protocols::sewing Namespace Reference

Namespaces
	sampling
	scoring

Classes
class	AddStartnodeFragments
class	AddStartnodeFragmentsCreator
class	AppendAssemblyMover
class	AppendAssemblyMoverCreator
class	Assembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	AssemblyConstraintsMover
class	AssemblyConstraintsMoverCreator
class	AssemblyFactory
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	AssemblyMover
class	AssemblyMoverCreator
struct	Basis
struct	basis_pair_equal_to
struct	basis_pair_hash
class	ContinuousAssembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
struct	coord_equal_to
struct	coord_hash
class	DisembodiedAssembly
	An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
class	EnumerateAssemblyMover
class	EnumerateAssemblyMoverCreator
class	GivenPathAssemblyMover
class	GivenPathAssemblyMoverCreator
class	GreedyAssemblyMover
class	GreedyAssemblyMoverCreator
class	HashEdge
class	Hasher
struct	HashResult
struct	HashValue
class	LoophashAssemblyMover
class	LoophashAssemblyMoverCreator
struct	Model
class	ModelConstIterator
class	ModelIterator
class	ModelNode
class	MonteCarloAssemblyMover
class	MonteCarloAssemblyMoverCreator
struct	NodeConstraint
class	NodeConstraintAssemblyMover
class	NodeConstraintAssemblyMoverCreator
class	ReadNativeRotamersFile
class	ReadNativeRotamersFileCreator
class	ReadRepeatNativeRotamersFile
class	ReadRepeatNativeRotamersFileCreator
class	RehashAssemblyMover
class	RehashAssemblyMoverCreator
class	RepeatAssemblyMover
class	RepeatAssemblyMoverCreator
struct	segment
class	SegmentGraph
struct	SewAtom
class	SewGraph
struct	SewResidue
struct	SewSegment

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 < AssemblyConstraintsMover >	AssemblyConstraintsMoverOP
typedef utility::pointer::shared_ptr < AssemblyConstraintsMover const >	AssemblyConstraintsMoverCOP
typedef utility::pointer::shared_ptr < AssemblyMover >	AssemblyMoverOP
typedef utility::pointer::shared_ptr < AssemblyMover const >	AssemblyMoverCOP
typedef utility::pointer::shared_ptr < EnumerateAssemblyMover >	EnumerateAssemblyMoverOP
typedef utility::pointer::shared_ptr < EnumerateAssemblyMover const >	EnumerateAssemblyMoverCOP
typedef utility::pointer::shared_ptr < LoophashAssemblyMover >	LoophashAssemblyMoverOP
typedef utility::pointer::shared_ptr < LoophashAssemblyMover const >	LoophashAssemblyMoverCOP
typedef utility::pointer::shared_ptr < MonteCarloAssemblyMover >	MonteCarloAssemblyMoverOP
typedef utility::pointer::shared_ptr < MonteCarloAssemblyMover const >	MonteCarloAssemblyMoverCOP
typedef utility::pointer::shared_ptr < NodeConstraintAssemblyMover >	NodeConstraintAssemblyMoverOP
typedef utility::pointer::shared_ptr < NodeConstraintAssemblyMover const >	NodeConstraintAssemblyMoverCOP
typedef utility::pointer::shared_ptr < RehashAssemblyMover >	RehashAssemblyMoverOP
typedef utility::pointer::shared_ptr < RehashAssemblyMover const >	RehashAssemblyMoverCOP
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.sewing.Assembly")
std::ostream &	operator<< (std::ostream &out, Assembly const &assembly)
static basic::Tracer	TR ("protocols.sewing.ContinuousAssembly")
static basic::Tracer	TR ("protocols.sewing.DisembodiedAssembly")
static basic::Tracer	TR ("protocols.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 hash_between)
std::map< int, Model >	get_5_ss_models_from_db (std::string 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.sewing.Hasher")
static basic::Tracer	TR ("protocols.sewing.AddStartnodeFragments")
static basic::Tracer	TR ("protocols.sewing.AppendAssemblyMover")
static basic::Tracer	TR ("protocols.sewing.AssemblyConstraintsMover")
static basic::Tracer	TR ("protocols.sewing.AssemblyMover")
static basic::Tracer	TR ("protocols.sewing.sampling.EnumerateAssemblyMover")
static basic::Tracer	TR ("protocols.sewing.sampling.GivenPathAssemblyMover")
static basic::Tracer	TR ("protocols.sewing.sampling.GreedyAssemblyMover")
static basic::Tracer	TR ("protocols.sewing.sampling.MonteCarloAssemblyMover")
static basic::Tracer	TR ("protocols.sewing.RepeatAssemblyMover")
static basic::Tracer	TR ("protocols.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)
static basic::Tracer	TR ("protocols.sewing.io")
void	write_native_residue_file (NativeRotamersMap native_residue_map, std::string filename)
NativeRotamersMap	read_native_residue_file (std::string 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 P_PA)
	Return true if given model is H bonded by terminal strands. More...
utility::vector1< BasisPair >	read_hashing_scores_from_file (std::string filename)
	Take the given StructureScores and save them to disk. More...
static basic::Tracer	TR ("protocols.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

