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 THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.ClassicMatchAlgorithm")
static THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.DownstreamAlgorithm")
static THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.SecondaryMatcherToDownstreamResidue")
static THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.LigandConformerBuilder")
static THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.RigidLigandBuilder")
static THREAD_LOCAL basic::Tracer	TR ("core.protocols.match.downstream")
static THREAD_LOCAL basic::Tracer	TR ("protocols.match.downstream.SecondaryMatcherToDownstreamResidue")
static THREAD_LOCAL 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< AtomAngleSecMatchRPE > protocols::match::downstream::AtomAngleSecMatchRPEOP

typedef utility::pointer::shared_ptr< AtomDihedralSecMatchRPE const > protocols::match::downstream::AtomDihedralSecMatchRPECOP

typedef utility::pointer::shared_ptr< AtomDihedralSecMatchRPE > protocols::match::downstream::AtomDihedralSecMatchRPEOP

typedef utility::pointer::shared_ptr< AtomDistanceSecMatchRPE const > protocols::match::downstream::AtomDistanceSecMatchRPECOP

typedef utility::pointer::shared_ptr< AtomDistanceSecMatchRPE > protocols::match::downstream::AtomDistanceSecMatchRPEOP

typedef utility::pointer::shared_ptr< AtomGeometrySecMatchRPE const > protocols::match::downstream::AtomGeometrySecMatchRPECOP

typedef utility::pointer::shared_ptr< AtomGeometrySecMatchRPE > protocols::match::downstream::AtomGeometrySecMatchRPEOP

typedef utility::pointer::shared_ptr< ClassicMatchAlgorithm const > protocols::match::downstream::ClassicMatchAlgorithmCOP

typedef utility::pointer::shared_ptr< ClassicMatchAlgorithm > protocols::match::downstream::ClassicMatchAlgorithmOP

typedef utility::pointer::shared_ptr< DownstreamAlgorithm const > protocols::match::downstream::DownstreamAlgorithmCOP

typedef utility::pointer::shared_ptr< DownstreamAlgorithm > protocols::match::downstream::DownstreamAlgorithmOP

typedef utility::pointer::shared_ptr< DownstreamBuilder const > protocols::match::downstream::DownstreamBuilderCOP

typedef utility::pointer::shared_ptr< DownstreamBuilder > protocols::match::downstream::DownstreamBuilderOP

typedef utility::pointer::shared_ptr< GeometrySecMatchRPE const > protocols::match::downstream::GeometrySecMatchRPECOP

typedef utility::pointer::shared_ptr< GeometrySecMatchRPE > protocols::match::downstream::GeometrySecMatchRPEOP

typedef utility::pointer::shared_ptr< LigandConformerBuilder const > protocols::match::downstream::LigandConformerBuilderCOP

typedef utility::pointer::shared_ptr< LigandConformerBuilder > protocols::match::downstream::LigandConformerBuilderOP

typedef utility::pointer::shared_ptr< RigidLigandBuilder const > protocols::match::downstream::RigidLigandBuilderCOP

typedef utility::pointer::shared_ptr< RigidLigandBuilder > protocols::match::downstream::RigidLigandBuilderOP

typedef utility::pointer::shared_ptr< ScoringSecMatchRPE const > protocols::match::downstream::ScoringSecMatchRPECOP

typedef utility::pointer::shared_ptr< ScoringSecMatchRPE > protocols::match::downstream::ScoringSecMatchRPEOP

typedef utility::pointer::shared_ptr< SecMatchResiduePairEvaluator const > protocols::match::downstream::SecMatchResiduePairEvaluatorCOP

typedef utility::pointer::shared_ptr< SecMatchResiduePairEvaluator > protocols::match::downstream::SecMatchResiduePairEvaluatorOP

typedef utility::pointer::shared_ptr< SecondaryMatcherToDownstreamResidue const > protocols::match::downstream::SecondaryMatcherToDownstreamResidueCOP

typedef utility::pointer::shared_ptr< SecondaryMatcherToDownstreamResidue > protocols::match::downstream::SecondaryMatcherToDownstreamResidueOP

typedef utility::pointer::shared_ptr< SecondaryMatcherToUpstreamResidue const > protocols::match::downstream::SecondaryMatcherToUpstreamResidueCOP

typedef utility::pointer::shared_ptr< SecondaryMatcherToUpstreamResidue > protocols::match::downstream::SecondaryMatcherToUpstreamResidueOP

typedef utility::pointer::shared_ptr< SecondaryMatchUpstreamResProcessor const > protocols::match::downstream::SecondaryMatchUpstreamResProcessorCOP

typedef utility::pointer::shared_ptr< SecondaryMatchUpstreamResProcessor > protocols::match::downstream::SecondaryMatchUpstreamResProcessorOP

typedef utility::pointer::shared_ptr< TargetRotamerCoords const > protocols::match::downstream::TargetRotamerCoordsCOP

typedef utility::pointer::shared_ptr< TargetRotamerCoords > protocols::match::downstream::TargetRotamerCoordsOP

Function Documentation

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

static

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

static

static THREAD_LOCAL 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 THREAD_LOCAL basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.RigidLigandBuilder"  )

static

static THREAD_LOCAL basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.SecondaryMatcherToUpstreamResidue"  )

static

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

static

static THREAD_LOCAL basic::Tracer protocols::match::downstream::TR ( "core.protocols.match.downstream"  )

static

static THREAD_LOCAL basic::Tracer protocols::match::downstream::TR ( "protocols.match.downstream.LigandConformerBuilder"  )

static