Classes
class	StructureSlicePredicate

class	StructureSlice

class	BuildPhases

class	SegmentPairSet

class	DivideAndConqueror
	Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece. More...

class	SolutionPredicate

class	PoseBuilder
	Builds a pose from StructureData. More...

class	ExtendedPoseBuilder

class	SolutionSorter

class	FoldGraph

class	NamedSolution

class	NamedSolutions

class	IdealAbegoGenerator
	Logic for selection of abego values. More...

class	NullPoseFolder
	Folds a pose using random phi/psi torsions. More...

class	VLBProtected

class	Picker
	class used for picking/caching fragments More...

class	EXCN_Fold
	Exception thrown by PoseFolder::apply to indicate folding was not successful. More...

class	PoseFolder
	Given a pose with all residues, and a StructureData object, assign a 3D conformation to the pose. More...

class	RandomTorsionPoseFolder
	Folds a pose using random phi/psi torsions. More...

class	RemodelLoopMoverPoseFolder
	Folds residues in a pose using RemodelLoopMover. More...

class	ResidueDihedrals

class	Segment
	manages information about segments of residues More...

class	SegmentPairing

class	HelixPairing

class	StrandPairing

class	HelixSheetPairing

class	SheetDB
	class used to create/manipulate a database of sheets using a list of pdb files More...

class	Alias

class	BondInfo

class	StructureData

class	EXCN_PoseInconsistent

class	StructureDataCreator

class	StructureDataFactory
	Singleton for creating StructureData objects. More...

class	EXCN_RemarksNotPresent

class	SegmentCounts

class	StructureDataObserver
	a cacheable observer that keeps track of what length events occured More...

class	StructureDataPerturber
	Classes for altering StructureData objects on the fly. More...

class	NullPerturber
	Perturber that does nothing. More...

class	ConnectionPerturber
	"mutates" a connection More...

class	HelixPerturber
	"mutates" a helix More...

class	CompoundPerturber
	"mutates" a set of mixed architects More...

class	VectorSelector
	Selects items from a vector using different methods. More...

class	RandomVectorSelector
	Selects items from a vector randomly. More...

class	EnumeratedVectorSelector
	Selects items sequentially from a vector. More...

Typedefs
typedef utility::pointer::shared_ptr< DivideAndConqueror >	DivideAndConquerorOP

typedef utility::pointer::shared_ptr< DivideAndConqueror const >	DivideAndConquerorCOP

typedef utility::pointer::shared_ptr< BuildPhases >	BuildPhasesOP

typedef utility::pointer::shared_ptr< BuildPhases const >	BuildPhasesCOP

typedef utility::vector1< StructureSlice >	StructureSlices

typedef utility::vector1< StructureSlices >	FoldingSolutions

typedef std::pair< SegmentName, SegmentName >	SegmentPair

typedef utility::pointer::shared_ptr< PoseBuilder >	PoseBuilderOP

typedef utility::pointer::shared_ptr< PoseBuilder const >	PoseBuilderCOP

typedef utility::pointer::shared_ptr< ExtendedPoseBuilder >	ExtendedPoseBuilderOP

typedef utility::pointer::shared_ptr< ExtendedPoseBuilder const >	ExtendedPoseBuilderCOP

typedef utility::pointer::shared_ptr< FoldGraph >	FoldGraphOP

typedef utility::pointer::shared_ptr< FoldGraph const >	FoldGraphCOP

typedef utility::pointer::weak_ptr< FoldGraph >	FoldGraphAP

typedef utility::pointer::weak_ptr< FoldGraph const >	FoldGraphCAP

typedef std::set< std::string >	NamedNodeSet

typedef utility::pointer::shared_ptr< IdealAbegoGenerator >	IdealAbegoGeneratorOP

typedef utility::pointer::shared_ptr< IdealAbegoGenerator const >	IdealAbegoGeneratorCOP

typedef utility::pointer::shared_ptr< NullPoseFolder >	NullPoseFolderOP

typedef utility::pointer::shared_ptr< NullPoseFolder const >	NullPoseFolderCOP

typedef utility::pointer::shared_ptr< Picker >	PickerOP

typedef utility::pointer::shared_ptr< Picker const >	PickerCOP

typedef utility::pointer::weak_ptr< Picker >	PickerAP

typedef utility::pointer::weak_ptr< Picker const >	PickerCAP

typedef utility::pointer::shared_ptr< PoseFolder >	PoseFolderOP

typedef utility::pointer::shared_ptr< PoseFolder const >	PoseFolderCOP

typedef utility::pointer::shared_ptr< RandomTorsionPoseFolder >	RandomTorsionPoseFolderOP

typedef utility::pointer::shared_ptr< RandomTorsionPoseFolder const >	RandomTorsionPoseFolderCOP

typedef utility::pointer::shared_ptr< RemodelLoopMoverPoseFolder >	RemodelLoopMoverPoseFolderOP

typedef utility::pointer::shared_ptr< RemodelLoopMoverPoseFolder const >	RemodelLoopMoverPoseFolderCOP

typedef long int	SegmentResid

typedef utility::pointer::shared_ptr< Segment >	SegmentOP

typedef utility::pointer::shared_ptr< Segment const >	SegmentCOP

typedef utility::pointer::weak_ptr< Segment >	SegmentAP

typedef utility::pointer::weak_ptr< Segment const >	SegmentCAP

typedef utility::vector1< SegmentOP >	SegmentOPs

typedef utility::vector1< SegmentCOP >	SegmentCOPs

typedef utility::vector1< StrandOrientation >	StrandOrientations

typedef long int	RegisterShift

typedef utility::vector1< RegisterShift >	RegisterShifts

typedef std::pair< core::Size, core::Size >	ResiduePair

typedef utility::vector1< ResiduePair >	ResiduePairs

typedef utility::pointer::shared_ptr< SegmentPairing >	SegmentPairingOP

typedef utility::pointer::shared_ptr< SegmentPairing const >	SegmentPairingCOP

typedef utility::vector1< SegmentPairingOP >	SegmentPairingOPs

typedef utility::vector1< SegmentPairingCOP >	SegmentPairingCOPs

typedef utility::pointer::shared_ptr< HelixPairing >	HelixPairingOP

typedef utility::pointer::shared_ptr< HelixPairing const >	HelixPairingCOP

typedef utility::vector1< HelixPairingOP >	HelixPairingOPs

typedef utility::vector1< HelixPairingCOP >	HelixPairingCOPs

typedef utility::pointer::shared_ptr< StrandPairing >	StrandPairingOP

typedef utility::pointer::shared_ptr< StrandPairing const >	StrandPairingCOP

typedef utility::vector1< StrandPairingOP >	StrandPairingOPs

typedef utility::vector1< StrandPairingCOP >	StrandPairingCOPs

typedef utility::pointer::shared_ptr< HelixSheetPairing >	HelixSheetPairingOP

typedef utility::pointer::shared_ptr< HelixSheetPairing const >	HelixSheetPairingCOP

typedef utility::vector1< HelixSheetPairingOP >	HelixSheetPairingOPs

typedef utility::vector1< HelixSheetPairingCOP >	HelixSheetPairingCOPs

typedef utility::pointer::shared_ptr< SheetDB >	SheetDBOP

typedef utility::pointer::shared_ptr< SheetDB const >	SheetDBCOP

typedef utility::pointer::weak_ptr< SheetDB >	SheetDBAP

typedef utility::pointer::weak_ptr< SheetDB const >	SheetDBCAP

typedef utility::vector1< core::pose::PoseCOP >	SheetList
	this is the actual map used to store the sheets More...

