protocols::match::output Namespace Reference

Classes
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	MatchConsolidator
class	BestMatchesCollection
class	MatchEvaluator
class	MatchFilter
class	StateAccumulatingMatchFilter
class	MatchGrouper
class	MatchOutputter
class	MatchProcessor
class	OutputWriter
class	PDBWriter
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	PoseMatchOutputWriter
	helper class for the MatcherMover that will put a match into a supplied pose More...
class	PoseInserter
class	ProcessorFactory
class	SameChiBinComboGrouper
class	SameRotamerComboGrouper
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	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	MatchCollisionFilter
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	ResidueKinemageWriter
class	WriteUpstreamCoordinateKinemage
class	WriteUpstreamHitKinemage
class	DownstreamCoordinateKinemageWriter
class	SingleDownstreamResidueWriter
	Class for writing conformations of the downstream partner in a kinemage description. More...

Typedefs
typedef utility::pointer::owning_ptr < DownstreamRMSEvaluator >	DownstreamRMSEvaluatorOP
typedef utility::pointer::owning_ptr < DownstreamRMSEvaluator const >	DownstreamRMSEvaluatorCOP
typedef utility::pointer::owning_ptr < LimitHitsPerRotamerFilter >	LimitHitsPerRotamerFilterOP
typedef utility::pointer::owning_ptr < LimitHitsPerRotamerFilter const >	LimitHitsPerRotamerFilterCOP
typedef utility::pointer::owning_ptr < MatchConsolidator >	MatchConsolidatorOP
typedef utility::pointer::owning_ptr < MatchConsolidator const >	MatchConsolidatorCOP
typedef utility::pointer::owning_ptr < BestMatchesCollection >	BestMatchesCollectionOP
typedef utility::pointer::owning_ptr < BestMatchesCollection const >	BestMatchesCollectionCOP
typedef utility::pointer::owning_ptr < MatchEvaluator >	MatchEvaluatorOP
typedef utility::pointer::owning_ptr < MatchEvaluator const >	MatchEvaluatorCOP
typedef utility::pointer::owning_ptr < MatchFilter >	MatchFilterOP
typedef utility::pointer::owning_ptr < MatchFilter const >	MatchFilterCOP
typedef utility::pointer::owning_ptr < StateAccumulatingMatchFilter >	StateAccumulatingMatchFilterOP
typedef utility::pointer::owning_ptr < StateAccumulatingMatchFilter const >	StateAccumulatingMatchFilterCOP
typedef utility::pointer::owning_ptr < MatchGrouper >	MatchGrouperOP
typedef utility::pointer::owning_ptr < MatchGrouper const >	MatchGrouperCOP
typedef utility::pointer::owning_ptr < MatchOutputter >	MatchOutputterOP
typedef utility::pointer::owning_ptr < MatchOutputter const >	MatchOutputterCOP
typedef utility::pointer::owning_ptr < MatchProcessor >	MatchProcessorOP
typedef utility::pointer::owning_ptr < MatchProcessor const >	MatchProcessorCOP
typedef utility::pointer::owning_ptr < OutputWriter >	OutputWriterOP
typedef utility::pointer::owning_ptr < OutputWriter const >	OutputWriterCOP
typedef utility::pointer::owning_ptr < PDBWriter >	PDBWriterOP
typedef utility::pointer::owning_ptr < PDBWriter const >	PDBWriterCOP
typedef utility::pointer::owning_ptr < CloudPDBWriter >	CloudPDBWriterOP
typedef utility::pointer::owning_ptr < CloudPDBWriter const >	CloudPDBWriterCOP
typedef utility::pointer::owning_ptr < PoseMatchOutputWriter >	PoseMatchOutputWriterOP
typedef utility::pointer::owning_ptr < PoseMatchOutputWriter const >	PoseMatchOutputWriterCOP
typedef utility::pointer::owning_ptr < PoseInserter >	PoseInserterOP
typedef utility::pointer::owning_ptr < PoseInserter const >	PoseInserterCOP
typedef utility::pointer::owning_ptr < ProcessorFactory >	ProcessorFactoryOP
