

static const double	EXT_OMG = 180

Typedef Documentation

typedef utility::pointer::owning_ptr< FoldTreeFromLoops const > protocols::loops::FoldTreeFromLoopsCOP

Definition at line 26 of file FoldTreeFromLoopsWrapper.fwd.hh.

typedef utility::pointer::owning_ptr< FoldTreeFromLoops > protocols::loops::FoldTreeFromLoopsOP

Definition at line 24 of file FoldTreeFromLoopsWrapper.fwd.hh.

typedef utility::pointer::owning_ptr< GuardedLoopsFromFile const > protocols::loops::GuardedLoopsFromFileCOP

Definition at line 39 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< GuardedLoopsFromFile > protocols::loops::GuardedLoopsFromFileOP

Definition at line 38 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< Loop const > protocols::loops::LoopCOP

Definition at line 32 of file Loop.fwd.hh.

typedef utility::pointer::owning_ptr< Loop > protocols::loops::LoopOP

Definition at line 30 of file Loop.fwd.hh.

typedef utility::pointer::owning_ptr< Loops const > protocols::loops::LoopsCOP

Definition at line 27 of file Loops.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileData const > protocols::loops::LoopsFileDataCOP

Definition at line 31 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileData > protocols::loops::LoopsFileDataOP

Definition at line 29 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileFallbackConfiguration const > protocols::loops::LoopsFileFallbackConfigurationCOP

Definition at line 24 of file LoopsFileFallbackConfiguration.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileFallbackConfiguration > protocols::loops::LoopsFileFallbackConfigurationOP

Definition at line 22 of file LoopsFileFallbackConfiguration.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileIO const > protocols::loops::LoopsFileIOCOP

Definition at line 36 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileIO > protocols::loops::LoopsFileIOOP

Definition at line 33 of file LoopsFileIO.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileLoader const > protocols::loops::LoopsFileLoaderCOP

Definition at line 25 of file LoopsFileLoader.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileLoader > protocols::loops::LoopsFileLoaderOP

Definition at line 23 of file LoopsFileLoader.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileOptions const > protocols::loops::LoopsFileOptionsCOP

Definition at line 27 of file LoopsFileOptions.fwd.hh.

typedef utility::pointer::owning_ptr< LoopsFileOptions > protocols::loops::LoopsFileOptionsOP

Definition at line 24 of file LoopsFileOptions.fwd.hh.

typedef utility::pointer::owning_ptr< Loops > protocols::loops::LoopsOP

Definition at line 24 of file Loops.fwd.hh.

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

Definition at line 34 of file Loop.fwd.hh.

Enumeration Type Documentation

enum protocols::loops::LoopConfiguration

Enumerator
extras
resSeq
iCode
chainID
skip_rate
extend
use_pose_numbering
number_of_configuration_keywords

Definition at line 334 of file LoopsFileIO.hh.

enum protocols::loops::ResidueIdentifier

The following enumerators are used for parsing JSON formatted loop files.

Enumerator
start
stop
cut_point
number_of_residue_identifiers

Definition at line 327 of file LoopsFileIO.hh.

Function Documentation

void protocols::loops::add_coordinate_constraints_to_pose	(	core::pose::Pose &	pose,
		const core::pose::Pose &	constraint_target_pose,
		protocols::loops::Loops &	exclude_regions
	)

Definition at line 342 of file util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::fold_tree(), protocols::loops::Loops::invert(), core::chemical::ResidueTypeSet::name_map(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::loophash::LoopHashLibrary::get_all(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), and protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut().

void protocols::loops::add_cutpoint_variants ( core::pose::Pose & pose)

Remove cutpoint variants

Add cutpoint variants to all the cutpoints

Definition at line 618 of file loops_main.cc.

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::constraint_set(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::residue(), and core::pack::tt().