Typedef Documentation

typedef utility::pointer::shared_ptr< AssemblyConstraintsMover const > protocols::sewing::AssemblyConstraintsMoverCOP

typedef utility::pointer::shared_ptr< AssemblyConstraintsMover > protocols::sewing::AssemblyConstraintsMoverOP

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

typedef utility::pointer::shared_ptr< AssemblyMover const > protocols::sewing::AssemblyMoverCOP

typedef utility::pointer::shared_ptr< AssemblyMover > protocols::sewing::AssemblyMoverOP

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

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

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

typedef utility::pointer::shared_ptr< EnumerateAssemblyMover const > protocols::sewing::EnumerateAssemblyMoverCOP

typedef utility::pointer::shared_ptr< EnumerateAssemblyMover > protocols::sewing::EnumerateAssemblyMoverOP

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

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

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

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

typedef utility::pointer::shared_ptr< LoophashAssemblyMover const > protocols::sewing::LoophashAssemblyMoverCOP

typedef utility::pointer::shared_ptr< LoophashAssemblyMover > protocols::sewing::LoophashAssemblyMoverOP

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

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

typedef utility::pointer::shared_ptr< MonteCarloAssemblyMover const > protocols::sewing::MonteCarloAssemblyMoverCOP

typedef utility::pointer::shared_ptr< MonteCarloAssemblyMover > protocols::sewing::MonteCarloAssemblyMoverOP

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

typedef utility::pointer::shared_ptr< NodeConstraintAssemblyMover const > protocols::sewing::NodeConstraintAssemblyMoverCOP

typedef utility::pointer::shared_ptr< NodeConstraintAssemblyMover > protocols::sewing::NodeConstraintAssemblyMoverOP

typedef utility::pointer::shared_ptr< RehashAssemblyMover const > protocols::sewing::RehashAssemblyMoverCOP

typedef utility::pointer::shared_ptr< RehashAssemblyMover > protocols::sewing::RehashAssemblyMoverOP

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::sewing::move_type

Enumerator
ADD_EDGE
DELETE_EDGE
SWITCH_EDGE

Function Documentation

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

void protocols::sewing::add_num_neighbors

(

std::map< int, Model > &

)

void protocols::sewing::create_alpha_beta_models_table

(

)

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

Model protocols::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::total_residue().

Referenced by protocols::sewing::AppendAssemblyMover::apply().

Model protocols::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::sewing::SegmentGraph::add_connection(), core::conformation::Residue::atom(), protocols::sewing::SewAtom::atomno_, protocols::sewing::SewResidue::basis_atoms_, core::conformation::Residue::chi(), protocols::sewing::SewResidue::chi_angles_, protocols::sewing::SewAtom::coords_, protocols::sewing::SewSegment::dssp_, protocols::sewing::SewSegment::hash_, protocols::sewing::SewSegment::model_id_, protocols::sewing::Model::model_id_, core::chemical::ResidueType::name(), core::pose::Pose::residue(), protocols::sewing::SewResidue::residue_type_, protocols::sewing::SewSegment::residues_, protocols::sewing::SewResidue::resnum_, core::pose::Pose::secstruct(), protocols::sewing::SewSegment::segment_id_, protocols::sewing::Model::segments_, core::conformation::Residue::type(), and core::conformation::Atom::xyz().

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

(

std::string

hash_between

)

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

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

(

)

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

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

(

std::string

hash_between

)

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

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

(

)

References result_to_models(), and TR().

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

(

)

References result_to_models(), and TR().

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

(

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

atom_map

)

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

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

References core::graph::Node::get_node_index(), protocols::sewing::ModelNode::model(), protocols::sewing::Model::model_id_, and protocols::sewing::ModelNode::segment_ids().

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

References protocols::sewing::HashEdge::basis_pair_.

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

References protocols::sewing::Assembly::all_segments_, and protocols::sewing::Assembly::segments_.

utility::vector1<BasisPair> protocols::sewing::read_hashing_scores_from_file

(

std::string

filename

)

Take the given StructureScores and save them to disk.

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

(

std::string

filename

)

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

Referenced by protocols::sewing::EnumerateAssemblyMover::generate_assembly(), protocols::sewing::RehashAssemblyMover::parse_my_tag(), protocols::sewing::AppendAssemblyMover::parse_my_tag(), and protocols::sewing::AssemblyMover::parse_my_tag().

