protocols::legacy_sewing Namespace Reference

Namespaces
	sampling
	scoring

Classes
class	Assembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	AssemblyFactory
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	ContinuousAssembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	DisembodiedAssembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
struct	segment
struct	SewAtom
struct	SewResidue
struct	SewSegment
class	ModelIterator
class	ModelConstIterator
class	SegmentGraph
struct	Model
struct	coord_hash
struct	coord_equal_to
struct	HashValue
struct	Basis
struct	basis_pair_hash
struct	basis_pair_equal_to
struct	HashResult
class	Hasher
class	LegacyAddStartnodeFragments
class	LegacyAddStartnodeFragmentsCreator
class	LegacyAppendAssemblyMover
class	LegacyAppendAssemblyMoverCreator
class	LegacyReadNativeRotamersFile
class	LegacyReadRepeatNativeRotamersFile
class	LegacyAssemblyConstraintsMover
class	LegacyAssemblyConstraintsMoverCreator
class	LegacyAssemblyMover
class	LegacyEnumerateAssemblyMover
class	LegacyEnumerateAssemblyMoverCreator
class	LegacyGivenPathAssemblyMover
class	LegacyGivenPathAssemblyMoverCreator
class	LegacyGreedyAssemblyMover
class	LegacyGreedyAssemblyMoverCreator
class	LegacyMonteCarloAssemblyMover
class	LegacyMonteCarloAssemblyMoverCreator
class	LegacyReadNativeRotamersFileCreator
class	LegacyReadRepeatNativeRotamersFileCreator
class	LegacyRepeatAssemblyMover
class	LegacyRepeatAssemblyMoverCreator
class	ModelNode
class	HashEdge
class	SewGraph

Typedefs
typedef utility::pointer::shared_ptr< Assembly >	AssemblyOP
typedef utility::pointer::shared_ptr< Assembly const >	AssemblyCOP
typedef utility::pointer::shared_ptr< Model >	ModelOP
typedef utility::pointer::shared_ptr< Model const >	ModelCOP
typedef utility::pointer::shared_ptr< SewSegment >	SewSegmentOP
typedef utility::pointer::shared_ptr< SewSegment const >	SewSegmentCOP
typedef utility::pointer::shared_ptr< Hasher >	HasherOP
typedef utility::pointer::shared_ptr< Hasher const >	HasherCOP
typedef utility::fixedsizearray1< int, 3 >	HashKey
typedef boost::unordered_map< HashKey, utility::vector1< HashValue >, coord_hash, coord_equal_to >	HashMap
typedef std::pair< Basis, Basis >	BasisPair
typedef std::pair< core::Size, core::Size >	SegmentPair
typedef std::map< core::id::AtomID, core::id::AtomID >	AtomMap
typedef std::map< BasisPair, HashResult >	ScoreResults
typedef std::pair< BasisPair, HashResult >	ScoreResult
typedef utility::pointer::shared_ptr< LegacyAssemblyConstraintsMover >	LegacyAssemblyConstraintsMoverOP
typedef utility::pointer::shared_ptr< LegacyAssemblyConstraintsMover const >	LegacyAssemblyConstraintsMoverCOP
typedef utility::pointer::shared_ptr< LegacyAssemblyMover >	LegacyAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyAssemblyMover const >	LegacyAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyEnumerateAssemblyMover >	LegacyEnumerateAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyEnumerateAssemblyMover const >	LegacyEnumerateAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyMonteCarloAssemblyMover >	LegacyMonteCarloAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyMonteCarloAssemblyMover const >	LegacyMonteCarloAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover >	LegacyNodeConstraintAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover const >	LegacyNodeConstraintAssemblyMoverCOP
typedef utility::pointer::shared_ptr< SewGraph >	SewGraphOP
typedef utility::pointer::shared_ptr< SewGraph const >	SewGraphCOP
typedef std::map< core::Size, utility::vector1< std::pair< bool, core::conformation::ResidueOP > > >	NativeRotamersMap

