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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...
 
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  HashEdge
 
class  Hasher
 
struct  HashResult
 
struct  HashValue
 
class  LegacyAddStartnodeFragments
 
class  LegacyAddStartnodeFragmentsCreator
 
class  LegacyAppendAssemblyMover
 
class  LegacyAppendAssemblyMoverCreator
 
class  LegacyAssemblyConstraintsMover
 
class  LegacyAssemblyConstraintsMoverCreator
 
class  LegacyAssemblyMover
 
class  LegacyEnumerateAssemblyMover
 
class  LegacyEnumerateAssemblyMoverCreator
 
class  LegacyGivenPathAssemblyMover
 
class  LegacyGivenPathAssemblyMoverCreator
 
class  LegacyGreedyAssemblyMover
 
class  LegacyGreedyAssemblyMoverCreator
 
class  LegacyMonteCarloAssemblyMover
 
class  LegacyMonteCarloAssemblyMoverCreator
 
class  LegacyReadNativeRotamersFile
 
class  LegacyReadNativeRotamersFileCreator
 
class  LegacyReadRepeatNativeRotamersFile
 
class  LegacyReadRepeatNativeRotamersFileCreator
 
class  LegacyRepeatAssemblyMover
 
class  LegacyRepeatAssemblyMoverCreator
 
struct  Model
 
class  ModelConstIterator
 
class  ModelIterator
 
class  ModelNode
 
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, BasisBasisPair
 
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
< LegacyLoophashAssemblyMover > 
LegacyLoophashAssemblyMoverOP
 
typedef
utility::pointer::shared_ptr
< LegacyLoophashAssemblyMover
const > 
LegacyLoophashAssemblyMoverCOP
 
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
< LegacyRehashAssemblyMover > 
LegacyRehashAssemblyMoverOP
 
typedef
utility::pointer::shared_ptr
< LegacyRehashAssemblyMover
const > 
LegacyRehashAssemblyMoverCOP
 
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, Modelresult_to_models (cppdb::result res)
 
std::map< int, Modelresult_to_five_ss_models (cppdb::result res)
 
std::map< int, Modelget_discontinuous_models_from_db ()
 
std::map< int, Modelget_strand_sew_models_from_db ()
 
std::map< int, Modelget_continuous_models_from_db (std::string const &hash_between)
 
std::map< int, Modelget_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, Modelget_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, Modelread_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.LegacyLoophashAssemblyMover")
 
static basic::Tracer TR ("protocols.legacy_sewing.sampling.LegacyMonteCarloAssemblyMover")
 
static basic::Tracer TR ("protocols.legacy_sewing.LegacyRehashAssemblyMover")
 
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< BasisPairscores_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

typedef utility::pointer::shared_ptr< Assembly const > protocols::legacy_sewing::AssemblyCOP
typedef utility::pointer::shared_ptr< Assembly > protocols::legacy_sewing::AssemblyOP
typedef utility::pointer::shared_ptr< Hasher const > protocols::legacy_sewing::HasherCOP
typedef utility::pointer::shared_ptr< Hasher > protocols::legacy_sewing::HasherOP
typedef utility::fixedsizearray1<int, 3> protocols::legacy_sewing::HashKey
typedef boost::unordered_map<HashKey,utility::vector1< HashValue >,coord_hash,coord_equal_to> protocols::legacy_sewing::HashMap
typedef utility::pointer::shared_ptr< LegacyAssemblyMover const > protocols::legacy_sewing::LegacyAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyLoophashAssemblyMover const > protocols::legacy_sewing::LegacyLoophashAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyLoophashAssemblyMover > protocols::legacy_sewing::LegacyLoophashAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover const > protocols::legacy_sewing::LegacyNodeConstraintAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyNodeConstraintAssemblyMover > protocols::legacy_sewing::LegacyNodeConstraintAssemblyMoverOP
typedef utility::pointer::shared_ptr< LegacyRehashAssemblyMover const > protocols::legacy_sewing::LegacyRehashAssemblyMoverCOP
typedef utility::pointer::shared_ptr< LegacyRehashAssemblyMover > protocols::legacy_sewing::LegacyRehashAssemblyMoverOP
typedef utility::pointer::shared_ptr< Model const > protocols::legacy_sewing::ModelCOP
typedef utility::pointer::shared_ptr< Model > protocols::legacy_sewing::ModelOP
typedef utility::pointer::shared_ptr< SewGraph const > protocols::legacy_sewing::SewGraphCOP
typedef utility::pointer::shared_ptr< SewGraph > protocols::legacy_sewing::SewGraphOP
typedef utility::pointer::shared_ptr< SewSegment const > protocols::legacy_sewing::SewSegmentCOP
typedef utility::pointer::shared_ptr< SewSegment > protocols::legacy_sewing::SewSegmentOP