typedef std::map< std::string, SheetList >	MapByLengths

typedef std::map< std::string, MapByLengths >	MapByOrientations

typedef std::map< core::Size, MapByOrientations >	MapByStrands

typedef core::Size	MovableGroup

typedef utility::pointer::shared_ptr< StructureData >	StructureDataOP

typedef utility::pointer::shared_ptr< StructureData const >	StructureDataCOP

typedef utility::pointer::weak_ptr< StructureData >	StructureDataAP

typedef utility::pointer::weak_ptr< StructureData const >	StructureDataCAP

typedef utility::vector1< StructureDataOP >	StructureDataOPs

typedef utility::vector1< StructureDataCOP >	StructureDataCOPs

typedef std::map< std::string, std::string >	StringMap

typedef std::map< std::string, Segment >	SegmentMap

typedef std::map< std::string, Alias >	AliasMap

typedef utility::vector1< BondInfo >	BondInfos

typedef utility::vector1< core::Size >	Cutpoints

typedef utility::vector1< MovableGroup >	MovableGroups

typedef utility::pointer::shared_ptr< StructureDataFactory >	StructureDataFactoryOP

typedef utility::pointer::shared_ptr< StructureDataFactory const >	StructureDataFactoryCOP

typedef utility::pointer::shared_ptr< StructureDataObserver >	StructureDataObserverOP

typedef utility::pointer::shared_ptr< StructureDataObserver const >	StructureDataObserverCOP

typedef utility::pointer::weak_ptr< StructureDataObserver >	StructureDataObserverAP

typedef utility::pointer::weak_ptr< StructureDataObserver const >	StructureDataObserverCAP

typedef utility::pointer::shared_ptr< StructureDataPerturber >	StructureDataPerturberOP

typedef utility::pointer::shared_ptr< StructureDataPerturber const >	StructureDataPerturberCOP

typedef utility::vector1< StructureDataPerturber >	StructureDataPerturbers

typedef utility::vector1< StructureDataPerturberOP >	StructureDataPerturberOPs

typedef utility::vector1< StructureDataPerturberCOP >	StructureDataPerturberCOPs

typedef utility::pointer::shared_ptr< ConnectionPerturber >	ConnectionPerturberOP

typedef utility::pointer::shared_ptr< ConnectionPerturber const >	ConnectionPerturberCOP

typedef utility::pointer::shared_ptr< CompoundPerturber >	CompoundPerturberOP

typedef utility::pointer::shared_ptr< CompoundPerturber const >	CompoundPerturberCOP

typedef utility::pointer::shared_ptr< HelixPerturber >	HelixPerturberOP

typedef utility::pointer::shared_ptr< HelixPerturber const >	HelixPerturberCOP

Enumerations
enum	StrandOrientation { UP = 1 , DOWN = 2 , ORIENTATIONS_END = 3 }
	Individual strands are oriented pointing either "UP" or "DOWN" If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel. More...

Functions
std::ostream &	operator<< (std::ostream &os, SegmentPairSet const &pairs)

std::ostream &	operator<< (std::ostream &os, StructureSlice const &slice)

std::string	create_debug_filename (std::string const &file_prefix, core::Size const index, std::string const &file_suffix)

void	add_terminus_variants (core::pose::Pose &pose, ExtendedPoseBuilder::Resids const &endings)

core::conformation::ResidueOP	rsd_op (core::pose::Pose const &pose, std::string const &res_type)
	helper function to create a ValineOP in the same typeset as the pose More...

void	append_new_chain_from_template_segment (core::pose::Pose &pose, Segment const &segment)

void	append_residues_from_template_segment (core::pose::Pose &pose, Segment const &prev_segment, Segment const &segment)

core::kinematics::FoldTree	modify_ft_for_residue_insertion (core::pose::Pose &pose, core::Size const safe_res)
	modifies teh ft in the pose, returns the original More...

void	set_dihedrals (core::pose::Pose &pose, core::Size const resid, ResidueDihedrals const &dihedrals)

void	prepend_new_residues (core::pose::Pose &pose, core::Size num_residues, core::Size insert_pos, core::Size const, std::string const &type, ResidueDihedrals const &lower_dihedrals)

void	append_new_residues (core::pose::Pose &pose, core::Size num_residues, core::Size insert_pos, core::Size const, std::string const &type, ResidueDihedrals const &upper_dihedrals)

template<class T >
void	insert_mg (std::map< core::Size, std::list< T > > &fixed_mgs, core::Size const mg, T const &segname)

std::map< core::Size, std::list< core::Size > >	map_mgs (StructureData const &sd, FoldGraph const &fg)

std::map< core::Size, core::Size >	map_nodes (StructureData const &sd, FoldGraph const &fg)

std::ostream &	operator<< (std::ostream &os, NamedSolutions const &solutions)

std::ostream &	operator<< (std::ostream &os, NamedSolution const &s)

char	get_secstruct_from_abego (char const abego)

utility::vector1< std::string >	truncate_abego (utility::vector1< std::string > const &complete_abego, core::Size const closest_chain_ending)

core::Size	get_closest_chain_ending (utility::vector1< core::Size > const &chain_endings, core::Size total_residue, core::Size const end_res)

void	check_residue (core::select::residue_selector::ResidueSubset const &subset, core::Size const resid)
	checks to ensure a residue is in the ResidueSubset exits with error if not More...

void	check_residue_subset (core::select::residue_selector::ResidueSubset const &subset, protocols::loops::Loops const &loops)
	checks to ensure loops are contained within the ResidueSubset exits with error if not More...

bool	residue_is_compatible (core::conformation::Residue const &rsd)

std::ostream &	operator<< (std::ostream &os, Segment const &res)
	output residueinfo More...

std::ostream &	operator<< (std::ostream &os, SegmentPairing const &pairing)

core::select::residue_selector::ResidueVector	get_strand_residues (StrandOrientation const &orient, core::Size const start, core::Size const stop, core::select::residue_selector::ResidueVector const &bulges)

core::select::residue_selector::ResidueVector	get_bulges (core::Size const start, core::Size const stop, std::string const &abego)

void	add_paired_residues (StructureData const &sd, StrandPairing const &p, protocols::fldsgn::topology::SS_Info2 const &ss_info, ResiduePairs &pairs)

core::Size	count_bulges (protocols::fldsgn::topology::Strand const &strand, std::string const &abego)

bool	pose_matches_description (core::pose::Pose const &pose, std::string const &in_lengths_shifts)
	tells whether the given pose matches up with the given descriptor More...

