Classes
class	BestMatchesCollection

class	CloudPDBWriter
	an output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections More...

class	DownstreamCoordinateKinemageWriter

class	DownstreamRMSEvaluator
	In the best of all possible worlds, this class would be sufficiently generic such that I could compare RMS for arbitrary subsets of atoms on the downstream partner, but in my first pass implementation, I'm writing while aiming at the RigidLigandBuilder – 1 residue – and I'll compare all heavy atoms. More...

class	LimitHitsPerRotamerFilter

class	MatchCollisionFilter

class	MatchConsolidator

class	MatchEvaluator

class	MatchFilter

class	MatchGrouper

class	MatchOutputter

class	MatchProcessor

class	MatchScoreWriter

class	OutputWriter

class	PDBWriter

class	PoseInserter

class	PoseMatchOutputWriter
	helper class for the MatcherMover that will put a match into a supplied pose More...

class	ProcessorFactory

class	ResidueKinemageWriter

class	SameChiBinComboGrouper

class	SameRotamerComboGrouper

class	SameSequenceAndDSPositionGrouper
	class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account More...

class	SameSequenceGrouper
	Class to group matches that represent the same amino acids at the same launch points. E.g. Two matches that both put a cys at launch point #33, a ser a launch point #42 and another ser at launch point #80 would be grouped together – even if they are different rotamers. More...

class	SingleDownstreamResidueWriter
	Class for writing conformations of the downstream partner in a kinemage description. More...

class	StateAccumulatingMatchFilter

class	UpstreamCollisionFilter
	This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol. More...

class	UpstreamDownstreamCollisionFilter
	This class is used to detect collisions between upstream residues and downstream poses. More...

class	UpstreamHitCacher

class	WriteKinemageOutputter

class	WriteUpstreamCoordinateKinemage

class	WriteUpstreamHitKinemage

Typedefs
typedef utility::pointer::shared_ptr < DownstreamRMSEvaluator >	DownstreamRMSEvaluatorOP

typedef utility::pointer::shared_ptr < DownstreamRMSEvaluator const >	DownstreamRMSEvaluatorCOP

typedef utility::pointer::shared_ptr < LimitHitsPerRotamerFilter >	LimitHitsPerRotamerFilterOP

typedef utility::pointer::shared_ptr < LimitHitsPerRotamerFilter const >	LimitHitsPerRotamerFilterCOP

typedef utility::pointer::shared_ptr < MatchConsolidator >	MatchConsolidatorOP

typedef utility::pointer::shared_ptr < MatchConsolidator const >	MatchConsolidatorCOP

typedef utility::pointer::shared_ptr < BestMatchesCollection >	BestMatchesCollectionOP

typedef utility::pointer::shared_ptr < BestMatchesCollection const >	BestMatchesCollectionCOP

typedef utility::pointer::shared_ptr < MatchEvaluator >	MatchEvaluatorOP

typedef utility::pointer::shared_ptr < MatchEvaluator const >	MatchEvaluatorCOP

typedef utility::pointer::shared_ptr < MatchFilter >	MatchFilterOP

typedef utility::pointer::shared_ptr < MatchFilter const >	MatchFilterCOP

typedef utility::pointer::shared_ptr < StateAccumulatingMatchFilter >	StateAccumulatingMatchFilterOP

typedef utility::pointer::shared_ptr < StateAccumulatingMatchFilter const >	StateAccumulatingMatchFilterCOP

typedef utility::pointer::shared_ptr < MatchGrouper >	MatchGrouperOP

typedef utility::pointer::shared_ptr < MatchGrouper const >	MatchGrouperCOP

typedef utility::pointer::shared_ptr < MatchOutputter >	MatchOutputterOP

typedef utility::pointer::shared_ptr < MatchOutputter const >	MatchOutputterCOP

typedef utility::pointer::shared_ptr < MatchProcessor >	MatchProcessorOP

typedef utility::pointer::shared_ptr < MatchProcessor const >	MatchProcessorCOP

typedef utility::pointer::shared_ptr < MatchScoreWriter >	MatchScoreWriterOP

typedef utility::pointer::shared_ptr < MatchScoreWriter const >	MatchScoreWriterCOP

typedef utility::pointer::shared_ptr < OutputWriter >	OutputWriterOP

typedef utility::pointer::shared_ptr < OutputWriter const >	OutputWriterCOP

typedef utility::pointer::shared_ptr < PDBWriter >	PDBWriterOP

typedef utility::pointer::shared_ptr < PDBWriter const >	PDBWriterCOP

typedef utility::pointer::shared_ptr < CloudPDBWriter >	CloudPDBWriterOP

typedef utility::pointer::shared_ptr < CloudPDBWriter const >	CloudPDBWriterCOP

typedef utility::pointer::shared_ptr < PoseMatchOutputWriter >	PoseMatchOutputWriterOP