typedef utility::pointer::owning_ptr < ProcessorFactory const >	ProcessorFactoryCOP
typedef utility::pointer::owning_ptr < SameChiBinComboGrouper >	SameChiBinComboGrouperOP
typedef utility::pointer::owning_ptr < SameChiBinComboGrouper const >	SameChiBinComboGrouperCOP
typedef utility::pointer::owning_ptr < SameRotamerComboGrouper >	SameRotamerComboGrouperOP
typedef utility::pointer::owning_ptr < SameRotamerComboGrouper const >	SameRotamerComboGrouperCOP
typedef utility::pointer::owning_ptr < SameSequenceGrouper >	SameSequenceGrouperOP
typedef utility::pointer::owning_ptr < SameSequenceGrouper const >	SameSequenceGrouperCOP
typedef utility::pointer::owning_ptr < SameSequenceAndDSPositionGrouper >	SameSequenceAndDSPositionGrouperOP
typedef utility::pointer::owning_ptr < SameSequenceAndDSPositionGrouper const >	SameSequenceAndDSPositionGrouperCOP
typedef utility::pointer::owning_ptr < UpstreamCollisionFilter >	UpstreamCollisionFilterOP
typedef utility::pointer::owning_ptr < UpstreamCollisionFilter const >	UpstreamCollisionFilterCOP
typedef utility::pointer::owning_ptr < UpstreamDownstreamCollisionFilter >	UpstreamDownstreamCollisionFilterOP
typedef utility::pointer::owning_ptr < UpstreamDownstreamCollisionFilter const >	UpstreamDownstreamCollisionFilterCOP
typedef utility::pointer::owning_ptr < UpstreamHitCacher >	UpstreamHitCacherOP
typedef utility::pointer::owning_ptr < UpstreamHitCacher const >	UpstreamHitCacherCOP
typedef utility::pointer::owning_ptr < WriteKinemageOutputter >	WriteKinemageOutputterOP
typedef utility::pointer::owning_ptr < WriteKinemageOutputter const >	WriteKinemageOutputterCOP
typedef utility::pointer::owning_ptr < WriteUpstreamCoordinateKinemage >	WriteUpstreamCoordinateKinemageOP
typedef utility::pointer::owning_ptr < WriteUpstreamCoordinateKinemage const >	WriteUpstreamCoordinateKinemageCOP
typedef utility::pointer::owning_ptr < WriteUpstreamHitKinemage >	WriteUpstreamHitKinemageOP
typedef utility::pointer::owning_ptr < WriteUpstreamHitKinemage const >	WriteUpstreamHitKinemageCOP
typedef utility::pointer::owning_ptr < DownstreamCoordinateKinemageWriter >	DownstreamCoordinateKinemageWriterOP
typedef utility::pointer::owning_ptr < DownstreamCoordinateKinemageWriter const >	DownstreamCoordinateKinemageWriterCOP
typedef utility::pointer::owning_ptr < SingleDownstreamResidueWriter >	SingleDownstreamResidueWriterOP
typedef utility::pointer::owning_ptr < SingleDownstreamResidueWriter const >	SingleDownstreamResidueWriterCOP

Functions
static basic::Tracer	TR ("protocols.match.output.MatchProcessor")
static basic::Tracer	TR ("protocols.match.output.PDBWriter")
static 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::owning_ptr< BestMatchesCollection const > protocols::match::output::BestMatchesCollectionCOP

Definition at line 35 of file MatchConsolidator.fwd.hh.

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

Definition at line 34 of file MatchConsolidator.fwd.hh.

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

Definition at line 33 of file PDBWriter.fwd.hh.

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

Definition at line 32 of file PDBWriter.fwd.hh.

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

Definition at line 37 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 35 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 29 of file DownstreamRMSEvaluator.fwd.hh.

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

Definition at line 27 of file DownstreamRMSEvaluator.fwd.hh.