std::string	orientations_str (StrandOrientations const &orientations)

utility::graph::Graph	graph_from_strandpairings (protocols::fldsgn::topology::StrandPairings const &spairs, std::map< core::Size, core::Size > &node_to_strand)

int	add_to_pose (core::pose::PoseOP newpose, core::pose::Pose const &pose, core::Size s_start, core::Size s_stop)

utility::vector1< core::pose::PoseOP >	extract_sheets_from_strandlist (utility::vector1< core::pose::PoseOP > const &strands, core::Size const nstrands)

core::pose::PoseOP	reorder_chains (core::pose::Pose &pose)

utility::vector1< core::pose::PoseOP >	extract_sheets_from_pose (core::pose::Pose const &pose, protocols::fldsgn::topology::StrandPairings const &spairs, protocols::fldsgn::topology::SS_Info2 const &ss_info, bool const idealize)

utility::vector1< bool >	calc_paired_residues (core::pose::Pose &pose, protocols::fldsgn::topology::StrandPairingSet const &spairs)
	creates a list of whether a pose residue is beta-sheet-type paired to anything More...

std::string	make_strand_info_str (architects::Lengths const &lengths, RegisterShifts const &shifts)
	creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts More...

std::string	make_lengths_str (core::pose::Pose const &pose, utility::vector1< bool > const &paired, Lengths const &lengths, StrandOrientations const &orients, protocols::fldsgn::topology::StrandPairingSet const &spairs)

std::pair< std::string, std::string >	prune_unpaired_residues (core::pose::Pose &pose)
	using the pose secondary structure, remove residues that aren't paired. returns a list of paired strand lengths, which do not necessarily correspond to pose lengths due to beta-bulges and other weird things. More...

core::Size	num_strands (core::pose::Pose const &pose)
	counts number of strands based on number of jumps. Pose must be a disconnected sheet More...

std::pair< std::string, std::string >	find_orientations_and_lengths (core::pose::Pose const &pose)
	gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set More...

std::string	reverse_orientations (std::string const &orient)

utility::vector1< bool >	parse_orientations (std::string const &orientations)

std::pair< utility::vector1< core::Size >, utility::vector1< int > >	parse_lengths (std::string const &lengths)

std::string	reverse_lengths (std::string const &orientations, std::string const &lengths)

std::pair< std::string, std::string >	canonicalize (std::string const &orientations, std::string const &lengths)

std::string const &	choose_canonical (std::string const &l1, std::string const &l2)

core::pose::PoseOP	reverse_chains (core::pose::Pose const &pose)

std::ostream &	operator<< (std::ostream &os, BondInfo const &b)

template<class T >
void	set_map_data (std::map< std::string, T > &map, std::string const &key, T const &value, bool const overwrite)

utility::vector1< core::Size >	compute_cutpoints (core::pose::Pose const &pose)

utility::vector1< core::Size >	compute_chain_beginnings (core::pose::Pose const &pose)

void	advance_past_virtual_residues (core::pose::Pose const &pose, utility::vector1< core::Size >::const_iterator &cur_resid, utility::vector1< core::Size >::const_iterator const &end_resids)

std::ostream &	operator<< (std::ostream &os, StructureData const &perm)
	output More...

std::ostream &	operator<< (std::ostream &os, Alias const &alias)

std::string	add_segment (StructureData &sd, Segment &seg, char const ss_type, SegmentCounts &counts)

void	add_segments_for_chain (std::string const &id_val, StructureData &sd, std::string const &chain_ss, std::string const &chain_abego, SegmentCounts &counts)
	Adds segments to the given SD. More...

basic::datacache::WriteableCacheableMap const &	get_writeable_cacheable_map (core::pose::Pose const &pose)

basic::datacache::WriteableCacheableMap &	get_writeable_cacheable_map (core::pose::Pose &pose)

void	clean_from_storage (std::string &st)
	prepare a string that was stored in string datacache More...

void	clean_for_storage (std::string &ss)
	prepare a string to be stored in the string datacache More...

Variables
static std::map< char, char > const	abego2secstruct

Typedef Documentation

◆ AliasMap

typedef std::map< std::string, Alias > protocols::denovo_design::components::AliasMap

◆ BondInfos

typedef utility::vector1< BondInfo > protocols::denovo_design::components::BondInfos

◆ BuildPhasesCOP

typedef utility::pointer::shared_ptr< BuildPhases const > protocols::denovo_design::components::BuildPhasesCOP

◆ BuildPhasesOP

typedef utility::pointer::shared_ptr< BuildPhases > protocols::denovo_design::components::BuildPhasesOP

◆ CompoundPerturberCOP

typedef utility::pointer::shared_ptr< CompoundPerturber const > protocols::denovo_design::components::CompoundPerturberCOP

◆ CompoundPerturberOP

typedef utility::pointer::shared_ptr< CompoundPerturber > protocols::denovo_design::components::CompoundPerturberOP

◆ ConnectionPerturberCOP

typedef utility::pointer::shared_ptr< ConnectionPerturber const > protocols::denovo_design::components::ConnectionPerturberCOP

◆ ConnectionPerturberOP

typedef utility::pointer::shared_ptr< ConnectionPerturber > protocols::denovo_design::components::ConnectionPerturberOP

◆ Cutpoints

typedef utility::vector1< core::Size > protocols::denovo_design::components::Cutpoints

◆ DivideAndConquerorCOP

typedef utility::pointer::shared_ptr< DivideAndConqueror const > protocols::denovo_design::components::DivideAndConquerorCOP

◆ DivideAndConquerorOP

typedef utility::pointer::shared_ptr< DivideAndConqueror > protocols::denovo_design::components::DivideAndConquerorOP

◆ ExtendedPoseBuilderCOP

typedef utility::pointer::shared_ptr< ExtendedPoseBuilder const > protocols::denovo_design::components::ExtendedPoseBuilderCOP

◆ ExtendedPoseBuilderOP

typedef utility::pointer::shared_ptr< ExtendedPoseBuilder > protocols::denovo_design::components::ExtendedPoseBuilderOP

◆ FoldGraphAP

typedef utility::pointer::weak_ptr< FoldGraph > protocols::denovo_design::components::FoldGraphAP

◆ FoldGraphCAP

typedef utility::pointer::weak_ptr< FoldGraph const > protocols::denovo_design::components::FoldGraphCAP

◆ FoldGraphCOP

typedef utility::pointer::shared_ptr< FoldGraph const > protocols::denovo_design::components::FoldGraphCOP

◆ FoldGraphOP

typedef utility::pointer::shared_ptr< FoldGraph > protocols::denovo_design::components::FoldGraphOP

◆ FoldingSolutions

typedef utility::vector1< StructureSlices > protocols::denovo_design::components::FoldingSolutions