Enumerations
enum	move_type { ADD_EDGE = 1 , DELETE_EDGE , SWITCH_EDGE }

Functions
static basic::Tracer	TR ("protocols.legacy_sewing.Assembly")
std::ostream &	operator<< (std::ostream &out, Assembly const &assembly)
static basic::Tracer	TR ("protocols.legacy_sewing.ContinuousAssembly")
static basic::Tracer	TR ("protocols.legacy_sewing.DisembodiedAssembly")
static basic::Tracer	TR ("protocols.legacy_sewing.Model")
Model	create_model_from_pose (core::pose::Pose const &pose, int model_id)
	Use the given segment-ranges to create a Model. Give this model an id that doesn't currently exist in the given map of models. More...
Model	create_model_from_pose (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &segments, int model_id)
	Use the given segment-ranges to create a Model. Give this model an id that doesn't currently exist in the given map of models. More...
std::map< int, Model >	result_to_models (cppdb::result res)
std::map< int, Model >	result_to_five_ss_models (cppdb::result res)
std::map< int, Model >	get_discontinuous_models_from_db ()
std::map< int, Model >	get_strand_sew_models_from_db ()
std::map< int, Model >	get_continuous_models_from_db (std::string const &hash_between)
std::map< int, Model >	get_5_ss_models_from_db (std::string const &hash_between)
void	remove_models_from_dssp (std::map< int, Model > &models, char dssp1, char dssp2)
	Will only work for smotif models!!! More...
void	add_num_neighbors (std::map< int, Model > &)
void	add_linker_segments (std::map< int, Model > &models)
std::map< int, Model >	get_alpha_beta_models_from_db ()
void	create_alpha_beta_models_table ()
void	write_model_file (std::string const &comments, std::map< int, Model > models, std::string filename)
std::map< int, Model >	read_model_file (std::string filename)
static basic::Tracer	TR ("protocols.legacy_sewing.Hasher")
static basic::Tracer	TR ("protocols.legacy_sewing.LegacyAddStartnodeFragments")
static basic::Tracer	TR ("protocols.legacy_sewing.LegacyAppendAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.LegacyAssemblyConstraintsMover")
static basic::Tracer	TR ("protocols.legacy_sewing.LegacyAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.sampling.LegacyEnumerateAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.sampling.LegacyGivenPathAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.sampling.LegacyGreedyAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.sampling.LegacyMonteCarloAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.LegacyRepeatAssemblyMover")
static basic::Tracer	TR ("protocols.legacy_sewing.SewGraph")
std::ostream &	operator<< (std::ostream &out, ModelNode const &node)
std::ostream &	operator<< (std::ostream &out, HashEdge const &edge)
utility::vector1< BasisPair >	scores_to_alignments (ScoreResults const &scores)
std::string	serialize_graph_json (SewGraphCOP graph, core::Size max_nodes)
	Take the given StructureScores and save them to disk. More...
static basic::Tracer	TR ("protocols.legacy_sewing.io")
void	write_native_residue_file (NativeRotamersMap native_residue_map, std::string const &filename)
NativeRotamersMap	read_native_residue_file (std::string const &filename)
void	write_hashing_scores_to_file (ScoreResults const &scores, std::string filename)
	Take the given StructureScores and save them to disk. More...
std::string	see_whether_model_is_H_bonded_by_terminal_strands (Model model, std::string const &P_PA)
	Return true if given model is H bonded by terminal strands. More...
static basic::Tracer	TR ("protocols.legacy_sewing.util")
std::map< core::id::AtomID, core::id::AtomID >	largest_continuous_atom_map (std::map< core::id::AtomID, core::id::AtomID > const &atom_map)

Variables
static int const	CHIMERA_SEGMENT = 0
static int const	POSE_SEGMENT = -1

Typedef Documentation

AssemblyCOP

typedef utility::pointer::shared_ptr< Assembly const > protocols::legacy_sewing::AssemblyCOP

AssemblyOP

typedef utility::pointer::shared_ptr< Assembly > protocols::legacy_sewing::AssemblyOP

AtomMap

typedef std::map< core::id::AtomID, core::id::AtomID > protocols::legacy_sewing::AtomMap

BasisPair

typedef std::pair< Basis, Basis > protocols::legacy_sewing::BasisPair

HasherCOP

typedef utility::pointer::shared_ptr< Hasher const > protocols::legacy_sewing::HasherCOP