Enumeration Type Documentation

Enumerator
ADD_EDGE 
DELETE_EDGE 
SWITCH_EDGE 

Function Documentation

void protocols::legacy_sewing::add_linker_segments ( std::map< int, Model > &  models)
void protocols::legacy_sewing::add_num_neighbors ( std::map< int, Model > &  )
void protocols::legacy_sewing::create_alpha_beta_models_table ( )
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().

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 
)
std::map< int, Model > protocols::legacy_sewing::get_5_ss_models_from_db ( std::string const &  hash_between)
std::map< int, Model > protocols::legacy_sewing::get_alpha_beta_models_from_db ( )
std::map< int, Model > protocols::legacy_sewing::get_continuous_models_from_db ( std::string const &  hash_between)
std::map< int, Model > protocols::legacy_sewing::get_discontinuous_models_from_db ( )

References result_to_models(), and TR().

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

References result_to_models(), and TR().

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)
std::ostream& protocols::legacy_sewing::operator<< ( std::ostream &  out,
ModelNode const &  node 
)
std::ostream& protocols::legacy_sewing::operator<< ( std::ostream &  out,
HashEdge const &  edge 
)
std::ostream& protocols::legacy_sewing::operator<< ( std::ostream &  out,
Assembly const &  assembly 
)
std::map< int, Model > protocols::legacy_sewing::read_model_file ( std::string  filename)
NativeRotamersMap protocols::legacy_sewing::read_native_residue_file ( std::string const &  filename)
void protocols::legacy_sewing::remove_models_from_dssp ( std::map< int, Model > &  models,
char  dssp1,
char  dssp2 
)
std::map< int, Model > protocols::legacy_sewing::result_to_five_ss_models ( cppdb::result  res)
std::map< int, Model > protocols::legacy_sewing::result_to_models ( cppdb::result  res)
utility::vector1< BasisPair > protocols::legacy_sewing::scores_to_alignments ( ScoreResults const &  scores)
std::string protocols::legacy_sewing::see_whether_model_is_H_bonded_by_terminal_strands ( Model  model,
std::string const &  P_PA 
)
std::string protocols::legacy_sewing::serialize_graph_json ( SewGraphCOP  graph,
core::Size  max_nodes 
)
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.io"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyGivenPathAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyGreedyAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyMonteCarloAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.Hasher"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.sampling.LegacyEnumerateAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.util"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.SewGraph"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAddStartnodeFragments"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAssemblyConstraintsMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.ContinuousAssembly"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.DisembodiedAssembly"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.Model"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAppendAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyRehashAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyLoophashAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyRepeatAssemblyMover"  )
static
static basic::Tracer protocols::legacy_sewing::TR ( "protocols.legacy_sewing.LegacyAssemblyMover"  )
static
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::DisembodiedAssembly::append_model(), protocols::legacy_sewing::ContinuousAssembly::append_model(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::legacy_sewing::LegacyReadNativeRotamersFile::apply(), protocols::legacy_sewing::LegacyAssemblyMover::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply_repeat(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), create_alpha_beta_models_table(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::delete_edge(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder(), protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::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(), get_strand_sew_models_from_db(), protocols::legacy_sewing::LegacyAppendAssemblyMover::hash_pdb_model(), 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().

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::hybridization::score, core::simple_metrics::metrics::sum, and TR().

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

Variable Documentation

int const protocols::legacy_sewing::CHIMERA_SEGMENT = 0
static
int const protocols::legacy_sewing::POSE_SEGMENT = -1
static