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	MatchScoreWriter
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::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 basic::Tracer	TR ("protocols.match.output.MatchProcessor")
std::ostream &	operator<< (std::ostream &output, MatchScoreWriter const &object_to_output)
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 const &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 const &extras="")
void	print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Residue const &res, std::string const &extras="")

Typedef Documentation

BestMatchesCollectionCOP

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

BestMatchesCollectionOP

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

CloudPDBWriterCOP

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

CloudPDBWriterOP

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

DownstreamCoordinateKinemageWriterCOP

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

DownstreamCoordinateKinemageWriterOP

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

DownstreamRMSEvaluatorCOP

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

DownstreamRMSEvaluatorOP

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

LimitHitsPerRotamerFilterCOP

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

LimitHitsPerRotamerFilterOP

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

MatchConsolidatorCOP

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

MatchConsolidatorOP

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

MatchEvaluatorCOP

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

MatchEvaluatorOP

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

MatchFilterCOP

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

MatchFilterOP

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

MatchGrouperCOP

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

MatchGrouperOP

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

MatchOutputterCOP

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

MatchOutputterOP

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

MatchProcessorCOP

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

MatchProcessorOP

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

MatchScoreWriterCOP

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

MatchScoreWriterOP

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

OutputWriterCOP

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

OutputWriterOP

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

PDBWriterCOP

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

PDBWriterOP

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

PoseInserterCOP

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

PoseInserterOP

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

PoseMatchOutputWriterCOP

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

PoseMatchOutputWriterOP

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

ProcessorFactoryCOP

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

ProcessorFactoryOP

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

SameChiBinComboGrouperCOP

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

SameChiBinComboGrouperOP

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

SameRotamerComboGrouperCOP

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

SameRotamerComboGrouperOP

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

SameSequenceAndDSPositionGrouperCOP

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

SameSequenceAndDSPositionGrouperOP

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

SameSequenceGrouperCOP

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

SameSequenceGrouperOP

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

SingleDownstreamResidueWriterCOP

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

SingleDownstreamResidueWriterOP

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

StateAccumulatingMatchFilterCOP

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

StateAccumulatingMatchFilterOP

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

UpstreamCollisionFilterCOP

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

UpstreamCollisionFilterOP

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

UpstreamDownstreamCollisionFilterCOP

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

UpstreamDownstreamCollisionFilterOP

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

UpstreamHitCacherCOP

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

UpstreamHitCacherOP

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

WriteKinemageOutputterCOP

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

WriteKinemageOutputterOP

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

WriteUpstreamCoordinateKinemageCOP

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

WriteUpstreamCoordinateKinemageOP

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

WriteUpstreamHitKinemageCOP

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

WriteUpstreamHitKinemageOP

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

Function Documentation

operator<<()

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

print_node() [1/3]

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

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

print_node() [2/3]

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 const &	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::ResidueTypeBase::name3(), and core::conformation::membrane::out.

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

print_node() [3/3]

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

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

TR() [1/3]

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(), protocols::match::output::CloudPDBWriter::write_match_groups(), and protocols::match::output::MatchScoreWriter::write_match_scores().

TR() [2/3]

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

static

TR() [3/3]

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

static