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::antibody2::AntibodyModelerProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::antibody2::CDRsMinPackMin::finalize_setup(), protocols::antibody2::RefineBetaBarrel::finalize_setup(), protocols::antibody2::H3RefineCCD::finalize_setup(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::antibody::AntibodyModeler::relax_cdrs(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

void protocols::loops::add_loop	(	Size	seg_begin,
		Size	seg_end,
		pose::Pose const &	pose,
		loops::Loops &	loops
	)

Definition at line 47 of file make_loops.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_pro, protocols::loops::Loops::add_loop(), core::pose::Pose::chain(), core::chemical::ResidueType::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and TR().

Referenced by loops_around_residues().

void protocols::loops::add_loop_flank_residues_bb_to_movemap	(	Loops const &	loops,
		core::kinematics::MoveMap &	mm,
		core::Size	flank_size
	)

add flank stem residues to the loop movemap

Definition at line 813 of file loops_main.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), and core::kinematics::MoveMap::set_bb().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply().

void protocols::loops::add_single_cutpoint_variant	(	core::pose::Pose &	pose,
		const Loop &	loop
	)

Add cutpoint variant around a sinlge cutpoint (defined by loop)

Definition at line 651 of file loops_main.cc.

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and core::pose::Pose::residue().

Referenced by protocols::antibody::AntibodyModeler::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

void protocols::loops::addScoresForLoopParts	(	core::pose::Pose &	pose,
		loops::Loops	loops,
		const core::scoring::ScoreFunction &	scorefxn,
		core::pose::Pose &	native_pose,
		core::Size	nloops
	)

Definition at line 222 of file util.cc.

References protocols::loops::Loops::add_loop(), core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::scoring::ScoreFunction::get_sub_score_exclude_res(), core::pose::initialize_atomid_map(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_protein(), loop_rmsd(), native_loop_core_CA_rmsd(), core::pose::Pose::residue(), core::pose::setPoseExtraScores(), protocols::loops::Loops::size(), start, stop, core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::ScoreMover::apply().

void protocols::loops::apply_sequence_mapping	(	pose::Pose &	pose,
		std::string const &	target_seq,
		id::SequenceMapping const &	start_mapping
	)

what can we assume about the starting fold_tree??

Definition at line 1070 of file loops_main.cc.

Referenced by core::kinematics::FoldTree::delete_jump_seqpos(), and core::kinematics::FoldTree::delete_seqpos_simple().

void protocols::loops::ccd_close_loops	(	pose::Pose &	pose,
		Loops const &	loops,
		kinematics::MoveMap const &	mm
	)

close loops by the CCD mechanism

take a pose and loop defintions, close each loop separately by the CCD algorithm. Currently hard-code all parameters related to CCD and then call fast_ccd_loop_closure for closing this single loop

Definition at line 840 of file loops_main.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), and protocols::loops::loop_closure::ccd::fast_ccd_loop_closure().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop().

loops::Loops protocols::loops::compute_ss_regions	(	core::Real	max_loop_frac,
		core::Size	min_length,
		core::fragment::SecondaryStructure const &	ss
	)

Definition at line 297 of file util.cc.

References protocols::loops::Loops::add_loop(), core::fragment::SecondaryStructure::loop_fraction(), start, and core::fragment::SecondaryStructure::total_residue().

void protocols::loops::define_scorable_core_from_secondary_structure	(	core::fragment::SecondaryStructure const &	ss_def,
		protocols::loops::Loops &	scored_core
	)

Definition at line 419 of file util.cc.

References protocols::loops::Loops::add_loop(), core::fragment::SecondaryStructure::helix_fraction(), protocols::loops::Loops::invert(), core::fragment::SecondaryStructure::loop_fraction(), and core::fragment::SecondaryStructure::total_residue().

void protocols::loops::extend_sequence_mapping	(	pose::Pose const &	pose,
		id::SequenceMapping &	mapping,
		std::string &	source_seq,
		std::string &	target_seq
	)

Definition at line 993 of file loops_main.cc.