◆ HelixPairingCOP

typedef utility::pointer::shared_ptr< HelixPairing const > protocols::denovo_design::components::HelixPairingCOP

◆ HelixPairingCOPs

typedef utility::vector1< HelixPairingCOP > protocols::denovo_design::components::HelixPairingCOPs

◆ HelixPairingOP

typedef utility::pointer::shared_ptr< HelixPairing > protocols::denovo_design::components::HelixPairingOP

◆ HelixPairingOPs

typedef utility::vector1< HelixPairingOP > protocols::denovo_design::components::HelixPairingOPs

◆ HelixPerturberCOP

typedef utility::pointer::shared_ptr< HelixPerturber const > protocols::denovo_design::components::HelixPerturberCOP

◆ HelixPerturberOP

typedef utility::pointer::shared_ptr< HelixPerturber > protocols::denovo_design::components::HelixPerturberOP

◆ HelixSheetPairingCOP

typedef utility::pointer::shared_ptr< HelixSheetPairing const > protocols::denovo_design::components::HelixSheetPairingCOP

◆ HelixSheetPairingCOPs

typedef utility::vector1< HelixSheetPairingCOP > protocols::denovo_design::components::HelixSheetPairingCOPs

◆ HelixSheetPairingOP

typedef utility::pointer::shared_ptr< HelixSheetPairing > protocols::denovo_design::components::HelixSheetPairingOP

◆ HelixSheetPairingOPs

typedef utility::vector1< HelixSheetPairingOP > protocols::denovo_design::components::HelixSheetPairingOPs

◆ IdealAbegoGeneratorCOP

typedef utility::pointer::shared_ptr< IdealAbegoGenerator const > protocols::denovo_design::components::IdealAbegoGeneratorCOP

◆ IdealAbegoGeneratorOP

typedef utility::pointer::shared_ptr< IdealAbegoGenerator > protocols::denovo_design::components::IdealAbegoGeneratorOP

◆ MapByLengths

typedef std::map< std::string, SheetList > protocols::denovo_design::components::MapByLengths

◆ MapByOrientations

typedef std::map< std::string, MapByLengths > protocols::denovo_design::components::MapByOrientations

◆ MapByStrands

typedef std::map< core::Size, MapByOrientations > protocols::denovo_design::components::MapByStrands

◆ MovableGroup

typedef core::Size protocols::denovo_design::components::MovableGroup

◆ MovableGroups

typedef utility::vector1< MovableGroup > protocols::denovo_design::components::MovableGroups

◆ NamedNodeSet

typedef std::set< std::string > protocols::denovo_design::components::NamedNodeSet

◆ NullPoseFolderCOP

typedef utility::pointer::shared_ptr< NullPoseFolder const > protocols::denovo_design::components::NullPoseFolderCOP

◆ NullPoseFolderOP

typedef utility::pointer::shared_ptr< NullPoseFolder > protocols::denovo_design::components::NullPoseFolderOP

◆ PickerAP

typedef utility::pointer::weak_ptr< Picker > protocols::denovo_design::components::PickerAP

◆ PickerCAP

typedef utility::pointer::weak_ptr< Picker const > protocols::denovo_design::components::PickerCAP

◆ PickerCOP

typedef utility::pointer::shared_ptr< Picker const > protocols::denovo_design::components::PickerCOP

◆ PickerOP

typedef utility::pointer::shared_ptr< Picker > protocols::denovo_design::components::PickerOP

◆ PoseBuilderCOP

typedef utility::pointer::shared_ptr< PoseBuilder const > protocols::denovo_design::components::PoseBuilderCOP

◆ PoseBuilderOP

typedef utility::pointer::shared_ptr< PoseBuilder > protocols::denovo_design::components::PoseBuilderOP

◆ PoseFolderCOP

typedef utility::pointer::shared_ptr< PoseFolder const > protocols::denovo_design::components::PoseFolderCOP

◆ PoseFolderOP

typedef utility::pointer::shared_ptr< PoseFolder > protocols::denovo_design::components::PoseFolderOP

◆ RandomTorsionPoseFolderCOP

typedef utility::pointer::shared_ptr< RandomTorsionPoseFolder const > protocols::denovo_design::components::RandomTorsionPoseFolderCOP

◆ RandomTorsionPoseFolderOP

typedef utility::pointer::shared_ptr< RandomTorsionPoseFolder > protocols::denovo_design::components::RandomTorsionPoseFolderOP

◆ RegisterShift

typedef long int protocols::denovo_design::components::RegisterShift

◆ RegisterShifts

typedef utility::vector1< RegisterShift > protocols::denovo_design::components::RegisterShifts

◆ RemodelLoopMoverPoseFolderCOP

typedef utility::pointer::shared_ptr< RemodelLoopMoverPoseFolder const > protocols::denovo_design::components::RemodelLoopMoverPoseFolderCOP

◆ RemodelLoopMoverPoseFolderOP

typedef utility::pointer::shared_ptr< RemodelLoopMoverPoseFolder > protocols::denovo_design::components::RemodelLoopMoverPoseFolderOP

◆ ResiduePair

typedef std::pair< core::Size, core::Size > protocols::denovo_design::components::ResiduePair

◆ ResiduePairs

typedef utility::vector1< ResiduePair > protocols::denovo_design::components::ResiduePairs

◆ SegmentAP

typedef utility::pointer::weak_ptr< Segment > protocols::denovo_design::components::SegmentAP

◆ SegmentCAP

typedef utility::pointer::weak_ptr< Segment const > protocols::denovo_design::components::SegmentCAP

◆ SegmentCOP

typedef utility::pointer::shared_ptr< Segment const > protocols::denovo_design::components::SegmentCOP

◆ SegmentCOPs

typedef utility::vector1< SegmentCOP > protocols::denovo_design::components::SegmentCOPs

◆ SegmentMap

typedef std::map< std::string, Segment > protocols::denovo_design::components::SegmentMap

◆ SegmentOP

typedef utility::pointer::shared_ptr< Segment > protocols::denovo_design::components::SegmentOP

◆ SegmentOPs

typedef utility::vector1< SegmentOP > protocols::denovo_design::components::SegmentOPs

◆ SegmentPair

typedef std::pair< SegmentName, SegmentName > protocols::denovo_design::components::SegmentPair

◆ SegmentPairingCOP

typedef utility::pointer::shared_ptr< SegmentPairing const > protocols::denovo_design::components::SegmentPairingCOP

◆ SegmentPairingCOPs

typedef utility::vector1< SegmentPairingCOP > protocols::denovo_design::components::SegmentPairingCOPs

◆ SegmentPairingOP

typedef utility::pointer::shared_ptr< SegmentPairing > protocols::denovo_design::components::SegmentPairingOP

◆ SegmentPairingOPs

typedef utility::vector1< SegmentPairingOP > protocols::denovo_design::components::SegmentPairingOPs

◆ SegmentResid

typedef long int protocols::denovo_design::components::SegmentResid

◆ SheetDBAP

typedef utility::pointer::weak_ptr< SheetDB > protocols::denovo_design::components::SheetDBAP