HasherOP

typedef utility::pointer::shared_ptr< Hasher > protocols::legacy_sewing::HasherOP

HashKey

typedef utility::fixedsizearray1<int, 3> protocols::legacy_sewing::HashKey

HashMap

typedef boost::unordered_map<HashKey,utility::vector1< HashValue >,coord_hash,coord_equal_to> protocols::legacy_sewing::HashMap

LegacyAssemblyConstraintsMoverCOP

typedef utility::pointer::shared_ptr< LegacyAssemblyConstraintsMover const > protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCOP

LegacyAssemblyConstraintsMoverOP

typedef utility::pointer::shared_ptr< LegacyAssemblyConstraintsMover > protocols::legacy_sewing::LegacyAssemblyConstraintsMoverOP

LegacyAssemblyMoverCOP

typedef utility::pointer::shared_ptr< LegacyAssemblyMover const > protocols::legacy_sewing::LegacyAssemblyMoverCOP

LegacyAssemblyMoverOP

typedef utility::pointer::shared_ptr< LegacyAssemblyMover > protocols::legacy_sewing::LegacyAssemblyMoverOP

LegacyEnumerateAssemblyMoverCOP

typedef utility::pointer::shared_ptr< LegacyEnumerateAssemblyMover const > protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCOP

LegacyEnumerateAssemblyMoverOP

typedef utility::pointer::shared_ptr< LegacyEnumerateAssemblyMover > protocols::legacy_sewing::LegacyEnumerateAssemblyMoverOP

LegacyMonteCarloAssemblyMoverCOP

typedef utility::pointer::shared_ptr< LegacyMonteCarloAssemblyMover const > protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCOP

LegacyMonteCarloAssemblyMoverOP

typedef utility::pointer::shared_ptr< LegacyMonteCarloAssemblyMover > protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverOP

LegacyNodeConstraintAssemblyMoverCOP

typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover const > protocols::legacy_sewing::LegacyNodeConstraintAssemblyMoverCOP

LegacyNodeConstraintAssemblyMoverOP

typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover > protocols::legacy_sewing::LegacyNodeConstraintAssemblyMoverOP

ModelCOP

typedef utility::pointer::shared_ptr< Model const > protocols::legacy_sewing::ModelCOP

ModelOP

typedef utility::pointer::shared_ptr< Model > protocols::legacy_sewing::ModelOP

NativeRotamersMap

typedef std::map<core::Size, utility::vector1<std::pair<bool, core::conformation::ResidueOP> > > protocols::legacy_sewing::NativeRotamersMap

ScoreResult

typedef std::pair< BasisPair, HashResult > protocols::legacy_sewing::ScoreResult

ScoreResults

typedef std::map< BasisPair, HashResult > protocols::legacy_sewing::ScoreResults

SegmentPair

typedef std::pair< core::Size, core::Size> protocols::legacy_sewing::SegmentPair

SewGraphCOP

typedef utility::pointer::shared_ptr< SewGraph const > protocols::legacy_sewing::SewGraphCOP

SewGraphOP

typedef utility::pointer::shared_ptr< SewGraph > protocols::legacy_sewing::SewGraphOP

SewSegmentCOP

typedef utility::pointer::shared_ptr< SewSegment const > protocols::legacy_sewing::SewSegmentCOP

SewSegmentOP

typedef utility::pointer::shared_ptr< SewSegment > protocols::legacy_sewing::SewSegmentOP

Enumeration Type Documentation

move_type

enum protocols::legacy_sewing::move_type

Enumerator
ADD_EDGE
DELETE_EDGE
SWITCH_EDGE

Function Documentation

add_linker_segments()

void protocols::legacy_sewing::add_linker_segments

(

std::map< int, Model > &

models

)

Go through the list of models and add extra 'linker' segments to Models that have secondary structure segments that are separated by a single "linker" segments. These linker segments will not be hashed by the Hasher class. Segments with linkers will have their next_segment_ populated so that the order is maintained in the assembly

References protocols::legacy_sewing::SegmentGraph::add_connection(), protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, protocols::simple_filters::coords(), protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::SewSegment::hash_, protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, protocols::legacy_sewing::Model::segments_, protocols::legacy_sewing::Model::structure_id_, and TR().