References core::id::SequenceMapping::insert_source_residue(), core::id::SequenceMapping::insert_target_residue(), core::id::SequenceMapping::push_back(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and core::pack::tt().

protocols::loops::Loops protocols::loops::extract_continuous_chunks	(	core::pose::Pose const &	pose,
		core::Size const	minimum_size,
		core::Real const	CA_CA_distance_cutoff
	)

Definition at line 705 of file util.cc.

References remove_short_chunks(), split_by_ca_ca_dist(), and split_by_resSeq().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::hybridization::HybridizeProtocol::add_template(), and protocols::hybridization::HybridizeProtocol::apply().

protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks	(	core::pose::Pose const &	pose,
		char const	extracted_ss_type
	)

Extract secondary structure chunks from the secondary structure.

Extract secondary structure chunks from the pose, using a given secondary structure type.

Definition at line 479 of file util.cc.

References core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::hybridization::HybridizeProtocol::apply(), and extract_secondary_structure_chunks().

protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks	(	core::pose::Pose const &	pose,
		std::string	extracted_ss_types,
		core::Size	gap_size,
		core::Size	minimum_length_of_chunk_helix,
		core::Size	minimum_length_of_chunk_strand,
		core::Real	CA_CA_distance_cutoff
	)

Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);.

Definition at line 661 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), extract_secondary_structure_chunks(), remove_short_chunks(), remove_small_gaps(), split_by_ca_ca_dist(), and split_by_resSeq().

void protocols::loops::filter_loop_neighbors_by_distance	(	pose::Pose const &	pose,
		utility::vector1< bool > &	map,
		Loops const &	loops,
		Real &	dist_cutoff
	)

filter set of loop neighbors to a certain CB distance

neighbors contains the set of potential neighbors to the loop residues given in loops. This set is reduced to only contain neighbors within dist_cutoff of any residue in loops.

Definition at line 952 of file loops_main.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by select_loop_residues().

protocols::loops::Loops protocols::loops::find_non_protein_chunks ( core::pose::Pose const & pose)

Definition at line 532 of file util.cc.

References protocols::loops::Loops::add_loop(), core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::residue_type(), protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), and core::pose::Pose::total_residue().

void protocols::loops::fix_with_coord_cst	(	Loops const &	rigid,
		core::pose::Pose &	pose,
		bool	bCstAllAtom,
		utility::vector1< core::Real > &	weights
	)

Definition at line 102 of file util.cc.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::abinitio::LoopJumpFoldCst::add_coord_cst(), and protocols::abinitio::AbrelaxApplication::do_distributed_rerun().

void protocols::loops::fold_tree_from_loops	(	core::pose::Pose const &	pose,
		Loops const &	loops,
		kinematics::FoldTree &	f,
		bool	terminal_cutpoint
	)

the main function for perform loop modeling

for each loop defined, add a fixed jump from the residue before loop_start and the residue after the loop_end. The cutpoint is from loop_cut. Support terminal loops, i.e., starting at residue 1 or ending at total_residue

voi/d loops_main( core::pose::Pose & pose ); construct a fold tree from loop definition

Definition at line 233 of file loops_main.cc.

References core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::is_protein(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::loops::Loops::sequential_order(), core::pose::symmetry::symmetrize_fold_tree(), and core::pose::Pose::total_residue().

Referenced by protocols::loops::FoldTreeFromLoops::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::LoopRefine::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::abinitio::AbrelaxApplication::fold(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

core::scoring::ScoreFunctionOP protocols::loops::get_cen_scorefxn ( )

Definition at line 327 of file util.cc.

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::LoopMover_Perturb_KIC(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD(), protocols::loop_build::LoopMover_SlidingWindow::LoopMover_SlidingWindow(), protocols::grafting::GraftMoverBase::set_default_cen_scorefunction(), and protocols::comparative_modeling::LoopRelaxMover::set_defaults_().

core::scoring::ScoreFunctionOP protocols::loops::get_fa_scorefxn ( )

Definition at line 337 of file util.cc.

