Namespaces
	filters

	loop_closure

	loop_mover

	loops_definers

Classes
class	EXCN_Loop_not_closed

class	FoldTreeFromLoops

class	FoldTreeFromLoopsCreator

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	JSONFormattedLoopsFileReader

class	Loop
	single loop definition More...

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

class	LoopFromFileData

class	LoopMoverFactory
	Create LoopMover Reporters. More...

class	Loops

class	LoopsFileData

class	LoopsFileIO

class	LoopsFileLoader
	LoopsFileLoader constructs a LoopsFileData instance from data provided by the ResourceManager. More...

class	LoopsFileLoaderCreator
	LoopsFileLoaderCreator allows the ResourceLoaderFactory to create a LoopsFileLoader instance. More...

class	PoseNumberedLoopFileReader

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

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

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

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

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

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

typedef utility::vector1 < SerializedLoop >	SerializedLoopList

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

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

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

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

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

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

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

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

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

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

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")

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

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

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

static basic::Tracer	tr ("loops")

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

LoopsOP	deep_copy (Loops const &source)

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

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)
	Add cutpoint variants to all the cutpoints in a Pose. More...

void	add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)
	Add cutpoint variants around a single cutpoint (defined by a Loop). More...

void	add_single_cutpoint_variant (core::pose::Pose &pose, const core::uint cutpoint)
	Add cutpoint variants around a single cutpoint (defined by residue number). More...

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

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

core::kinematics::MoveMapOP	move_map_from_loops (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
	Create a new MoveMapOP for use in minimizing the given loop. More...

core::kinematics::MoveMapOP	move_map_from_loop (core::pose::Pose &pose, Loop const &loop, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
	Create a new MoveMapOP for use in minimizing the given loop. 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	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...

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

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

utility::vector1< bool >	select_loop_residues (core::pose::Pose const &pose, Loop const &loop, bool const include_neighbors, core::Real neighbor_dist=10.0)
	mark loop residues and its neighbors as necessary for one loop. More...

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 Takes distance from selection to neighbors to trim neighbors. 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)
	Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed. More...

bool	set_secstruct_from_psipred_ss2 (core::pose::Pose &pose, std::string const &filename=std::string())
	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 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...

core::pose::ResidueIndexDescriptionCOP	make_rid_posenum (std::string const &fname, core::Size lineno, core::Size resnum)

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	loops_around_residues (Loops &loops, core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_indices, core::Size gapsize=6, core::Size extend=2)
	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, 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 (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 (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::Size minimum_length_of_chunk_loop=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)

std::pair< bool, core::Size >	has_severe_pep_bond_geom_issues (core::pose::Pose const &pose, const Loop &loop, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
	Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...

std::pair< bool, core::Size >	has_severe_pep_bond_geom_issues (core::pose::Pose const &pose, core::Size resnum, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
	Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...

Variables
static const core::Real	EXT_PHI = -150

static const core::Real	EXT_PSI = +150

static const core::Real	EXT_OMG = 180

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::loops::LoopConfiguration

Enumerator
extras
resSeq
iCode
chainID
skip_rate
extend
use_pose_numbering
number_of_configuration_keywords

enum protocols::loops::ResidueIdentifier

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

Enumerator
start
stop
cut_point
number_of_residue_identifiers

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
	)

References protocols::cluster::calibur::aa, 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::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), TR(), and core::pose::virtual_type_for_pose().

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 )

Add cutpoint variants to all the cutpoints in a Pose.

References add_single_cutpoint_variant(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::num_cutpoint().

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_pro, protocols::loops::Loops::add_loop(), core::pose::Pose::chain(), core::chemical::ResidueTypeBase::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

References core::kinematics::MoveMap::set_bb().

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

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

Add cutpoint variants around a single cutpoint (defined by a Loop).

References add_single_cutpoint_variant(), and protocols::loops::Loop::cut().

Referenced by protocols::antibody_legacy::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::add_single_cutpoint_variant	(	core::pose::Pose &	pose,
		const core::uint	cutpoint
	)

Add cutpoint variants around a single cutpoint (defined by residue number).

Referenced by add_cutpoint_variants(), and add_single_cutpoint_variant().

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

References protocols::loops::Loops::add_loop(), core::conformation::Residue::atom_index(), core::id::AtomID::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(), protocols::hybridization::score, core::id::AtomID::set(), core::pose::setPoseExtraScore(), protocols::loops::Loops::size(), core::pose::Pose::size(), start, stop, and core::scoring::superimpose_pose().

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??

