Classes
class	ActiveSiteGrid

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	AtomGeometrySecMatchRPE
	helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes 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	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	GeometrySecMatchRPE
	holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues. More...

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...

struct	hash_upstream_hit

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	TargetRotamerCoords

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...

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::owning_ptr < ActiveSiteGrid >	ActiveSiteGridOP

typedef utility::pointer::owning_ptr < ActiveSiteGrid const >	ActiveSiteGridCOP

typedef utility::pointer::owning_ptr < ClassicMatchAlgorithm >	ClassicMatchAlgorithmOP

typedef utility::pointer::owning_ptr < ClassicMatchAlgorithm const >	ClassicMatchAlgorithmCOP

typedef utility::pointer::owning_ptr < DownstreamAlgorithm >	DownstreamAlgorithmOP

typedef utility::pointer::owning_ptr < DownstreamAlgorithm const >	DownstreamAlgorithmCOP

typedef utility::pointer::owning_ptr < DownstreamBuilder >	DownstreamBuilderOP

typedef utility::pointer::owning_ptr < DownstreamBuilder const >	DownstreamBuilderCOP

typedef utility::pointer::owning_ptr < AtomGeometrySecMatchRPE >	AtomGeometrySecMatchRPEOP

typedef utility::pointer::owning_ptr < AtomGeometrySecMatchRPE const >	AtomGeometrySecMatchRPECOP

typedef utility::pointer::owning_ptr < AtomDistanceSecMatchRPE >	AtomDistanceSecMatchRPEOP

typedef utility::pointer::owning_ptr < AtomDistanceSecMatchRPE const >	AtomDistanceSecMatchRPECOP

typedef utility::pointer::owning_ptr < AtomAngleSecMatchRPE >	AtomAngleSecMatchRPEOP

typedef utility::pointer::owning_ptr < AtomAngleSecMatchRPE const >	AtomAngleSecMatchRPECOP

typedef utility::pointer::owning_ptr < AtomDihedralSecMatchRPE >	AtomDihedralSecMatchRPEOP

typedef utility::pointer::owning_ptr < AtomDihedralSecMatchRPE const >	AtomDihedralSecMatchRPECOP

typedef utility::pointer::owning_ptr < GeometrySecMatchRPE >	GeometrySecMatchRPEOP

typedef utility::pointer::owning_ptr < GeometrySecMatchRPE const >	GeometrySecMatchRPECOP

typedef utility::pointer::owning_ptr < LigandConformerBuilder >	LigandConformerBuilderOP

typedef utility::pointer::owning_ptr < LigandConformerBuilder const >	LigandConformerBuilderCOP

typedef utility::pointer::owning_ptr < RigidLigandBuilder >	RigidLigandBuilderOP

typedef utility::pointer::owning_ptr < RigidLigandBuilder const >	RigidLigandBuilderCOP

typedef utility::pointer::owning_ptr < ScoringSecMatchRPE >	ScoringSecMatchRPEOP

typedef utility::pointer::owning_ptr < ScoringSecMatchRPE const >	ScoringSecMatchRPECOP

typedef utility::pointer::owning_ptr < SecMatchResiduePairEvaluator >	SecMatchResiduePairEvaluatorOP

typedef utility::pointer::owning_ptr < SecMatchResiduePairEvaluator const >	SecMatchResiduePairEvaluatorCOP

typedef utility::pointer::owning_ptr < SecondaryMatcherToDownstreamResidue >	SecondaryMatcherToDownstreamResidueOP

typedef utility::pointer::owning_ptr < SecondaryMatcherToDownstreamResidue const >	SecondaryMatcherToDownstreamResidueCOP

typedef utility::pointer::owning_ptr < SecondaryMatcherToUpstreamResidue >	SecondaryMatcherToUpstreamResidueOP

typedef utility::pointer::owning_ptr < SecondaryMatcherToUpstreamResidue const >	SecondaryMatcherToUpstreamResidueCOP

typedef utility::pointer::owning_ptr < TargetRotamerCoords >	TargetRotamerCoordsOP

typedef utility::pointer::owning_ptr < TargetRotamerCoords const >	TargetRotamerCoordsCOP

typedef utility::pointer::owning_ptr < SecondaryMatchUpstreamResProcessor >	SecondaryMatchUpstreamResProcessorOP

typedef utility::pointer::owning_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")