References core::scoring::getScoreFunction().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_new_ramping_scorefxn(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC(), and protocols::comparative_modeling::LoopRelaxMover::set_defaults_().

void protocols::loops::get_tenA_neighbor_residues	(	pose::Pose const &	pose,
		utility::vector1< bool > &	residue_positions
	)

get neighbor residues within 10 A CB distance cutoff

use TenANeighborGraph. As input, residue_positions[i] is true for residues to be counted. As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.

Definition at line 875 of file loops_main.cc.

References core::pose::Pose::energies(), core::chemical::ResidueType::name(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::type().

Referenced by select_loop_residues().

void protocols::loops::idealize_loop	(	core::pose::Pose &	pose,
		Loop const &	loop
	)

set ideal BB geometry; this must occur so that loops with missing density work.

Definition at line 1445 of file loops_main.cc.

References core::pose::Pose::conformation(), core::conformation::idealize_position(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), and set_extended_torsions().

core::Real protocols::loops::loop_local_rmsd	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Loops const &	loops
	)

calculate rmsd of loop residues with repect to native (loop fit)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of each loop after fitting it onto the reference loop and when there are multiple loops, return the mean value.

Definition at line 1671 of file loops_main.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), protocols::loops::Loops::num_loop(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

core::Real protocols::loops::loop_rmsd	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Loops const &	loops,
		bool	CA_only,
		bool	bb_only
	)

calculate rmsd of loop residues with repect to native (template aligned)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

Definition at line 1607 of file loops_main.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atoms(), protocols::loops::Loops::begin(), core::sequence::end, protocols::loops::Loops::end(), core::pose::Pose::residue(), core::scoring::rms, start, core::pose::Pose::total_residue(), core::pack::tt(), and core::conformation::Residue::xyz().

core::Real protocols::loops::loop_rmsd_with_superimpose	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Loops const &	loops,
		bool	CA_only,
		bool	bb_only
	)

As above but actuall superimposes the non-loop part.

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

Definition at line 1554 of file loops_main.cc.

References loop_rmsd_with_superimpose_core().

Referenced by protocols::cluster::ClusterPhilStyle_Loop::get_distance_measure().

core::Real protocols::loops::loop_rmsd_with_superimpose_core	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Loops const &	loops,
		Loops const &	core,
		bool	CA_only,
		bool	bb_only
	)

As above but actually superimposes only the core part (in case there are multiple loops...)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

Definition at line 1573 of file loops_main.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), protocols::loops::Loops::is_loop_residue(), loop_rmsd(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), protocols::loops::Loops::size(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_filters::LoopRmsdEvaluator::apply(), and loop_rmsd_with_superimpose().

void protocols::loops::loopfinder	(	core::pose::Pose &	pose,
		loops::Loops &	loops
	)

Definition at line 54 of file loopfinder.cc.

References protocols::loops::Loops::add_loop(), core::conformation::Residue::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), cut_point, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::protein_interface_design::movers::LoopFinder::apply().

void protocols::loops::loops_around_residues	(	loops::Loops &	loops,
		pose::Pose const &	pose,
		vector1< Size > const &	residue_indices,
		Size	gapsize,
		Size	extend
	)

add a set of loops 'built' around the provided residue indices

A maximum of gapsize residues are allowed between specified residues for any given loop, loop ends are extended by extend residues, and chain discontinuity starts a new loop

Author: ashworth

Definition at line 95 of file make_loops.cc.

References add_loop(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, extend, protocols::loops::Loops::num_loop(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::apply().

LoopsOP protocols::loops::loops_from_string	(	std::string const	loop_str,
		core::pose::Pose const &	pose
	)

loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop

Definition at line 390 of file util.cc.

References core::pose::parse_resnum(), and core::pose::Pose::total_residue().