References core::pose::add_variant_type_to_pose_residue(), core::id::SequenceMapping::all_aligned(), core::pose::Pose::chain(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::delete_residue_slow(), core::id::SequenceMapping::delete_source_residue(), core::pose::Pose::fold_tree(), core::id::SequenceMapping::insert_aligned_residue(), core::kinematics::FoldTree::is_cutpoint(), core::id::SequenceMapping::is_identity(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::pose::Pose::sequence(), core::pose::Pose::set_omega(), core::id::SequenceMapping::show(), core::pose::Pose::size(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), tt(), core::conformation::Residue::type(), and core::chemical::ResidueTypeBase::variant_types().

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

This function takes a pose and loop definitions and closes each loop separately by the CCD algorithm. All parameters related to CCD are hard-coded. If one wishes more control over the options, s/he should use the CCDLoopClosureMover.

References protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop(), and protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap().

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
	)

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

LoopsOP protocols::loops::deep_copy ( Loops const & source )

inline

References protocols::loops::Loops::clone().

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

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
	)

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 tt().

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

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::update_template().

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.

References core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), and protocols::hybridization::HybridizeProtocol::update_template().

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::Size	minimum_length_of_chunk_loop,
		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);.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), 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 Takes distance from selection to neighbors to trim neighbors.

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.

References core::select::filter_neighbors_by_distance(), and core::pose::Pose::size().

Referenced by select_loop_residues().

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

References protocols::loops::Loops::add_loop(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::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::size().

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

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

References protocols::cluster::calibur::aa, 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_carbohydrate(), core::pose::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::is_upper_terminus(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), protocols::make_rot_lib::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::loops::Loops::sequential_order(), core::pose::Pose::size(), and core::pose::symmetry::symmetrize_fold_tree().

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::antibody::design::GeneralAntibodyModeler::extend_CDR(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::tcr::remodel_tcr_cdr_loops(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), set_single_loop_fold_tree(), protocols::loop_modeling::LoopMover::setup_fold_tree(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), protocols::antibody::AntibodyInfo::setup_simple_fold_tree(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

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

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::loop_modeler::LoopModeler::LoopModeler(), 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(), and protocols::comparative_modeling::LoopRelaxMover::set_defaults_().

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

References core::scoring::get_score_function().

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::loop_modeler::LoopModeler::LoopModeler(), 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_().

std::pair< bool, core::Size > protocols::loops::has_severe_pep_bond_geom_issues	(	core::pose::Pose const &	pose,
		const Loop &	loop,
		bool	check_bonds = `true`,
		bool	check_angles = `true`,
		core::Real	max_c_n_dis = `2.0`,
		core::Real	allowed_ca_c_n_deviation = `25.0`,
		core::Real	allowed_c_n_ca_deviation = `25.0`
	)

Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1.

Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values out of this range. -JAB Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009) Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325. deviation is +/- from the min/max values of the CDL.

Parameters

Stringent cutoffs are: 1.5, 15, 15

Author: Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References has_severe_pep_bond_geom_issues(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::antibody::design::check_cb(), protocols::antibody::AntibodyInfo::check_cdr_quality(), protocols::grafting::graft_closed(), and protocols::antibody::design::AntibodyDesignMover::run_graft().

std::pair< bool, core::Size > protocols::loops::has_severe_pep_bond_geom_issues	(	core::pose::Pose const &	pose,
		core::Size	resnum,
		bool	check_bonds = `true`,
		bool	check_angles = `true`,
		core::Real	max_c_n_dis = `2.0`,
		core::Real	allowed_ca_c_n_deviation = `25.0`,
		core::Real	allowed_c_n_ca_deviation = `25.0`
	)

Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1.

Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values out of this range. -JAB Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009) Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325. deviation is +/- from the min/max values of the CDL.

Parameters

Stringent cutoffs are: 1.5, 15, 15

Author: Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), TR(), and core::conformation::Atom::xyz().

Referenced by has_severe_pep_bond_geom_issues().

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.

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

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::loop_modeling::LoopBuilder::idealize_loop(), 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.

References protocols::loops::Loops::num_loop(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), 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.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atoms(), core::sequence::end, core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), start, core::pose::Pose::total_residue(), 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.

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.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_index(), core::id::AtomID::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::pose::Pose::size(), and core::scoring::superimpose_pose().

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

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

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, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), 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

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

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::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

References add_loop(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, extend, protocols::mean_field::min(), protocols::loops::Loops::num_loop(), core::pose::Pose::size(), 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

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

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
	)

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

References loops_set_move_map().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loop_modeling::refiners::MinimizationRefiner::do_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	(	pose::Pose &	pose,
		Loops const &	loops,
		bool const	fix_template_sc,
		core::kinematics::MoveMap &	mm,
		Real	neighbor_dist,
		bool const	allow_omega_move,
		bool const	allow_takeoff_torsion_move
	)

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

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

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

References loops_set_move_map().