typedef utility::pointer::shared_ptr < PoseMatchOutputWriter const >	PoseMatchOutputWriterCOP

typedef utility::pointer::shared_ptr < PoseInserter >	PoseInserterOP

typedef utility::pointer::shared_ptr < PoseInserter const >	PoseInserterCOP

typedef utility::pointer::shared_ptr < ProcessorFactory >	ProcessorFactoryOP

typedef utility::pointer::shared_ptr < ProcessorFactory const >	ProcessorFactoryCOP

typedef utility::pointer::shared_ptr < SameChiBinComboGrouper >	SameChiBinComboGrouperOP

typedef utility::pointer::shared_ptr < SameChiBinComboGrouper const >	SameChiBinComboGrouperCOP

typedef utility::pointer::shared_ptr < SameRotamerComboGrouper >	SameRotamerComboGrouperOP

typedef utility::pointer::shared_ptr < SameRotamerComboGrouper const >	SameRotamerComboGrouperCOP

typedef utility::pointer::shared_ptr < SameSequenceGrouper >	SameSequenceGrouperOP

typedef utility::pointer::shared_ptr < SameSequenceGrouper const >	SameSequenceGrouperCOP

typedef utility::pointer::shared_ptr < SameSequenceAndDSPositionGrouper >	SameSequenceAndDSPositionGrouperOP

typedef utility::pointer::shared_ptr < SameSequenceAndDSPositionGrouper const >	SameSequenceAndDSPositionGrouperCOP

typedef utility::pointer::shared_ptr < UpstreamCollisionFilter >	UpstreamCollisionFilterOP

typedef utility::pointer::shared_ptr < UpstreamCollisionFilter const >	UpstreamCollisionFilterCOP

typedef utility::pointer::shared_ptr < UpstreamDownstreamCollisionFilter >	UpstreamDownstreamCollisionFilterOP

typedef utility::pointer::shared_ptr < UpstreamDownstreamCollisionFilter const >	UpstreamDownstreamCollisionFilterCOP

typedef utility::pointer::shared_ptr < UpstreamHitCacher >	UpstreamHitCacherOP

typedef utility::pointer::shared_ptr < UpstreamHitCacher const >	UpstreamHitCacherCOP

typedef utility::pointer::shared_ptr < WriteKinemageOutputter >	WriteKinemageOutputterOP

typedef utility::pointer::shared_ptr < WriteKinemageOutputter const >	WriteKinemageOutputterCOP

typedef utility::pointer::shared_ptr < WriteUpstreamCoordinateKinemage >	WriteUpstreamCoordinateKinemageOP

typedef utility::pointer::shared_ptr < WriteUpstreamCoordinateKinemage const >	WriteUpstreamCoordinateKinemageCOP

typedef utility::pointer::shared_ptr < WriteUpstreamHitKinemage >	WriteUpstreamHitKinemageOP

typedef utility::pointer::shared_ptr < WriteUpstreamHitKinemage const >	WriteUpstreamHitKinemageCOP

typedef utility::pointer::shared_ptr < DownstreamCoordinateKinemageWriter >	DownstreamCoordinateKinemageWriterOP

typedef utility::pointer::shared_ptr < DownstreamCoordinateKinemageWriter const >	DownstreamCoordinateKinemageWriterCOP

typedef utility::pointer::shared_ptr < SingleDownstreamResidueWriter >	SingleDownstreamResidueWriterOP

typedef utility::pointer::shared_ptr < SingleDownstreamResidueWriter const >	SingleDownstreamResidueWriterCOP

Functions
static thread_local basic::Tracer	TR ("protocols.match.output.MatchProcessor")

std::ostream &	operator<< (std::ostream &output, MatchScoreWriter const &object_to_output)

static thread_local basic::Tracer	TR ("protocols.match.output.PDBWriter")

static thread_local basic::Tracer	TR ("protocols.match.output.ProcessorFactory")

void	print_node (std::ostream &out, int residue_num, int atom_num, core::Vector const &atom_xyz, core::chemical::ResidueType const &res, std::string extras="")
	TWO FUNCTIONS STOLEN FROM IAN: and slightly modified. More...

void	print_node (std::ostream &out, int residue_num, int atom_num, core::conformation::Residue const &res, std::string extras="")

void	print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Residue const &res, std::string extras="")

