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protocols::match::downstream Namespace Reference

Classes

class  ActiveSiteGrid
 
class  AtomAngleSecMatchRPE
 RPE to figure out if three atoms are within a given angle atoms need to be set through the parent class add_at_ind function. More...
 
class  AtomDihedralSecMatchRPE
 RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima. More...
 
class  AtomDistanceSecMatchRPE
 RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function. More...
 
class  AtomGeometrySecMatchRPE
 helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes More...
 
class  ClassicMatchAlgorithm
 Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner. More...
 
class  DownstreamAlgorithm
 A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits. More...
 
class  DownstreamBuilder
 
class  GeometrySecMatchRPE
 holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues. More...
 
struct  hash_upstream_hit
 
class  LigandConformerBuilder
 
class  RigidLigandBuilder
 
class  ScoringSecMatchRPE
 
class  SecMatchEvaluatorFactory
 a collection of functions making a single score_function More...
 
class  SecMatchResiduePairEvaluator
 base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue More...
 
class  SecondaryMatcherToDownstreamResidue
 A class for an algorithm. Given a conformation of the downstream partner, the algorithm is responsible for producing a set of hits. More...
 
class  SecondaryMatcherToUpstreamResidue
 A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits. More...
 
class  SecondaryMatchUpstreamResProcessor
 A simple class to respond to the UpstreamBuilder's process_hit method and pass on the coordinates to its "owning" SecondaryMatcherToUpstreamResidue object. More...
 
class  TargetRotamerCoords
 
struct  us_secmatch_hit_compare
 A simple struct to use in list.sort() to ensure that the hits returned by a secondary matcher which has possibly generated upstream hits out-of-order, will return an ordered-hit-list in its build_hits_at_all_positions() method. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< ActiveSiteGrid
ActiveSiteGridOP
 
typedef
utility::pointer::shared_ptr
< ActiveSiteGrid const > 
ActiveSiteGridCOP
 
typedef
utility::pointer::shared_ptr
< ClassicMatchAlgorithm
ClassicMatchAlgorithmOP
 
typedef
utility::pointer::shared_ptr
< ClassicMatchAlgorithm const > 
ClassicMatchAlgorithmCOP
 
typedef
utility::pointer::shared_ptr
< DownstreamAlgorithm
DownstreamAlgorithmOP
 
typedef
utility::pointer::shared_ptr
< DownstreamAlgorithm const > 
DownstreamAlgorithmCOP
 
typedef
utility::pointer::shared_ptr
< DownstreamBuilder
DownstreamBuilderOP
 
typedef
utility::pointer::shared_ptr
< DownstreamBuilder const > 
DownstreamBuilderCOP
 
typedef
utility::pointer::shared_ptr
< AtomGeometrySecMatchRPE
AtomGeometrySecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< AtomGeometrySecMatchRPE
const > 
AtomGeometrySecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< AtomDistanceSecMatchRPE
AtomDistanceSecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< AtomDistanceSecMatchRPE
const > 
AtomDistanceSecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< AtomAngleSecMatchRPE
AtomAngleSecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< AtomAngleSecMatchRPE const > 
AtomAngleSecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< AtomDihedralSecMatchRPE
AtomDihedralSecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< AtomDihedralSecMatchRPE
const > 
AtomDihedralSecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< GeometrySecMatchRPE
GeometrySecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< GeometrySecMatchRPE const > 
GeometrySecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< LigandConformerBuilder
LigandConformerBuilderOP
 
typedef
utility::pointer::shared_ptr
< LigandConformerBuilder const > 
LigandConformerBuilderCOP
 
typedef
utility::pointer::shared_ptr
< RigidLigandBuilder
RigidLigandBuilderOP
 
typedef
utility::pointer::shared_ptr
< RigidLigandBuilder const > 
RigidLigandBuilderCOP
 
typedef
utility::pointer::shared_ptr
< ScoringSecMatchRPE
ScoringSecMatchRPEOP
 
typedef
utility::pointer::shared_ptr
< ScoringSecMatchRPE const > 
ScoringSecMatchRPECOP
 