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

Definition at line 29 of file LimitHitsPerRotamerFilter.fwd.hh.

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

Definition at line 26 of file LimitHitsPerRotamerFilter.fwd.hh.

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

Definition at line 32 of file MatchConsolidator.fwd.hh.

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

Definition at line 29 of file MatchConsolidator.fwd.hh.

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

Definition at line 29 of file MatchEvaluator.fwd.hh.

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

Definition at line 26 of file MatchEvaluator.fwd.hh.

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

Definition at line 29 of file MatchFilter.fwd.hh.

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

Definition at line 26 of file MatchFilter.fwd.hh.

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

Definition at line 38 of file MatchGrouper.fwd.hh.

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

Definition at line 35 of file MatchGrouper.fwd.hh.

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

Definition at line 30 of file MatchOutputter.fwd.hh.

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

Definition at line 27 of file MatchOutputter.fwd.hh.

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

Definition at line 29 of file MatchProcessor.fwd.hh.

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

Definition at line 26 of file MatchProcessor.fwd.hh.

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

Definition at line 29 of file OutputWriter.fwd.hh.

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

Definition at line 26 of file OutputWriter.fwd.hh.

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

Definition at line 30 of file PDBWriter.fwd.hh.

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

Definition at line 27 of file PDBWriter.fwd.hh.

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

Definition at line 27 of file PoseInserter.fwd.hh.

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

Definition at line 25 of file PoseInserter.fwd.hh.

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

Definition at line 36 of file PDBWriter.fwd.hh.

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

Definition at line 35 of file PDBWriter.fwd.hh.

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

Definition at line 29 of file ProcessorFactory.fwd.hh.

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

Definition at line 27 of file ProcessorFactory.fwd.hh.

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

Definition at line 29 of file SameChiBinComboGrouper.fwd.hh.

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

Definition at line 26 of file SameChiBinComboGrouper.fwd.hh.

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

Definition at line 29 of file SameRotamerComboGrouper.fwd.hh.

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

Definition at line 26 of file SameRotamerComboGrouper.fwd.hh.

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

Definition at line 32 of file SameSequenceGrouper.fwd.hh.

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

Definition at line 31 of file SameSequenceGrouper.fwd.hh.

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

Definition at line 30 of file SameSequenceGrouper.fwd.hh.

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

Definition at line 27 of file SameSequenceGrouper.fwd.hh.

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

Definition at line 41 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 39 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 34 of file MatchFilter.fwd.hh.

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

Definition at line 31 of file MatchFilter.fwd.hh.

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

Definition at line 29 of file UpstreamCollisionFilter.fwd.hh.

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

Definition at line 26 of file UpstreamCollisionFilter.fwd.hh.

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

Definition at line 29 of file UpstreamDownstreamCollisionFilter.fwd.hh.

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

Definition at line 26 of file UpstreamDownstreamCollisionFilter.fwd.hh.

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

Definition at line 29 of file UpstreamHitCacher.fwd.hh.

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

Definition at line 26 of file UpstreamHitCacher.fwd.hh.

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

Definition at line 29 of file WriteKinemageOutputter.fwd.hh.

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

Definition at line 26 of file WriteKinemageOutputter.fwd.hh.

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

Definition at line 29 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 27 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 33 of file WriteUpstreamCoordinateKineamge.fwd.hh.

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

Definition at line 31 of file WriteUpstreamCoordinateKineamge.fwd.hh.

Function Documentation

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.

Definition at line 46 of file WriteUpstreamCoordinateKineamge.cc.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), protocols::loops::extras, core::chemical::AtomType::name(), and core::chemical::ResidueType::name3().

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 = ""
	)

Definition at line 69 of file WriteUpstreamCoordinateKineamge.cc.

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 = ""
	)

Definition at line 81 of file WriteUpstreamCoordinateKineamge.cc.

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

static 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(), and protocols::match::output::CloudPDBWriter::write_match_groups().

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

static

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

static