NativeRotamersMap protocols::sewing::read_native_residue_file

(

std::string

filename

)

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

Referenced by protocols::sewing::AssemblyConstraintsMover::parse_my_tag(), and protocols::sewing::ReadNativeRotamersFile::parse_tag().

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

Will only work for smotif models!!!

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

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

(

cppdb::result

res

)

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

Referenced by get_5_ss_models_from_db().

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

(

cppdb::result

res

)

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

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

(

ScoreResults const &

scores

)

std::string protocols::sewing::see_whether_model_is_H_bonded_by_terminal_strands	(	Model	model,
		std::string	P_PA
	)

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

References protocols::stepwise::modeler::rna::file_exists(), protocols::features::strand_assembly::find_sheet(), protocols::sewing::Model::pdb_code_, core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), protocols::sewing::Model::segments_, and TR().

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

References protocols::sewing::HashEdge::basis_pair(), core::graph::Node::const_upper_edge_list_begin(), core::graph::Node::const_upper_edge_list_end(), core::graph::Edge::get_other_ind(), protocols::sewing::ModelNode::model(), protocols::sewing::Model::model_id_, protocols::sewing::Model::pdb_code_, protocols::sewing::Model::pose_number(), and TR().

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.sampling.GivenPathAssemblyMover"  )

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.sampling.GreedyAssemblyMover"  )

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.sampling.MonteCarloAssemblyMover"  )

static

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

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.sampling.EnumerateAssemblyMover"  )

static

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

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.AssemblyConstraintsMover"  )

static

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

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.AddStartnodeFragments"  )

static

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

static

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

static

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

static

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

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.AppendAssemblyMover"  )

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.RepeatAssemblyMover"  )

static

static basic::Tracer protocols::sewing::TR ( "protocols.sewing.AssemblyMover"  )

static

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

static

Referenced by protocols::sewing::MonteCarloAssemblyMover::add_edge(), protocols::sewing::SewGraph::add_edges_from_binary(), add_linker_segments(), protocols::sewing::RepeatAssemblyMover::add_repeats(), protocols::sewing::DisembodiedAssembly::append_model(), protocols::sewing::ContinuousAssembly::append_model(), protocols::sewing::AddStartnodeFragments::apply(), protocols::sewing::ReadNativeRotamersFile::apply(), protocols::sewing::AssemblyMover::apply(), protocols::sewing::AppendAssemblyMover::apply(), protocols::sewing::NodeConstraintAssemblyMover::apply(), protocols::sewing::ReadRepeatNativeRotamersFile::apply(), protocols::sewing::AssemblyConstraintsMover::apply(), protocols::sewing::AssemblyConstraintsMover::apply_repeat(), protocols::sewing::MonteCarloAssemblyMover::boltzman(), protocols::sewing::NodeConstraintAssemblyMover::check_all_nodes(), create_alpha_beta_models_table(), protocols::sewing::MonteCarloAssemblyMover::delete_edge(), protocols::sewing::RepeatAssemblyMover::dfs_cycle_finder(), protocols::sewing::AssemblyMover::follow_random_edge_from_node(), protocols::sewing::GreedyAssemblyMover::generate_assembly(), protocols::sewing::EnumerateAssemblyMover::generate_assembly(), protocols::sewing::RehashAssemblyMover::generate_assembly(), protocols::sewing::MonteCarloAssemblyMover::generate_assembly(), protocols::sewing::RepeatAssemblyMover::generate_assembly(), protocols::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(), get_strand_sew_models_from_db(), protocols::sewing::AppendAssemblyMover::hash_pdb_model(), protocols::sewing::AssemblyMover::output_stats(), protocols::sewing::AssemblyMover::parse_my_tag(), protocols::sewing::AssemblyMover::parse_requirements(), read_model_file(), read_native_residue_file(), protocols::sewing::RehashAssemblyMover::rearrange_assembly(), protocols::sewing::AppendAssemblyMover::refine_assembly(), protocols::sewing::Hasher::remove_connection_inconsistencies(), protocols::sewing::Hasher::remove_duplicates(), remove_models_from_dssp(), protocols::sewing::SewGraph::report_binary_stats(), result_to_five_ss_models(), protocols::sewing::Hasher::score(), protocols::sewing::Hasher::score_one(), see_whether_model_is_H_bonded_by_terminal_strands(), serialize_graph_json(), protocols::sewing::SewGraph::SewGraph(), protocols::sewing::Hasher::trim_scores(), and write_hashing_scores_to_file().

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

Take the given StructureScores and save them to disk.

References TR().

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

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

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

void protocols::sewing::write_native_residue_file	(	NativeRotamersMap	native_residue_map,
		std::string	filename
	)

Referenced by protocols::sewing::AssemblyMover::output_stats().

Variable Documentation

int const protocols::sewing::CHIMERA_SEGMENT = 0

static

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