typedef
utility::pointer::shared_ptr
< SecMatchResiduePairEvaluator
SecMatchResiduePairEvaluatorOP
 
typedef
utility::pointer::shared_ptr
< SecMatchResiduePairEvaluator
const > 
SecMatchResiduePairEvaluatorCOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatcherToDownstreamResidue
SecondaryMatcherToDownstreamResidueOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatcherToDownstreamResidue
const > 
SecondaryMatcherToDownstreamResidueCOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatcherToUpstreamResidue
SecondaryMatcherToUpstreamResidueOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatcherToUpstreamResidue
const > 
SecondaryMatcherToUpstreamResidueCOP
 
typedef
utility::pointer::shared_ptr
< TargetRotamerCoords
TargetRotamerCoordsOP
 
typedef
utility::pointer::shared_ptr
< TargetRotamerCoords const > 
TargetRotamerCoordsCOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatchUpstreamResProcessor
SecondaryMatchUpstreamResProcessorOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatchUpstreamResProcessor
const > 
SecondaryMatchUpstreamResProcessorCOP
 

Functions

static basic::Tracer TR ("protocols.match.downstream.ClassicMatchAlgorithm")
 
static basic::Tracer TR ("protocols.match.downstream.DownstreamAlgorithm")
 
static basic::Tracer TR ("protocols.match.downstream.SecondaryMatcherToDownstreamResidue")
 
static basic::Tracer TR ("protocols.match.downstream.LigandConformerBuilder")
 
static basic::Tracer TR ("protocols.match.downstream.RigidLigandBuilder")
 
static basic::Tracer TR ("core.protocols.match.downstream")
 
static basic::Tracer TR ("protocols.match.downstream.SecondaryMatcherToDownstreamResidue")
 
static basic::Tracer TR ("protocols.match.downstream.SecondaryMatcherToUpstreamResidue")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ActiveSiteGrid const > protocols::match::downstream::ActiveSiteGridCOP
typedef utility::pointer::shared_ptr< ActiveSiteGrid > protocols::match::downstream::ActiveSiteGridOP
typedef utility::pointer::shared_ptr< AtomAngleSecMatchRPE const > protocols::match::downstream::AtomAngleSecMatchRPECOP
typedef utility::pointer::shared_ptr< DownstreamAlgorithm const > protocols::match::downstream::DownstreamAlgorithmCOP
typedef utility::pointer::shared_ptr< DownstreamBuilder const > protocols::match::downstream::DownstreamBuilderCOP
typedef utility::pointer::shared_ptr< GeometrySecMatchRPE const > protocols::match::downstream::GeometrySecMatchRPECOP
typedef utility::pointer::shared_ptr< RigidLigandBuilder const > protocols::match::downstream::RigidLigandBuilderCOP
typedef utility::pointer::shared_ptr< ScoringSecMatchRPE const > protocols::match::downstream::ScoringSecMatchRPECOP
typedef utility::pointer::shared_ptr< TargetRotamerCoords const > protocols::match::downstream::TargetRotamerCoordsCOP

Function Documentation

static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.SecondaryMatcherToDownstreamResidue"  )
static
static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.DownstreamAlgorithm"  )
static
static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.ClassicMatchAlgorithm"  )
static

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::ScoringSecMatchRPE::check2bsc(), protocols::match::downstream::LigandConformerBuilder::determine_redundant_conformer_groups(), protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues(), protocols::match::downstream::ScoringSecMatchRPE::eval_longRange_2b_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::match::downstream::ClassicMatchAlgorithm::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::ClassicMatchAlgorithm::respond_to_primary_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_primary_hitlist_change(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_primary_hitlist_change(), and protocols::match::downstream::ScoringSecMatchRPE::ScoringSecMatchRPE().

static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.RigidLigandBuilder"  )
static
static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.SecondaryMatcherToUpstreamResidue"  )
static
static basic::Tracer protocols::match::downstream::TR ( "core.protocols.match.downstream"  )
static
static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.SecondaryMatcherToDownstreamResidue"  )
static
static basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.LigandConformerBuilder"  )
static