add_num_neighbors()

void protocols::legacy_sewing::add_num_neighbors

(

std::map< int, Model > &

)

create_alpha_beta_models_table()

void protocols::legacy_sewing::create_alpha_beta_models_table

(

)

References protocols::legacy_sewing::segment::dssp, protocols::simple_filters::dssp(), protocols::legacy_sewing::segment::segment_id, protocols::legacy_sewing::segment::struct_id, and TR().

create_model_from_pose() [1/2]

Model protocols::legacy_sewing::create_model_from_pose	(	core::pose::Pose const &	pose,
		int	model_id
	)

Use the given segment-ranges to create a Model. Give this model an id that doesn't currently exist in the given map of models.

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

Referenced by protocols::legacy_sewing::LegacyAppendAssemblyMover::apply().

create_model_from_pose() [2/2]

Model protocols::legacy_sewing::create_model_from_pose	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	segments,
		int	model_id
	)

Use the given segment-ranges to create a Model. Give this model an id that doesn't currently exist in the given map of models.

create a Model from the pose

References protocols::legacy_sewing::SegmentGraph::add_connection(), core::conformation::Residue::atom(), protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, core::conformation::Residue::chi(), protocols::legacy_sewing::SewResidue::chi_angles_, protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::Model::model_id_, core::chemical::ResidueTypeBase::name(), core::pose::Pose::residue(), protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewResidue::resnum_, core::pose::Pose::secstruct(), protocols::legacy_sewing::Model::segments_, core::conformation::Residue::type(), and core::conformation::Atom::xyz().

get_5_ss_models_from_db()

std::map< int, Model > protocols::legacy_sewing::get_5_ss_models_from_db

(

std::string const &

hash_between

)

References result_to_five_ss_models(), protocols::legacy_sewing::Model::segments_, and TR().

get_alpha_beta_models_from_db()

std::map< int, Model > protocols::legacy_sewing::get_alpha_beta_models_from_db

(

)

References protocols::legacy_sewing::Model::model_id_, result_to_models(), protocols::legacy_sewing::Model::segments_, and TR().

get_continuous_models_from_db()

std::map< int, Model > protocols::legacy_sewing::get_continuous_models_from_db

(

std::string const &

hash_between

)

References protocols::legacy_sewing::Model::model_id_, result_to_models(), protocols::legacy_sewing::Model::segments_, and TR().

get_discontinuous_models_from_db()

std::map< int, Model > protocols::legacy_sewing::get_discontinuous_models_from_db

(

)

References result_to_models(), and TR().

get_strand_sew_models_from_db()

std::map< int, Model > protocols::legacy_sewing::get_strand_sew_models_from_db

(

)

References result_to_models(), and TR().

largest_continuous_atom_map()

std::map< core::id::AtomID, core::id::AtomID > protocols::legacy_sewing::largest_continuous_atom_map

(

std::map< core::id::AtomID, core::id::AtomID > const &

atom_map

)

Referenced by protocols::legacy_sewing::Assembly::create_chimera_segment().

operator<<() [1/3]

std::ostream& protocols::legacy_sewing::operator<<	(	std::ostream &	out,
		Assembly const &	assembly
	)

operator<<() [2/3]

std::ostream& protocols::legacy_sewing::operator<<	(	std::ostream &	out,
		HashEdge const &	edge
	)

operator<<() [3/3]

std::ostream& protocols::legacy_sewing::operator<<	(	std::ostream &	out,
		ModelNode const &	node
	)

read_model_file()

std::map< int, Model > protocols::legacy_sewing::read_model_file

(

std::string

filename

)

References protocols::legacy_sewing::SegmentGraph::add_connection(), protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::Model::distance_, protocols::legacy_sewing::SewSegment::dssp_, protocols::abinitio::filename(), protocols::legacy_sewing::SewSegment::hash_, protocols::legacy_sewing::Model::hoist_angle_degrees_, protocols::legacy_sewing::Model::meridian_angle_degrees_, protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::SewResidue::num_neighbors_, protocols::legacy_sewing::Model::packing_angle_degrees_, protocols::legacy_sewing::Model::pdb_code_, protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, protocols::legacy_sewing::Model::segments_, protocols::legacy_sewing::Model::structure_id_, and TR().