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

References core::id::BB, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by loops_set_move_map(), and move_map_from_loops().

core::pose::ResidueIndexDescriptionCOP protocols::loops::make_rid_posenum	(	std::string const &	fname,
		core::Size	lineno,
		core::Size	resnum
	)

core::kinematics::MoveMapOP protocols::loops::move_map_from_loop	(	core::pose::Pose &	pose,
		Loop const &	loop,
		bool const	fix_template_sc,
		core::Real	neighbor_dist,
		bool const	flanking_residues
	)

Create a new MoveMapOP for use in minimizing the given loop.

Wrapper around loops_set_move_map which works on a single loop object and returns a MoveMapOP. See the detailed documentation for loops_set_move_map for more information about the generated MoveMap.

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

core::kinematics::MoveMapOP protocols::loops::move_map_from_loops	(	core::pose::Pose &	pose,
		Loops const &	loops,
		bool const	fix_template_sc,
		core::Real	neighbor_dist,
		bool const	flanking_residues
	)

Create a new MoveMapOP for use in minimizing the given loop.

Wrapper around loops_set_move_map which works on a single loop object and returns a MoveMapOP. See the detailed documentation for loops_set_move_map for more information about the generated MoveMap.

References add_loop_flank_residues_bb_to_movemap(), and loops_set_move_map().

Referenced by move_map_from_loop().

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
	)

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

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

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

References protocols::loops::Loop::show().

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

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

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

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

Referenced by protocols::RBSegmentRelaxImpl::apply(), protocols::loop_build::LoopmodelWrapper::apply(), protocols::indel::IndelOptimizationMover::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::coupled_moves::CoupledMovesProtocol::parse_my_tag(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::antibody::H3PerturbCCD::read_and_store_fragments(), protocols::antibody_legacy::AntibodyModeler::read_and_store_fragments(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::comparative_modeling::LoopRelaxThreadingMover::setup(), and protocols::loop_modeler::LoopModeler::setup_kic_with_fragments_config().

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

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

Remove cutpoint variants.

Remove cutpoint variants

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::size().

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

Rebuild a loop via fragment insertion + ccd closure + minimization

References set_extended_torsions(), and set_single_loop_fold_tree().

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

Remove small chunks.

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().

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.

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

Referenced by extract_secondary_structure_chunks().

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.

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.

References core::fragment::FragSet::add(), core::id::BB, core::fragment::FragSet::frames(), core::fragment::FragSet::generate_insert_map(), core::kinematics::MoveMap::set_bb(), 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

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References core::select::fill_tenA_neighbor_residues(), filter_loop_neighbors_by_distance(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::residue(), and core::conformation::Residue::type().

utility::vector1< bool > protocols::loops::select_loop_residues	(	pose::Pose const &	pose,
		Loops const &	loops,
		bool const	include_neighbors,
		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

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References select_loop_residues(), and core::pose::Pose::size().

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

mark loop residues and its neighbors as necessary for one loop.

for one loop only

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

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

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

mark loop residues and its neighbors as necessary for one loop.

for one loop only

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References core::pose::Pose::size().

Referenced by loops_set_move_map(), and select_loop_residues().

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

Set a loop to extended torsion angles.

References idealize_loop(), protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and tt().

Referenced by 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
	)

References protocols::loops::Loops::add_loop(), core::pose::Pose::conformation(), protocols::loops::Loops::empty(), EXT_OMG, EXT_PHI, EXT_PSI, core::conformation::idealize_position(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), and TR().

Referenced by protocols::pose_creation::ExtendedPoseMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::pose_creation::PoseFromSequenceMover::apply(), protocols::antibody::design::GeneralAntibodyModeler::extend_CDR(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), safe_set_extended_torsions_and_idealize_loops(), and protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

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

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::fold_tree(), core::conformation::Residue::lower_connect_atom(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), tt(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree().

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.

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?

References protocols::cluster::calibur::aa, core::pose::Pose::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and 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,
		std::string const &	filename
	)

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.

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

References protocols::loops::Loops::add_loop(), core::pose::Pose::fold_tree(), fold_tree_from_loops(), and tt().

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::kinematic_closure::BalancedKicMover::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(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), remove_missing_density(), and protocols::forge::remodel::RemodelLoopMover::set_segment_stage().

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.

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().

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

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

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

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().

Referenced by extract_continuous_chunks(), extract_secondary_structure_chunks(), and split_by_resSeq().

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

static

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.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.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.

References protocols::mean_field::min(), core::id::SequenceMapping::reverse(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and tt().

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

static

Referenced by add_single_cutpoint_variant(), apply_sequence_mapping(), extend_sequence_mapping(), loop_rmsd(), read_loop_fragments(), set_extended_torsions(), set_loop_cutpoint_in_pose_fold_tree(), set_secstruct_from_dssp(), set_secstruct_from_psipred_ss2(), set_single_loop_fold_tree(), and trim_back_sequence_mapping().

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
	)