Referenced by protocols::loops::loops_definers::load_loop_definitions().

void protocols::loops::loops_set_move_map	(	pose::Pose &	pose,
		Loops const &	loops,
		bool const	fix_template_sc,
		core::kinematics::MoveMap &	mm,
		Real	neighbor_dist
	)

create a MoveMap for use of minimization based on loop definition (wrapper)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable. Default neighbors are 10A CB dist from loop residues; neighbor_dist can be used to further filter the neighbors. This is a wrapper function which determine moveable sidechains and then call actual loop_set_move_map function to set up move map properly

Definition at line 683 of file loops_main.cc.

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), select_loop_residues(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors().

void protocols::loops::loops_set_move_map	(	Loops const &	loops,
		utility::vector1< bool > const &	allow_sc_move,
		core::kinematics::MoveMap &	mm
	)

create a MoveMap for use of minimization based on loop definition

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable.

Definition at line 711 of file loops_main.cc.

References core::id::BB, protocols::loops::Loops::begin(), protocols::loops::Loops::end(), protocols::loops::Loops::num_loop(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

core::Real protocols::loops::native_loop_core_CA_rmsd	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose,
		loops::Loops	loops,
		int &	corelength
	)

Definition at line 1507 of file loops_main.cc.

References core::scoring::CA_rmsd(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), protocols::loops::Loops::size(), start, and core::pose::Pose::total_residue().

Referenced by addScoresForLoopParts(), and protocols::comparative_modeling::LoopRelaxMover::apply().

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

inline

Definition at line 164 of file Loop.hh.

References protocols::loops::Loop::cut_, protocols::loops::Loop::extended_, protocols::loops::Loop::skip_rate_, protocols::loops::Loop::start_, and protocols::loops::Loop::stop_.

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

Definition at line 164 of file Loops.cc.

References protocols::loops::Loops::begin(), and protocols::loops::Loops::end().

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

Definition at line 457 of file LoopsFileIO.cc.

void protocols::loops::read_loop_fragments ( std::vector< core::fragment::FragSetOP > & frag_libs)

Definition at line 110 of file loops_main.cc.

References core::pack::dunbrack::c, core::import_pose::centroid_pose_from_pdb(), core::fragment::chop_fragments(), core::fragment::FragmentIO::read_data(), core::fragment::steal_frag_set_from_pose(), and core::pack::tt().

Referenced by protocols::RBSegmentRelaxImpl::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::flexpep_docking::FlexPepDockingAbInitio::FlexPepDockingAbInitio(), protocols::flexpep_docking::FlexPepDockingLowRes::FlexPepDockingLowRes(), protocols::loop_build::LoopBuild_main(), protocols::LoopRebuild::LoopRebuild(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::antibody2::H3PerturbCCD::read_and_store_fragments(), protocols::antibody::AntibodyModeler::read_and_store_fragments(), read_loop_fragments(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), and protocols::comparative_modeling::LoopRelaxThreadingMover::setup().

void protocols::loops::read_loop_fragments ( utility::vector1< core::fragment::FragSetOP > & frag_libs)

Definition at line 212 of file loops_main.cc.

References read_loop_fragments().

void protocols::loops::remove_cutpoint_variants	(	core::pose::Pose &	pose,
		bool	force
	)

Remove cutpoint variants

Definition at line 558 of file loops_main.cc.

References core::pose::Pose::constraint_set(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::num_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void protocols::loops::remove_missing_density	(	core::pose::Pose &	pose,
		Loop const &	loop
	)

Rebuild a loop via fragment insertion + ccd closure + minimization

Definition at line 1492 of file loops_main.cc.

References protocols::loops::Loop::cut(), set_extended_torsions(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

protocols::loops::Loops protocols::loops::remove_short_chunks	(	protocols::loops::Loops const &	input_chunks,
		core::Size	minimum_length_of_chunk
	)

Remove small chunks.

Definition at line 645 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), and protocols::loops::Loops::end().

Referenced by extract_continuous_chunks(), and extract_secondary_structure_chunks().

protocols::loops::Loops protocols::loops::remove_small_gaps	(	protocols::loops::Loops const &	input_chunks,
		core::Size	gap_size
	)

If two chunks are separated by a small gap of size <= <gap_size>, combine them.