Referenced by protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyAppendAssemblyMover::parse_my_tag(), and protocols::legacy_sewing::LegacyAssemblyMover::parse_my_tag().

read_native_residue_file()

NativeRotamersMap protocols::legacy_sewing::read_native_residue_file

(

std::string const &

filename

)

References core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, protocols::abinitio::filename(), TR(), and protocols::kinmatch::xyz().

Referenced by protocols::legacy_sewing::LegacyAssemblyConstraintsMover::parse_my_tag(), and protocols::legacy_sewing::LegacyReadNativeRotamersFile::parse_tag().

remove_models_from_dssp()

void protocols::legacy_sewing::remove_models_from_dssp	(	std::map< int, Model > &	models,
		char	dssp1,
		char	dssp2
	)

Will only work for smotif models!!!

References protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::Model::segments_, core::id::to_string(), and TR().

result_to_five_ss_models()

std::map< int, Model > protocols::legacy_sewing::result_to_five_ss_models

(

cppdb::result

res

)

References protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, protocols::simple_filters::coords(), protocols::legacy_sewing::SewAtom::coords_, protocols::simple_filters::dssp(), protocols::legacy_sewing::SewSegment::dssp_, protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::Model::pdb_code_, protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, protocols::legacy_sewing::Model::segments_, protocols::legacy_sewing::Model::structure_id_, and TR().

Referenced by get_5_ss_models_from_db().

result_to_models()

std::map< int, Model > protocols::legacy_sewing::result_to_models

(

cppdb::result

res

)

References protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, protocols::simple_filters::coords(), protocols::legacy_sewing::SewAtom::coords_, core::kinematics::distance(), protocols::legacy_sewing::Model::distance_, protocols::simple_filters::dssp(), protocols::legacy_sewing::SewSegment::dssp_, protocols::legacy_sewing::Model::hoist_angle_degrees_, protocols::legacy_sewing::Model::meridian_angle_degrees_, protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::Model::packing_angle_degrees_, protocols::legacy_sewing::Model::pdb_code_, protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::Model::structure_id_.

Referenced by get_alpha_beta_models_from_db(), get_continuous_models_from_db(), get_discontinuous_models_from_db(), and get_strand_sew_models_from_db().

scores_to_alignments()

utility::vector1< BasisPair > protocols::legacy_sewing::scores_to_alignments

(

ScoreResults const &

scores

)

References protocols::hybridization::score.

see_whether_model_is_H_bonded_by_terminal_strands()

std::string protocols::legacy_sewing::see_whether_model_is_H_bonded_by_terminal_strands	(	Model	model,
		std::string const &	P_PA
	)

Return true if given model is H bonded by terminal strands.

References protocols::features::strand_assembly::find_sheet(), protocols::legacy_sewing::Model::pdb_code_, core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), protocols::legacy_sewing::Model::segments_, and TR().

serialize_graph_json()

std::string protocols::legacy_sewing::serialize_graph_json	(	SewGraphCOP	graph,
		core::Size	max_nodes
	)

Take the given StructureScores and save them to disk.

References protocols::legacy_sewing::ModelNode::model(), protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::Model::pdb_code_, protocols::legacy_sewing::Model::pose_number(), and TR().

TR() [1/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.Assembly"  )