◆ SheetDBCAP

typedef utility::pointer::weak_ptr< SheetDB const > protocols::denovo_design::components::SheetDBCAP

◆ SheetDBCOP

typedef utility::pointer::shared_ptr< SheetDB const > protocols::denovo_design::components::SheetDBCOP

◆ SheetDBOP

typedef utility::pointer::shared_ptr< SheetDB > protocols::denovo_design::components::SheetDBOP

◆ SheetList

typedef utility::vector1< core::pose::PoseCOP > protocols::denovo_design::components::SheetList

this is the actual map used to store the sheets

◆ StrandOrientations

typedef utility::vector1< StrandOrientation > protocols::denovo_design::components::StrandOrientations

◆ StrandPairingCOP

typedef utility::pointer::shared_ptr< StrandPairing const > protocols::denovo_design::components::StrandPairingCOP

◆ StrandPairingCOPs

typedef utility::vector1< StrandPairingCOP > protocols::denovo_design::components::StrandPairingCOPs

◆ StrandPairingOP

typedef utility::pointer::shared_ptr< StrandPairing > protocols::denovo_design::components::StrandPairingOP

◆ StrandPairingOPs

typedef utility::vector1< StrandPairingOP > protocols::denovo_design::components::StrandPairingOPs

◆ StringMap

typedef std::map< std::string, std::string > protocols::denovo_design::components::StringMap

◆ StructureDataAP

typedef utility::pointer::weak_ptr< StructureData > protocols::denovo_design::components::StructureDataAP

◆ StructureDataCAP

typedef utility::pointer::weak_ptr< StructureData const > protocols::denovo_design::components::StructureDataCAP

◆ StructureDataCOP

typedef utility::pointer::shared_ptr< StructureData const > protocols::denovo_design::components::StructureDataCOP

◆ StructureDataCOPs

typedef utility::vector1< StructureDataCOP > protocols::denovo_design::components::StructureDataCOPs

◆ StructureDataFactoryCOP

typedef utility::pointer::shared_ptr< StructureDataFactory const > protocols::denovo_design::components::StructureDataFactoryCOP

◆ StructureDataFactoryOP

typedef utility::pointer::shared_ptr< StructureDataFactory > protocols::denovo_design::components::StructureDataFactoryOP

◆ StructureDataObserverAP

typedef utility::pointer::weak_ptr< StructureDataObserver > protocols::denovo_design::components::StructureDataObserverAP

◆ StructureDataObserverCAP

typedef utility::pointer::weak_ptr< StructureDataObserver const > protocols::denovo_design::components::StructureDataObserverCAP

◆ StructureDataObserverCOP

typedef utility::pointer::shared_ptr< StructureDataObserver const > protocols::denovo_design::components::StructureDataObserverCOP

◆ StructureDataObserverOP

typedef utility::pointer::shared_ptr< StructureDataObserver > protocols::denovo_design::components::StructureDataObserverOP

◆ StructureDataOP

typedef utility::pointer::shared_ptr< StructureData > protocols::denovo_design::components::StructureDataOP

◆ StructureDataOPs

typedef utility::vector1< StructureDataOP > protocols::denovo_design::components::StructureDataOPs

◆ StructureDataPerturberCOP

typedef utility::pointer::shared_ptr< StructureDataPerturber const > protocols::denovo_design::components::StructureDataPerturberCOP

◆ StructureDataPerturberCOPs

typedef utility::vector1< StructureDataPerturberCOP > protocols::denovo_design::components::StructureDataPerturberCOPs

◆ StructureDataPerturberOP

typedef utility::pointer::shared_ptr< StructureDataPerturber > protocols::denovo_design::components::StructureDataPerturberOP

◆ StructureDataPerturberOPs

typedef utility::vector1< StructureDataPerturberOP > protocols::denovo_design::components::StructureDataPerturberOPs

◆ StructureDataPerturbers

typedef utility::vector1< StructureDataPerturber > protocols::denovo_design::components::StructureDataPerturbers

◆ StructureSlices

typedef utility::vector1< StructureSlice > protocols::denovo_design::components::StructureSlices

Enumeration Type Documentation

◆ StrandOrientation

enum protocols::denovo_design::components::StrandOrientation

Individual strands are oriented pointing either "UP" or "DOWN" If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel.

Enumerator
UP
DOWN
ORIENTATIONS_END

Function Documentation

◆ add_paired_residues()

void protocols::denovo_design::components::add_paired_residues	(	StructureData const &	sd,
		StrandPairing const &	p,
		protocols::fldsgn::topology::SS_Info2 const &	ss_info,
		ResiduePairs &	pairs
	)

References core::scoring::abego, protocols::denovo_design::components::StructureData::abego(), core::sequence::end, get_bulges(), get_strand_residues(), protocols::denovo_design::components::StrandPairing::orient1(), protocols::denovo_design::components::StrandPairing::orient2(), protocols::denovo_design::components::Segment::safe(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::SegmentPairing::segments(), protocols::denovo_design::components::StrandPairing::shift(), protocols::fldsgn::topology::SS_Info2::strand_id(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::TR().

Referenced by protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs().

◆ add_segment()

std::string protocols::denovo_design::components::add_segment	(	StructureData &	sd,
		Segment &	seg,
		char const	ss_type,
		SegmentCounts &	counts
	)

References protocols::denovo_design::components::StructureData::add_segment(), protocols::denovo_design::components::Segment::id(), protocols::denovo_design::components::SegmentCounts::new_segment_name(), protocols::denovo_design::PARENT_DELIMETER, protocols::denovo_design::components::StructureData::pose_length(), protocols::denovo_design::components::Segment::set_id(), and protocols::TR().

Referenced by protocols::backrub::BackrubMover::add_mainchain_segments(), add_segments_for_chain(), and protocols::rbsegment_relax::ConfChangeMover::parse_my_tag().

◆ add_segments_for_chain()

void protocols::denovo_design::components::add_segments_for_chain	(	std::string const &	id_val,
		StructureData &	sd,
		std::string const &	chain_ss,
		std::string const &	chain_abego,
		SegmentCounts &	counts
	)

Adds segments to the given SD.

Parameters

[in]	id_val	Parent ID of the segments. Can be empty
[in,out]	sd	StructureData to be modified
[in]	chain_ss	Secondary structure of the full chain
[in]	chain_abego	Abego for the full chain
[in,out]	counts	Secondary structure element counters for naming segments

References core::pose::motif::a(), add_segment(), protocols::denovo_design::components::StructureData::mark_connected(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_motifs(), protocols::denovo_design::architects::BlueprintArchitect::design(), and protocols::denovo_design::components::StructureDataFactory::infer_from_pose().

◆ add_terminus_variants()

void protocols::denovo_design::components::add_terminus_variants	(	core::pose::Pose &	pose,
		ExtendedPoseBuilder::Resids const &	endings
	)

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), and core::pose::Pose::size().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ add_to_pose()

int protocols::denovo_design::components::add_to_pose	(	core::pose::PoseOP	newpose,
		core::pose::Pose const &	pose,
		core::Size	s_start,
		core::Size	s_stop
	)

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::conformation::Conformation::size(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

Referenced by extract_sheets_from_pose(), and prune_unpaired_residues().

◆ advance_past_virtual_residues()

void protocols::denovo_design::components::advance_past_virtual_residues	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size >::const_iterator &	cur_resid,
		utility::vector1< core::Size >::const_iterator const &	end_resids
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, and core::pose::Pose::residue().

Referenced by protocols::denovo_design::components::StructureData::check_chains().

◆ append_new_chain_from_template_segment()

void protocols::denovo_design::components::append_new_chain_from_template_segment	(	core::pose::Pose &	pose,
		Segment const &	segment
	)

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose().

◆ append_new_residues()

void protocols::denovo_design::components::append_new_residues	(	core::pose::Pose &	pose,
		core::Size	num_residues,
		core::Size	insert_pos,
		core::Size const	,
		std::string const &	type,
		ResidueDihedrals const &	upper_dihedrals
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::is_upper_terminus(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::denovo_design::components::ResidueDihedrals::phi(), protocols::denovo_design::components::ResidueDihedrals::psi(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), rsd_op(), protocols::denovo_design::components::ResidueDihedrals::set_in_pose(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ append_residues_from_template_segment()

void protocols::denovo_design::components::append_residues_from_template_segment	(	core::pose::Pose &	pose,
		Segment const &	prev_segment,
		Segment const &	segment
	)

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose().

◆ calc_paired_residues()

utility::vector1< bool > protocols::denovo_design::components::calc_paired_residues	(	core::pose::Pose &	pose,
		protocols::fldsgn::topology::StrandPairingSet const &	spairs
	)

creates a list of whether a pose residue is beta-sheet-type paired to anything

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), core::pose::Pose::size(), protocols::fldsgn::topology::StrandPairingSet::strand_pairing(), and protocols::TR().

Referenced by prune_unpaired_residues().

◆ canonicalize()

std::pair< std::string, std::string > protocols::denovo_design::components::canonicalize	(	std::string const &	orientations,
		std::string const &	lengths
	)

References choose_canonical(), protocols::denovo_design::components::SheetDB::orientations(), reverse_lengths(), reverse_orientations(), and protocols::TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheet(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), and protocols::denovo_design::components::SheetDB::set_sheetlist().

◆ check_residue()

void protocols::denovo_design::components::check_residue	(	core::select::residue_selector::ResidueSubset const &	subset,
		core::Size const	resid
	)

checks to ensure a residue is in the ResidueSubset exits with error if not

References protocols::denovo_design::components::RandomTorsionPoseFolder::class_name().

Referenced by protocols::pose_sewing::movers::SewAnythingAddMover::apply(), and check_residue_subset().

◆ check_residue_subset()

void protocols::denovo_design::components::check_residue_subset	(	core::select::residue_selector::ResidueSubset const &	subset,
		protocols::loops::Loops const &	loops
	)

checks to ensure loops are contained within the ResidueSubset exits with error if not

References check_residue().

Referenced by protocols::denovo_design::components::RandomTorsionPoseFolder::apply().

◆ choose_canonical()

std::string const & protocols::denovo_design::components::choose_canonical	(	std::string const &	l1,
		std::string const &	l2
	)

References protocols::antibody::l1, and protocols::antibody::l2.

Referenced by canonicalize().

◆ clean_for_storage()

void protocols::denovo_design::components::clean_for_storage ( std::string & ss )

prepare a string to be stored in the string datacache

Referenced by protocols::denovo_design::components::StructureData::write().

◆ clean_from_storage()

void protocols::denovo_design::components::clean_from_storage ( std::string & st )

prepare a string that was stored in string datacache

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data().

◆ compute_chain_beginnings()

utility::vector1< core::Size > protocols::denovo_design::components::compute_chain_beginnings ( core::pose::Pose const & pose )

References core::conformation::Conformation::chain_endings(), and core::pose::Pose::conformation().

Referenced by protocols::denovo_design::components::StructureData::check_chains().

◆ compute_cutpoints()

utility::vector1< core::Size > protocols::denovo_design::components::compute_cutpoints ( core::pose::Pose const & pose )

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::denovo_design::components::StructureData::check_chains().

◆ count_bulges()

core::Size protocols::denovo_design::components::count_bulges	(	protocols::fldsgn::topology::Strand const &	strand,
		std::string const &	abego
	)

References core::scoring::abego, and protocols::loops::loop_closure::ccd::strand.

Referenced by protocols::denovo_design::components::StrandPairing::nobu_register_shift().

◆ create_debug_filename()

std::string protocols::denovo_design::components::create_debug_filename	(	std::string const &	file_prefix,
		core::Size const	index,
		std::string const &	file_suffix
	)

References protocols::abinitio::filename().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose(), and protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ extract_sheets_from_pose()

utility::vector1< core::pose::PoseOP > protocols::denovo_design::components::extract_sheets_from_pose	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::StrandPairings const &	spairs,
		protocols::fldsgn::topology::SS_Info2 const &	ss_info,
		bool const	idealize
	)

References add_to_pose(), protocols::idealize::IdealizeMover::apply(), graph_from_strandpairings(), reorder_chains(), protocols::loops::start, protocols::loops::stop, protocols::fldsgn::topology::SS_Info2::strand(), protocols::loops::loop_closure::ccd::strand, and protocols::TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_spairs().

◆ extract_sheets_from_strandlist()

utility::vector1< core::pose::PoseOP > protocols::denovo_design::components::extract_sheets_from_strandlist	(	utility::vector1< core::pose::PoseOP > const &	strands,
		core::Size const	nstrands
	)

References protocols::TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_spairs().

◆ find_orientations_and_lengths()

std::pair< std::string, std::string > protocols::denovo_design::components::find_orientations_and_lengths ( core::pose::Pose const & pose )

gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set

References protocols::fldsgn::topology::calc_strand_pairing_set(), protocols::environment::NOT_SET, num_strands(), protocols::denovo_design::components::SheetDB::orientations(), orientations_str(), core::scoring::pair, core::pose::Pose::secstruct(), protocols::fldsgn::topology::StrandPairingSet::size(), core::id::to_string(), and protocols::TR().

◆ get_bulges()

core::select::residue_selector::ResidueVector protocols::denovo_design::components::get_bulges	(	core::Size const	start,
		core::Size const	stop,
		std::string const &	abego
	)

References core::scoring::abego, protocols::loops::start, and protocols::loops::stop.

Referenced by add_paired_residues().

◆ get_closest_chain_ending()

core::Size protocols::denovo_design::components::get_closest_chain_ending	(	utility::vector1< core::Size > const &	chain_endings,
		core::Size	total_residue,
		core::Size const	end_res
	)

Referenced by protocols::denovo_design::components::Picker::get_framelist().

◆ get_secstruct_from_abego()

char protocols::denovo_design::components::get_secstruct_from_abego ( char const abego )

References core::scoring::abego, and abego2secstruct.

Referenced by protocols::denovo_design::components::IdealAbegoGenerator::generate().

◆ get_strand_residues()

core::select::residue_selector::ResidueVector protocols::denovo_design::components::get_strand_residues	(	StrandOrientation const &	orient,
		core::Size const	start,
		core::Size const	stop,
		core::select::residue_selector::ResidueVector const &	bulges
	)

References DOWN, core::select::resids(), protocols::loops::start, protocols::loops::stop, protocols::TR(), and UP.

Referenced by add_paired_residues().

◆ get_writeable_cacheable_map() [1/2]

basic::datacache::WriteableCacheableMap& protocols::denovo_design::components::get_writeable_cacheable_map ( core::pose::Pose & pose )

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

◆ get_writeable_cacheable_map() [2/2]

basic::datacache::WriteableCacheableMap const& protocols::denovo_design::components::get_writeable_cacheable_map ( core::pose::Pose const & pose )

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

Referenced by protocols::denovo_design::components::StructureDataFactory::has_cached_data(), protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data(), and protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data_ptr().

◆ graph_from_strandpairings()

utility::graph::Graph protocols::denovo_design::components::graph_from_strandpairings	(	protocols::fldsgn::topology::StrandPairings const &	spairs,
		std::map< core::Size, core::Size > &	node_to_strand
	)

References protocols::denovo_design::components::SheetDB::MIN_STRAND_LEN, and protocols::TR().

Referenced by extract_sheets_from_pose().

◆ insert_mg()

template<class T >

void protocols::denovo_design::components::insert_mg	(	std::map< core::Size, std::list< T > > &	fixed_mgs,
		core::Size const	mg,
		T const &	segname
	)

References core::scoring::mg.

Referenced by protocols::denovo_design::components::FoldGraph::check_solution(), and map_mgs().

◆ make_lengths_str()

std::string protocols::denovo_design::components::make_lengths_str	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	paired,
		Lengths const &	lengths,
		StrandOrientations const &	orients,
		protocols::fldsgn::topology::StrandPairingSet const &	spairs
	)

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), DOWN, make_strand_info_str(), core::conformation::Conformation::num_chains(), protocols::loops::start, protocols::loops::stop, protocols::fldsgn::topology::StrandPairingSet::strand_pairing(), protocols::TR(), and UP.

Referenced by prune_unpaired_residues().

◆ make_strand_info_str()

std::string protocols::denovo_design::components::make_strand_info_str	(	Lengths const &	lengths,
		RegisterShifts const &	shifts
	)

creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts

References core::id::to_string().

Referenced by protocols::denovo_design::components::SheetDB::has_data(), make_lengths_str(), reverse_lengths(), protocols::denovo_design::components::SheetDB::sheet_list(), and protocols::denovo_design::components::SheetDB::sheet_list_const().

◆ map_mgs()

std::map< core::Size, std::list< core::Size > > protocols::denovo_design::components::map_mgs	(	StructureData const &	sd,
		FoldGraph const &	fg
	)

References insert_mg(), protocols::denovo_design::components::Segment::movable_group(), protocols::denovo_design::components::FoldGraph::nodeidx(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), and protocols::denovo_design::components::StructureData::segments_end().

◆ map_nodes()

std::map< core::Size, core::Size > protocols::denovo_design::components::map_nodes	(	StructureData const &	sd,
		FoldGraph const &	fg
	)

References protocols::denovo_design::components::Segment::movable_group(), protocols::denovo_design::components::FoldGraph::nodeidx(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), and protocols::denovo_design::components::StructureData::segments_end().

◆ modify_ft_for_residue_insertion()

core::kinematics::FoldTree protocols::denovo_design::components::modify_ft_for_residue_insertion	(	core::pose::Pose &	pose,
		core::Size const	safe_res
	)

modifies teh ft in the pose, returns the original

References core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), and protocols::TR().

◆ num_strands()

core::Size protocols::denovo_design::components::num_strands ( core::pose::Pose const & pose )

counts number of strands based on number of jumps. Pose must be a disconnected sheet

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::num_jump().

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_spairs(), find_orientations_and_lengths(), and protocols::features::strand_assembly::get_num_strands_in_this_sheet().

◆ operator<<() [1/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		Alias const &	alias
	)

◆ operator<<() [2/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		BondInfo const &	b
	)

◆ operator<<() [3/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		NamedSolution const &	s
	)

◆ operator<<() [4/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		NamedSolutions const &	solutions
	)

◆ operator<<() [5/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		Segment const &	res
	)

output residueinfo

◆ operator<<() [6/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		SegmentPairing const &	pairing
	)

◆ operator<<() [7/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		SegmentPairSet const &	pairs
	)

◆ operator<<() [8/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		StructureData const &	perm
	)

output

for output

◆ operator<<() [9/9]

std::ostream& protocols::denovo_design::components::operator<<	(	std::ostream &	os,
		StructureSlice const &	slice
	)

References protocols::stepwise::modeler::slice().

◆ orientations_str()

std::string protocols::denovo_design::components::orientations_str ( StrandOrientations const & orientations )

References DOWN, and UP.

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::add_orientations(), find_orientations_and_lengths(), protocols::denovo_design::components::SheetDB::has_data(), prune_unpaired_residues(), protocols::denovo_design::components::SheetDB::sheet_list(), and protocols::denovo_design::components::SheetDB::sheet_list_const().

◆ parse_lengths()

std::pair< utility::vector1< core::Size >, utility::vector1< int > > protocols::denovo_design::components::parse_lengths ( std::string const & lengths )

Referenced by pose_matches_description(), and reverse_lengths().

◆ parse_orientations()

utility::vector1< bool > protocols::denovo_design::components::parse_orientations ( std::string const & orientations )

References protocols::denovo_design::components::SheetDB::orientations(), and protocols::TR().

Referenced by reverse_lengths().

◆ pose_matches_description()

bool protocols::denovo_design::components::pose_matches_description	(	core::pose::Pose const &	pose,
		std::string const &	in_lengths_shifts
	)

tells whether the given pose matches up with the given descriptor

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Conformation::num_chains(), parse_lengths(), core::pose::Pose::residue(), and protocols::TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheet().

◆ prepend_new_residues()

void protocols::denovo_design::components::prepend_new_residues	(	core::pose::Pose &	pose,
		core::Size	num_residues,
		core::Size	insert_pos,
		core::Size const	,
		std::string const &	type,
		ResidueDihedrals const &	lower_dihedrals
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::is_lower_terminus(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::denovo_design::components::ResidueDihedrals::phi(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), protocols::denovo_design::components::ResidueDihedrals::psi(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), rsd_op(), protocols::denovo_design::components::ResidueDihedrals::set_in_pose(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), protocols::loops::stop, protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ prune_unpaired_residues()

std::pair< std::string, std::string > protocols::denovo_design::components::prune_unpaired_residues ( core::pose::Pose & pose )

using the pose secondary structure, remove residues that aren't paired. returns a list of paired strand lengths, which do not necessarily correspond to pose lengths due to beta-bulges and other weird things.

References add_to_pose(), calc_paired_residues(), protocols::fldsgn::topology::calc_strand_pairing_set(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::clear(), core::pose::Pose::conformation(), DOWN, protocols::simple_filters::dssp(), make_lengths_str(), protocols::denovo_design::components::SheetDB::MIN_STRAND_LEN, core::conformation::Conformation::num_chains(), orientations_str(), core::pose::Pose::secstruct(), protocols::loops::start, protocols::loops::stop, protocols::fldsgn::topology::StrandPairingSet::strand_pairing(), protocols::TR(), and UP.

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_spairs().

◆ reorder_chains()

core::pose::PoseOP protocols::denovo_design::components::reorder_chains ( core::pose::Pose & pose )

References protocols::fldsgn::topology::calc_strand_pairing_set(), core::pose::Pose::conformation(), protocols::simple_filters::dssp(), protocols::fldsgn::topology::StrandPairingSet::neighbor_strands(), core::conformation::Conformation::num_chains(), protocols::fldsgn::topology::StrandPairingSet::num_strands(), core::pose::Pose::secstruct(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), protocols::loops::loop_closure::ccd::strand, and protocols::TR().

Referenced by extract_sheets_from_pose().

◆ residue_is_compatible()

bool protocols::denovo_design::components::residue_is_compatible ( core::conformation::Residue const & rsd )

References core::conformation::Residue::is_carbohydrate(), and core::conformation::Residue::is_ligand().

Referenced by protocols::denovo_design::components::ResidueDihedrals::set_in_pose().

◆ reverse_chains()

core::pose::PoseOP protocols::denovo_design::components::reverse_chains ( core::pose::Pose const & pose )

References core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), core::pose::Pose::size(), and core::pose::Pose::split_by_chain().

Referenced by protocols::denovo_design::components::SheetDB::add_sheet(), and protocols::denovo_design::components::SheetDB::set_sheetlist().

◆ reverse_lengths()

std::string protocols::denovo_design::components::reverse_lengths	(	std::string const &	orientations,
		std::string const &	lengths
	)

References make_strand_info_str(), protocols::denovo_design::components::SheetDB::orientations(), parse_lengths(), and parse_orientations().

Referenced by protocols::denovo_design::components::SheetDB::add_sheet(), canonicalize(), and protocols::denovo_design::components::SheetDB::set_sheetlist().

◆ reverse_orientations()

std::string protocols::denovo_design::components::reverse_orientations ( std::string const & orient )

References protocols::TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheet(), canonicalize(), and protocols::denovo_design::components::SheetDB::set_sheetlist().

◆ rsd_op()

core::conformation::ResidueOP protocols::denovo_design::components::rsd_op	(	core::pose::Pose const &	pose,
		std::string const &	res_type
	)

helper function to create a ValineOP in the same typeset as the pose

References core::conformation::ResidueFactory::create_residue(), core::pose::get_restype_for_pose(), and core::pose::Pose::size().

Referenced by append_new_chain_from_template_segment(), append_new_residues(), append_residues_from_template_segment(), and prepend_new_residues().

◆ set_dihedrals()

void protocols::denovo_design::components::set_dihedrals	(	core::pose::Pose &	pose,
		core::Size const	resid,
		ResidueDihedrals const &	dihedrals
	)

References protocols::denovo_design::components::ResidueDihedrals::omega(), protocols::denovo_design::components::ResidueDihedrals::phi(), protocols::denovo_design::components::ResidueDihedrals::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

◆ set_map_data()

template<class T >

void protocols::denovo_design::components::set_map_data	(	std::map< std::string, T > &	map,
		std::string const &	key,
		T const &	value,
		bool const	overwrite
	)

References protocols::TR().

Referenced by protocols::denovo_design::components::StructureData::copy_data().

◆ truncate_abego()

utility::vector1< std::string > protocols::denovo_design::components::truncate_abego	(	utility::vector1< std::string > const &	complete_abego,
		core::Size const	closest_chain_ending
	)

Referenced by protocols::denovo_design::components::Picker::get_framelist().

Variable Documentation

◆ abego2secstruct

std::map< char, char > const protocols::denovo_design::components::abego2secstruct

static

Initial value:

= boost::assign::map_list_of

( 'A', 'H' ) ( 'B', 'E' ) ( 'X', 'L' )

Referenced by get_secstruct_from_abego().

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ AliasMap

◆ BondInfos

◆ BuildPhasesCOP

◆ BuildPhasesOP

◆ CompoundPerturberCOP

◆ CompoundPerturberOP

◆ ConnectionPerturberCOP

◆ ConnectionPerturberOP

◆ Cutpoints

◆ DivideAndConquerorCOP

◆ DivideAndConquerorOP

◆ ExtendedPoseBuilderCOP

◆ ExtendedPoseBuilderOP

◆ FoldGraphAP

◆ FoldGraphCAP

◆ FoldGraphCOP

◆ FoldGraphOP

◆ FoldingSolutions

◆ HelixPairingCOP

◆ HelixPairingCOPs

◆ HelixPairingOP

◆ HelixPairingOPs

◆ HelixPerturberCOP

◆ HelixPerturberOP

◆ HelixSheetPairingCOP

◆ HelixSheetPairingCOPs

◆ HelixSheetPairingOP

◆ HelixSheetPairingOPs

◆ IdealAbegoGeneratorCOP

◆ IdealAbegoGeneratorOP

◆ MapByLengths

◆ MapByOrientations

◆ MapByStrands

◆ MovableGroup

◆ MovableGroups

◆ NamedNodeSet

◆ NullPoseFolderCOP

◆ NullPoseFolderOP

◆ PickerAP

◆ PickerCAP

◆ PickerCOP

◆ PickerOP

◆ PoseBuilderCOP

◆ PoseBuilderOP

◆ PoseFolderCOP

◆ PoseFolderOP

◆ RandomTorsionPoseFolderCOP

◆ RandomTorsionPoseFolderOP

◆ RegisterShift

◆ RegisterShifts

◆ RemodelLoopMoverPoseFolderCOP

◆ RemodelLoopMoverPoseFolderOP

◆ ResiduePair

◆ ResiduePairs

◆ SegmentAP

◆ SegmentCAP

◆ SegmentCOP

◆ SegmentCOPs

◆ SegmentMap

◆ SegmentOP

◆ SegmentOPs

◆ SegmentPair

◆ SegmentPairingCOP

◆ SegmentPairingCOPs

◆ SegmentPairingOP

◆ SegmentPairingOPs

◆ SegmentResid

◆ SheetDBAP

◆ SheetDBCAP

◆ SheetDBCOP

◆ SheetDBOP

◆ SheetList

◆ StrandOrientations

◆ StrandPairingCOP