Typedef Documentation

typedef utility::pointer::shared_ptr< BestMatchesCollection const > protocols::match::output::BestMatchesCollectionCOP

typedef utility::pointer::shared_ptr< BestMatchesCollection > protocols::match::output::BestMatchesCollectionOP

typedef utility::pointer::shared_ptr< CloudPDBWriter const > protocols::match::output::CloudPDBWriterCOP

typedef utility::pointer::shared_ptr< CloudPDBWriter > protocols::match::output::CloudPDBWriterOP

typedef utility::pointer::shared_ptr< DownstreamCoordinateKinemageWriter const > protocols::match::output::DownstreamCoordinateKinemageWriterCOP

typedef utility::pointer::shared_ptr< DownstreamCoordinateKinemageWriter > protocols::match::output::DownstreamCoordinateKinemageWriterOP

typedef utility::pointer::shared_ptr< DownstreamRMSEvaluator const > protocols::match::output::DownstreamRMSEvaluatorCOP

typedef utility::pointer::shared_ptr< DownstreamRMSEvaluator > protocols::match::output::DownstreamRMSEvaluatorOP

typedef utility::pointer::shared_ptr< LimitHitsPerRotamerFilter const > protocols::match::output::LimitHitsPerRotamerFilterCOP

typedef utility::pointer::shared_ptr< LimitHitsPerRotamerFilter > protocols::match::output::LimitHitsPerRotamerFilterOP

typedef utility::pointer::shared_ptr< MatchConsolidator const > protocols::match::output::MatchConsolidatorCOP

typedef utility::pointer::shared_ptr< MatchConsolidator > protocols::match::output::MatchConsolidatorOP

typedef utility::pointer::shared_ptr< MatchEvaluator const > protocols::match::output::MatchEvaluatorCOP

typedef utility::pointer::shared_ptr< MatchEvaluator > protocols::match::output::MatchEvaluatorOP

typedef utility::pointer::shared_ptr< MatchFilter const > protocols::match::output::MatchFilterCOP

typedef utility::pointer::shared_ptr< MatchFilter > protocols::match::output::MatchFilterOP

typedef utility::pointer::shared_ptr< MatchGrouper const > protocols::match::output::MatchGrouperCOP

typedef utility::pointer::shared_ptr< MatchGrouper > protocols::match::output::MatchGrouperOP

typedef utility::pointer::shared_ptr< MatchOutputter const > protocols::match::output::MatchOutputterCOP

typedef utility::pointer::shared_ptr< MatchOutputter > protocols::match::output::MatchOutputterOP

typedef utility::pointer::shared_ptr< MatchProcessor const > protocols::match::output::MatchProcessorCOP

typedef utility::pointer::shared_ptr< MatchProcessor > protocols::match::output::MatchProcessorOP

typedef utility::pointer::shared_ptr<MatchScoreWriter const> protocols::match::output::MatchScoreWriterCOP

typedef utility::pointer::shared_ptr<MatchScoreWriter> protocols::match::output::MatchScoreWriterOP

typedef utility::pointer::shared_ptr< OutputWriter const > protocols::match::output::OutputWriterCOP

typedef utility::pointer::shared_ptr< OutputWriter > protocols::match::output::OutputWriterOP

typedef utility::pointer::shared_ptr< PDBWriter const > protocols::match::output::PDBWriterCOP

typedef utility::pointer::shared_ptr< PDBWriter > protocols::match::output::PDBWriterOP

typedef utility::pointer::shared_ptr< PoseInserter const > protocols::match::output::PoseInserterCOP

typedef utility::pointer::shared_ptr< PoseInserter > protocols::match::output::PoseInserterOP

typedef utility::pointer::shared_ptr< PoseMatchOutputWriter const > protocols::match::output::PoseMatchOutputWriterCOP

typedef utility::pointer::shared_ptr< PoseMatchOutputWriter > protocols::match::output::PoseMatchOutputWriterOP

typedef utility::pointer::shared_ptr< ProcessorFactory const > protocols::match::output::ProcessorFactoryCOP

typedef utility::pointer::shared_ptr< ProcessorFactory > protocols::match::output::ProcessorFactoryOP

typedef utility::pointer::shared_ptr< SameChiBinComboGrouper const > protocols::match::output::SameChiBinComboGrouperCOP

typedef utility::pointer::shared_ptr< SameChiBinComboGrouper > protocols::match::output::SameChiBinComboGrouperOP

typedef utility::pointer::shared_ptr< SameRotamerComboGrouper const > protocols::match::output::SameRotamerComboGrouperCOP

typedef utility::pointer::shared_ptr< SameRotamerComboGrouper > protocols::match::output::SameRotamerComboGrouperOP

typedef utility::pointer::shared_ptr< SameSequenceAndDSPositionGrouper const > protocols::match::output::SameSequenceAndDSPositionGrouperCOP