static

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::add_edge(), protocols::legacy_sewing::SewGraph::add_edges_from_binary(), add_linker_segments(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::add_repeats(), protocols::legacy_sewing::ContinuousAssembly::append_model(), protocols::legacy_sewing::DisembodiedAssembly::append_model(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(), protocols::legacy_sewing::LegacyAssemblyMover::apply(), protocols::legacy_sewing::LegacyReadNativeRotamersFile::apply(), protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply_repeat(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), create_alpha_beta_models_table(), protocols::legacy_sewing::Assembly::create_chimera_segment(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::delete_edge(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder(), protocols::legacy_sewing::Assembly::find_possible_orders(), protocols::legacy_sewing::Assembly::follow_edge(), protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly(), protocols::legacy_sewing::SewGraph::generate_binary_score_file(), get_5_ss_models_from_db(), get_alpha_beta_models_from_db(), get_continuous_models_from_db(), get_discontinuous_models_from_db(), protocols::legacy_sewing::Assembly::get_matching_model_segments(), get_strand_sew_models_from_db(), protocols::legacy_sewing::LegacyAppendAssemblyMover::hash_pdb_model(), protocols::legacy_sewing::Assembly::map_residues(), protocols::legacy_sewing::Assembly::native_positions(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::legacy_sewing::LegacyAssemblyMover::parse_my_tag(), protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(), read_model_file(), read_native_residue_file(), protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly(), protocols::legacy_sewing::Hasher::remove_connection_inconsistencies(), protocols::legacy_sewing::Hasher::remove_duplicates(), remove_models_from_dssp(), protocols::legacy_sewing::SewGraph::report_binary_stats(), result_to_five_ss_models(), protocols::legacy_sewing::Hasher::score(), protocols::legacy_sewing::Hasher::score_one(), see_whether_model_is_H_bonded_by_terminal_strands(), serialize_graph_json(), protocols::legacy_sewing::SewGraph::SewGraph(), protocols::legacy_sewing::Hasher::trim_scores(), and write_hashing_scores_to_file().

TR() [2/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.ContinuousAssembly"  )

static

TR() [3/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.DisembodiedAssembly"  )

static

TR() [4/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.Hasher"  )

static

TR() [5/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.io"  )

static

TR() [6/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAddStartnodeFragments"  )

static

TR() [7/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAppendAssemblyMover"  )

static

TR() [8/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAssemblyConstraintsMover"  )

static

TR() [9/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAssemblyMover"  )

static

TR() [10/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyRepeatAssemblyMover"  )

static

TR() [11/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.Model"  )

static

TR() [12/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyEnumerateAssemblyMover"  )

static

TR() [13/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyGivenPathAssemblyMover"  )

static

TR() [14/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyGreedyAssemblyMover"  )

static

TR() [15/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyMonteCarloAssemblyMover"  )

static

TR() [16/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.SewGraph"  )

static

TR() [17/17]

static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.util"  )

static

write_hashing_scores_to_file()

void protocols::legacy_sewing::write_hashing_scores_to_file	(	ScoreResults const &	scores,
		std::string	filename
	)

Take the given StructureScores and save them to disk.

References protocols::abinitio::filename(), protocols::hybridization::score, core::simple_metrics::metrics::sum, and TR().

write_model_file()

void protocols::legacy_sewing::write_model_file	(	std::string const &	comments,
		std::map< int, Model >	models,
		std::string	filename
	)

References protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::Model::distance_, protocols::legacy_sewing::SewSegment::dssp_, protocols::abinitio::filename(), protocols::legacy_sewing::SewSegment::hash_, protocols::legacy_sewing::Model::hoist_angle_degrees_, protocols::legacy_sewing::Model::meridian_angle_degrees_, protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::SewResidue::num_neighbors_, protocols::legacy_sewing::Model::packing_angle_degrees_, protocols::legacy_sewing::Model::pdb_code_, protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::Model::structure_id_.

Referenced by protocols::legacy_sewing::ContinuousAssembly::append_model().

write_native_residue_file()

void protocols::legacy_sewing::write_native_residue_file	(	NativeRotamersMap	native_residue_map,
		std::string const &	filename
	)

References protocols::abinitio::filename().

Referenced by protocols::legacy_sewing::LegacyAssemblyMover::output_stats().

Variable Documentation

CHIMERA_SEGMENT

int const protocols::legacy_sewing::CHIMERA_SEGMENT = 0

static

Referenced by protocols::legacy_sewing::Assembly::create_chimera_segment(), and protocols::legacy_sewing::scoring::LegacyCalciumMotifScorer::full_motif_score().

POSE_SEGMENT

int const protocols::legacy_sewing::POSE_SEGMENT = -1

static

Referenced by protocols::legacy_sewing::scoring::LegacyCalciumMotifScorer::full_motif_score().