Definition at line 620 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::num_loop(), protocols::loops::Loop::set_stop(), and stop.

Referenced by extract_secondary_structure_chunks().

static numeric::random::RandomGenerator protocols::loops::RG ( 429 )

static

Referenced by protocols::loops::LoopsFileFallbackConfiguration::get_loops_filename_from_options(), and protocols::loops::Loops::read_loops_options().

static numeric::random::RandomGenerator protocols::loops::RG ( 1337 )

static

static numeric::random::RandomGenerator protocols::loops::RG ( 430 )

static

static numeric::random::RandomGenerator protocols::loops::RG ( 31413 )

static

void protocols::loops::safe_set_extended_torsions_and_idealize_loops	(	const protocols::loops::Loops &	loops,
		core::pose::Pose *	pose
	)

Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops.

Definition at line 188 of file util.cc.

References protocols::loops::Loops::empty(), and set_extended_torsions_and_idealize_loops().

void protocols::loops::select_loop_frags	(	loops::Loops const &	loops,
		core::fragment::FragSet &	source,
		core::fragment::FragSet &	loop_frags,
		Size	shorten
	)

get frags that are fully within the Loop — shorten(=true/false) frags that are close to the end of loops.

Definition at line 143 of file util.cc.

References core::fragment::FragSet::add(), core::id::BB, for(), core::fragment::FragSet::frames(), core::fragment::FragSet::generate_insert_map(), core::kinematics::MoveMap::set_bb(), core::io::serialization::size(), protocols::loops::Loops::switch_movemap(), and TR().

void protocols::loops::select_loop_residues	(	pose::Pose const &	pose,
		Loops const &	loops,
		bool const	include_neighbors,
		utility::vector1< bool > &	map,
		Real	neighbor_dist
	)

mark loop residues and its neighbors as necessary in a sequence map.

use 10A CB distance cutoff as neighboring residue defintion. The function is used for conveniently setting up sidechain movable residues in loop modeling. The 10A residue set is further reduced if neighbor_dist < 10.0

Definition at line 903 of file loops_main.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), filter_loop_neighbors_by_distance(), get_tenA_neighbor_residues(), core::chemical::ResidueType::name(), core::pose::Pose::residue(), and core::conformation::Residue::type().

void protocols::loops::select_loop_residues	(	pose::Pose const &	pose,
		Loop const &	loop,
		bool const	include_neighbors,
		utility::vector1< bool > &	map,
		Real	neighbor_dist
	)

for one loop only

Definition at line 933 of file loops_main.cc.

References protocols::loops::Loops::add_loop(), and select_loop_residues().

void protocols::loops::set_extended_torsions	(	core::pose::Pose &	pose,
		Loop const &	loop
	)

Set a loop to extended torsion angles.

Definition at line 1459 of file loops_main.cc.

References idealize_loop(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and core::pack::tt().

Referenced by protocols::antibody2::ModelCDRH3::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), and remove_missing_density().

void protocols::loops::set_extended_torsions_and_idealize_loops	(	core::pose::Pose &	pose,
		loops::Loops	loops
	)

void protocols::loops::set_loop_cutpoint_in_pose_fold_tree	(	Size const	new_cutpoint,
		pose::Pose &	pose,
		Size const	loop_begin,
		Size const	loop_end
	)

Slide a loop cutpoint to a (potentially) new position

Note: Updates the pose's foldtree, either moving or adding a loop cutpoint; Updates CUTPOINT_UPPER and CUTPOINT_LOWER variant status of residues in loop to match new cutpoint location

Definition at line 518 of file loops_main.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::pose::remove_variant_type_from_pose_residue(), and core::pack::tt().

void protocols::loops::set_move_map_for_centroid_loop	(	Loop const &	loop,
		core::kinematics::MoveMap &	mm
	)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable.

Definition at line 768 of file loops_main.cc.

References core::id::BB, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop().

bool protocols::loops::set_secstruct_from_dssp	(	pose::Pose &	pose,
		std::string const &	filename
	)

another helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a DSSP file and set that to a Pose. (Rhiju's copy of Chu's psipred reader). Chu, should these functions be moved somewhere to core, along with pdb readers, etc?

Definition at line 1368 of file loops_main.cc.

References core::pose::Pose::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::total_residue(), and core::pack::tt().

Referenced by protocols::loop_build::LoopBuildMover::apply(), and protocols::comparative_modeling::initialize_ss().

bool protocols::loops::set_secstruct_from_psipred_ss2 ( pose::Pose & pose)

helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a psipred_ss2 file and set that to a Pose. A temporary setup since there is very limited ss support in Pose right now.

Definition at line 1336 of file loops_main.cc.

References core::pose::read_psipred_ss2_file(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::set_ss_from_phipsi(), and core::pack::tt().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::LoopRebuild::apply(), protocols::comparative_modeling::initialize_ss(), and protocols::hybridization::FoldTreeHybridize::setup_foldtree().

void protocols::loops::set_single_loop_fold_tree	(	core::pose::Pose &	pose,
		Loop const &	loop
	)

Make a single fold tree that brackets the loop

Set the fold tree to contain a single chain break at the loops' position

Definition at line 376 of file loops_main.cc.

References core::chemical::aa_vrt, core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::is_protein(), core::kinematics::FoldTree::nres(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::symmetry::set_asymm_unit_fold_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and core::pack::tt().

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop().

protocols::loops::Loops protocols::loops::split_by_ca_ca_dist	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	input_chunks,
		core::Real const	CA_CA_distance_cutoff
	)

Split into separate chunks if CA-CA distance is over the cutoff.

Definition at line 581 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), and core::conformation::Residue::xyz().

Referenced by extract_continuous_chunks(), and extract_secondary_structure_chunks().

protocols::loops::Loops protocols::loops::split_by_resSeq ( core::pose::Pose const & pose)

Definition at line 518 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), and core::pose::Pose::total_residue().

Referenced by extract_continuous_chunks(), and extract_secondary_structure_chunks().

protocols::loops::Loops protocols::loops::split_by_resSeq	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	input_chunks
	)

Definition at line 553 of file util.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::pose::Pose::pdb_info(), protocols::loops::Loop::set_start(), and protocols::loops::Loop::set_stop().

static basic::Tracer protocols::loops::TR ( "protocols.loops.FoldTreeFromLoopsWrapper" )

static

Referenced by add_loop(), protocols::loops::FoldTreeFromLoops::apply(), and loops_around_residues().

static basic::Tracer protocols::loops::tr ( "protocols.loops.Loop" )

static

Referenced by protocols::loops::Loops::add_loop(), protocols::loops::Loop::choose_cutpoint(), protocols::loops::LoopMoverFactory::create_loop_mover(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::read_loop_file(), protocols::loops::Loops::read_loops_options(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), and protocols::loops::Loops::verify_against().

static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopsFileIO" )

static

static basic::Tracer protocols::loops::TR	(	"protocols.loops.make_loops"	,
		t_info
	)

static

static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopMoverFactory" )

static

static basic::Tracer protocols::loops::tr ( "loops" )

static

void protocols::loops::trim_back_sequence_mapping	(	id::SequenceMapping &	mapping,
		std::string const &	source_seq,
		std::string const &	target_seq,
		Size const	min_loop_size
	)

Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.

Definition at line 1250 of file loops_main.cc.

References core::id::SequenceMapping::reverse(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and core::pack::tt().

basic::Tracer protocols::loops::tt ( "protocols.loops.loops_main" )

void protocols::loops::validate_loop_start_stop	(	bool	prohibit_single_residue_loops,
		core::Size	start,
		core::Size	stop,
		std::string const &	filename,
		core::Size	linecount
	)