typedef utility::pointer::shared_ptr< SameSequenceAndDSPositionGrouper > protocols::match::output::SameSequenceAndDSPositionGrouperOP

typedef utility::pointer::shared_ptr< SameSequenceGrouper const > protocols::match::output::SameSequenceGrouperCOP

typedef utility::pointer::shared_ptr< SameSequenceGrouper > protocols::match::output::SameSequenceGrouperOP

typedef utility::pointer::shared_ptr< SingleDownstreamResidueWriter const > protocols::match::output::SingleDownstreamResidueWriterCOP

typedef utility::pointer::shared_ptr< SingleDownstreamResidueWriter > protocols::match::output::SingleDownstreamResidueWriterOP

typedef utility::pointer::shared_ptr< StateAccumulatingMatchFilter const > protocols::match::output::StateAccumulatingMatchFilterCOP

typedef utility::pointer::shared_ptr< StateAccumulatingMatchFilter > protocols::match::output::StateAccumulatingMatchFilterOP

typedef utility::pointer::shared_ptr< UpstreamCollisionFilter const > protocols::match::output::UpstreamCollisionFilterCOP

typedef utility::pointer::shared_ptr< UpstreamCollisionFilter > protocols::match::output::UpstreamCollisionFilterOP

typedef utility::pointer::shared_ptr< UpstreamDownstreamCollisionFilter const > protocols::match::output::UpstreamDownstreamCollisionFilterCOP

typedef utility::pointer::shared_ptr< UpstreamDownstreamCollisionFilter > protocols::match::output::UpstreamDownstreamCollisionFilterOP

typedef utility::pointer::shared_ptr< UpstreamHitCacher const > protocols::match::output::UpstreamHitCacherCOP

typedef utility::pointer::shared_ptr< UpstreamHitCacher > protocols::match::output::UpstreamHitCacherOP

typedef utility::pointer::shared_ptr< WriteKinemageOutputter const > protocols::match::output::WriteKinemageOutputterCOP

typedef utility::pointer::shared_ptr< WriteKinemageOutputter > protocols::match::output::WriteKinemageOutputterOP

typedef utility::pointer::shared_ptr< WriteUpstreamCoordinateKinemage const > protocols::match::output::WriteUpstreamCoordinateKinemageCOP

typedef utility::pointer::shared_ptr< WriteUpstreamCoordinateKinemage > protocols::match::output::WriteUpstreamCoordinateKinemageOP

typedef utility::pointer::shared_ptr< WriteUpstreamHitKinemage const > protocols::match::output::WriteUpstreamHitKinemageCOP

typedef utility::pointer::shared_ptr< WriteUpstreamHitKinemage > protocols::match::output::WriteUpstreamHitKinemageOP

Function Documentation

std::ostream& protocols::match::output::operator<<	(	std::ostream &	output,
		MatchScoreWriter const &	object_to_output
	)

References protocols::match::output::MatchScoreWriter::show().

void protocols::match::output::print_node	(	std::ostream &	out,
		int	residue_num,
		int	atom_num,
		core::Vector const &	atom_xyz,
		core::chemical::ResidueType const &	res,
		std::string	extras = `""`
	)

TWO FUNCTIONS STOLEN FROM IAN: and slightly modified.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), protocols::loops::extras, core::chemical::AtomType::name(), core::chemical::ResidueType::name3(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by print_node(), protocols::match::output::SingleDownstreamResidueWriter::write_downstream_coordinates(), and protocols::match::output::ResidueKinemageWriter::write_rsd_coords().

void protocols::match::output::print_node	(	std::ostream &	out,
		int	residue_num,
		int	atom_num,
		core::conformation::Residue const &	res,
		std::string	extras = `""`
	)

References protocols::loops::extras, print_node(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

void protocols::match::output::print_node	(	std::ostream &	out,
		int	residue_num,
		std::string	atom_name,
		core::conformation::Residue const &	res,
		std::string	extras = `""`
	)

References core::conformation::Residue::atom_index(), protocols::loops::extras, and print_node().

static thread_local basic::Tracer protocols::match::output::TR ( "protocols.match.output.MatchProcessor" )

static

Referenced by protocols::match::output::ProcessorFactory::create_processor(), protocols::match::output::CloudPDBWriter::end_output_writing(), protocols::match::output::MatchProcessor::end_processing(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::CloudPDBWriter::write_match_groups(), and protocols::match::output::MatchScoreWriter::write_match_scores().

static thread_local basic::Tracer protocols::match::output::TR ( "protocols.match.output.PDBWriter" )

static

static thread_local basic::Tracer protocols::match::output::TR ( "protocols.match.output.ProcessorFactory" )

static

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation