Namespaces
	helixAssembly

	RelevantResiduesMode

	strand_assembly

Classes
class	AtomAtomPairFeatures

class	AtomAtomPairFeaturesCreator
	creator for the AtomAtomPairFeatures class More...

class	AtomInResidueAtomInResiduePairFeatures

class	AtomInResidueAtomInResiduePairFeaturesCreator
	creator for the AtomInResidueAtomInResiduePairFeatures class More...

class	AtomTypesFeatures

class	AtomTypesFeaturesCreator
	creator for the AtomTypesFeatures class More...

class	BatchFeatures

class	BetaTurnDetection

class	BetaTurnDetectionFeatures

class	BetaTurnDetectionFeaturesCreator
	creator for the BetaTurnDetectionFeatures class More...

class	ChargeChargeFeatures

class	ChargeChargeFeaturesCreator
	creator for the ChargeChargeFeatures class More...

class	DatabaseFilter

class	TopCountOfEachInput

class	TopCountOfAllInputs

class	TopPercentOfEachInput

class	TopPercentOfAllInputs

class	DatabaseJobInputter

class	DatabaseJobInputterCreator

class	DatabaseJobOutputter

class	DatabaseJobOutputterCreator

class	DdGFeatures

class	DdGFeaturesCreator
	creator for the DdGFeatures class More...

class	FeaturesReporter

class	FeaturesReporterCreator
	The Creator class is responsible for creating a particular mover class. More...

class	FeaturesReporterFactory
	Create Features Reporters. More...

class	FeaturesReporterRegistrator
	This templated class will register an instance of an FeaturesReporterCreator (class T) with the FeaturesReporterFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	GeometricSolvationFeatures

class	GeometricSolvationFeaturesCreator
	creator for the GeometricSolvationFeatures class More...

class	HBondFeatures

class	HBondFeaturesCreator
	creator for the HBondFeatures class More...

class	HBondParameterFeatures

class	HBondParameterFeaturesCreator
	creator for the HBondParameterFeatures class More...

class	HelixCapFeatures

class	HelixCapFeaturesCreator
	creator for the HelixCapFeaturesCreator class More...

class	InterfaceDdGMover
	Calculates ddG of binding. More...

class	InterfaceDdGMoverCreator

class	InterfaceFeatures
	Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS. More...

class	InterfaceFeaturesCreator
	creator for the HBondParameterFeatures class More...

class	JobDataFeatures

class	JobDataFeaturesCreator
	creator for the JobDataFeatures class More...

class	LoopAnchorFeatures

class	LoopAnchorFeaturesCreator
	creator for the LoopAnchorFeatures class More...

struct	clique_saver

struct	Segment

class	ModelFeatures

class	ModelFeaturesCreator
	creator for the ModelFeatures class More...

class	OrbitalsFeatures

class	OrbitalsFeaturesCreator
	creator for the OrbitalsFeatures class More...

class	PairFeatures

class	PairFeaturesCreator
	creator for the PairFeatures class More...

class	PdbDataFeatures

class	PdbDataFeaturesCreator
	creator for the PdbDataFeatures class More...

class	PoseCommentsFeatures

class	PoseCommentsFeaturesCreator
	creator for the PoseCommentsFeatures class More...

class	PoseConformationFeatures

class	PoseConformationFeaturesCreator
	creator for the PoseConformationFeatures class More...

class	ProteinBackboneAtomAtomPairFeatures

class	ProteinBackboneAtomAtomPairFeaturesCreator
	creator for the ProteinBackboneAtomAtomPairFeatures class More...

class	ProteinBackboneTorsionAngleFeatures

class	ProteinBackboneTorsionAngleFeaturesCreator
	creator for the ProteinBackboneTorsionAngleFeatures class More...

class	ProteinBondGeometryFeatures

class	ProteinBondGeometryFeaturesCreator
	creator for the ProteinBondGeometryFeatures class More...

class	ProteinResidueConformationFeatures

class	ProteinResidueConformationFeaturesCreator
	creator for the ProteinResidueConformationFeatures class More...

class	ProteinRMSDFeatures

class	ProteinRMSDFeaturesCreator
	creator for the ProteinRMSDFeatures class More...

class	ProteinRMSDNoSuperpositionFeatures

class	ProteinRMSDNoSuperpositionFeaturesCreator
	creator for the ProteinRMSDNoSuperpositionFeatures class More...

class	ProteinSilentReport

class	ProtocolFeatures

class	RadiusOfGyrationFeatures

class	RadiusOfGyrationFeaturesCreator
	creator for the RadiusOfGyrationFeatures class More...

class	Report

class	ReportToDB

class	ReportToDBCreator

class	ResidueBurialFeatures

class	ResidueBurialFeaturesCreator
	creator for the ResidueBurialFeatures class More...

class	ResidueConformationFeatures

class	ResidueConformationFeaturesCreator
	creator for the ResidueConformationFeatures class More...

class	ResidueFeatures

class	ResidueFeaturesCreator
	creator for the ResidueFeatures class More...

class	ResidueGridScoresFeatures

class	ResidueGridScoresFeaturesCreator
	creator for the ResidueGridScoresFeatures class More...

class	ResidueScoresFeatures

class	ResidueScoresFeaturesCreator
	creator for the ResidueScoresFeatures class More...

class	ResidueSecondaryStructureFeatures

class	ResidueSecondaryStructureFeaturesCreator
	creator for the ResidueSecondaryStructureFeatures class More...

class	ResidueTotalScoresFeatures

class	ResidueTotalScoresFeaturesCreator
	creator for the ResidueTotalScoresFeatures class More...

class	ResidueTypesFeatures

class	ResidueTypesFeaturesCreator
	creator for the ResidueTypesFeatures class More...

class	RotamerBoltzmannWeightFeatures

class	RotamerBoltzmannWeightFeaturesCreator
	creator for the RotamerBoltzmannWeightFeatures class More...

class	RotamerInitializer

class	RotamerFeatures

class	RotamerFeaturesCreator
	creator for the RotamerFeatures class More...

class	RotamerRecoveryFeatures

class	RotamerRecoveryFeaturesCreator
	creator for the RotamerRecoveryFeatures class More...

class	RuntimeFeatures

class	RuntimeFeaturesCreator

class	SaltBridgeFeatures

class	SaltBridgeFeaturesCreator
	creator for the SaltBridgeFeatures class More...

class	ScoreFunctionFeatures

class	ScoreFunctionFeaturesCreator
	creator for the ScoreFunctionFeatures class More...

class	ScoreTypeFeatures

class	ScoreTypeFeaturesCreator
	creator for the ScoreTypeFeatures class More...

class	ScreeningFeatures

class	ScreeningFeaturesCreator
	creator for the ScreeningFeaturesCreator class More...

class	SecondaryStructureSegmentFeatures

class	SecondaryStructureSegmentFeaturesCreator
	creator for the SecondaryStructureSegmentFeaturesCreator class More...

struct	MetricData

class	SimpleMetricFeatures

class	SimpleMetricFeaturesCreator
	creator for the SimpleMetricFeatures class More...

struct	SecondaryStructureSegment

class	SmotifFeatures

class	SmotifFeaturesCreator
	creator for the SmotifFeaturesCreator class More...

class	StructureFeatures

class	StructureFeaturesCreator
	creator for the StructureFeatures class More...

class	StructureScoresFeatures

class	StructureScoresFeaturesCreator
	creator for the StructureScoresFeatures class More...

class	TaskOperationFeatures

class	TaskOperationFeaturesCreator
	creator for the TaskOperationFeatures class More...

class	TotalScoreFeatures

class	TotalScoreFeaturesCreator

class	TrajectoryMapFeatures

class	TrajectoryMapFeaturesCreator
	creator for the TrajectoryMapFeatures class More...

class	TrajectoryReportToDB

class	TrajectoryReportToDBCreator

class	UnrecognizedAtomFeatures

class	UnrecognizedAtomFeaturesCreator
	creator for the UnrecognizedAtomFeatures class More...

class	WaterFeatures

class	WaterFeaturesCreator
	creator for the WaterFeatures class More...

Typedefs
typedef utility::pointer::shared_ptr< AtomAtomPairFeatures >	AtomAtomPairFeaturesOP

typedef utility::pointer::shared_ptr< AtomAtomPairFeatures const >	AtomAtomPairFeaturesCOP

typedef utility::pointer::shared_ptr< AtomInResidueAtomInResiduePairFeatures >	AtomInResidueAtomInResiduePairFeaturesOP

typedef utility::pointer::shared_ptr< AtomInResidueAtomInResiduePairFeatures const >	AtomInResidueAtomInResiduePairFeaturesCOP

typedef utility::pointer::shared_ptr< AtomTypesFeatures >	AtomTypesFeaturesOP

typedef utility::pointer::shared_ptr< AtomTypesFeatures const >	AtomTypesFeaturesCOP

typedef utility::pointer::shared_ptr< BatchFeatures >	BatchFeaturesOP

typedef utility::pointer::shared_ptr< BatchFeatures const >	BatchFeaturesCOP

typedef utility::pointer::shared_ptr< BetaTurnDetection >	BetaTurnDetectionOP

typedef utility::pointer::shared_ptr< BetaTurnDetection const >	BetaTurnDetectionCOP

typedef utility::pointer::shared_ptr< BetaTurnDetectionFeatures >	BetaTurnDetectionFeaturesOP

typedef utility::pointer::shared_ptr< BetaTurnDetectionFeatures const >	BetaTurnDetectionFeaturesCOP

typedef utility::pointer::shared_ptr< ChargeChargeFeatures >	ChargeChargeFeaturesOP

typedef utility::pointer::shared_ptr< ChargeChargeFeatures const >	ChargeChargeFeaturesCOP

typedef utility::pointer::shared_ptr< DatabaseFilter >	DatabaseFilterOP

typedef utility::pointer::shared_ptr< DatabaseFilter const >	DatabaseFilterCOP

typedef std::pair< bool, utility::vector1< StructureID > >	WriteDeletePair

typedef utility::pointer::shared_ptr< DatabaseJobInputter >	DatabaseJobInputterOP

typedef utility::pointer::shared_ptr< DatabaseJobOutputter >	DatabaseJobOutputterOP

typedef utility::pointer::shared_ptr< DdGFeatures >	DdGFeaturesOP

typedef utility::pointer::shared_ptr< DdGFeatures const >	DdGFeaturesCOP

typedef utility::pointer::shared_ptr< FeaturesReporter >	FeaturesReporterOP

typedef utility::pointer::shared_ptr< FeaturesReporter const >	FeaturesReporterCOP

typedef std::uint64_t	StructureID

typedef utility::pointer::shared_ptr< FeaturesReporterCreator >	FeaturesReporterCreatorOP

typedef utility::pointer::shared_ptr< FeaturesReporterCreator const >	FeaturesReporterCreatorCOP

typedef utility::pointer::shared_ptr< GeometricSolvationFeatures >	GeometricSolvationFeaturesOP

typedef utility::pointer::shared_ptr< GeometricSolvationFeatures const >	GeometricSolvationFeaturesCOP

typedef utility::pointer::shared_ptr< HBondFeatures >	HBondFeaturesOP

typedef utility::pointer::shared_ptr< HBondFeatures const >	HBondFeaturesCOP

typedef utility::pointer::shared_ptr< HBondParameterFeatures >	HBondParameterFeaturesOP

typedef utility::pointer::shared_ptr< HBondParameterFeatures const >	HBondParameterFeaturesCOP

typedef utility::pointer::shared_ptr< InterfaceDdGMover >	InterfaceDdGMoverOP

typedef utility::pointer::shared_ptr< InterfaceDdGMover const >	InterfaceDdGMoverCOP

typedef utility::pointer::shared_ptr< protocols::features::InterfaceFeatures >	InterfaceFeaturesOP

typedef utility::pointer::shared_ptr< InterfaceFeatures const >	InterfaceFeaturesCOP

typedef utility::pointer::shared_ptr< JobDataFeatures >	JobDataFeaturesOP

typedef utility::pointer::shared_ptr< JobDataFeatures const >	JobDataFeaturesCOP

typedef utility::pointer::shared_ptr< LoopAnchorFeatures >	LoopAnchorFeaturesOP

typedef utility::pointer::shared_ptr< LoopAnchorFeatures const >	LoopAnchorFeaturesCOP

typedef utility::pointer::shared_ptr< ModelFeatures >	ModelFeaturesOP

typedef utility::pointer::shared_ptr< ModelFeatures const >	ModelFeaturesCOP

typedef boost::undirected_graph< core::Size >	SegmentGraph

typedef boost::graph_traits< SegmentGraph >::vertex_descriptor	SegmentVertex

typedef boost::graph_traits< SegmentGraph >::edge_descriptor	InteractionEdge

typedef utility::pointer::shared_ptr< OrbitalsFeatures >	OrbitalsFeaturesOP

typedef utility::pointer::shared_ptr< OrbitalsFeatures const >	OrbitalsFeaturesCOP

typedef utility::pointer::shared_ptr< PairFeatures >	PairFeaturesOP

typedef utility::pointer::shared_ptr< PairFeatures const >	PairFeaturesCOP

typedef utility::pointer::shared_ptr< PdbDataFeatures >	PdbDataFeaturesOP

typedef utility::pointer::shared_ptr< PoseCommentsFeatures >	PoseCommentsFeaturesOP

typedef utility::pointer::shared_ptr< PoseCommentsFeatures const >	PoseCommentsFeaturesCOP

typedef utility::pointer::shared_ptr< PoseConformationFeatures >	PoseConformationFeaturesOP

typedef utility::pointer::shared_ptr< PoseConformationFeatures const >	PoseConformationFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBackboneAtomAtomPairFeatures >	ProteinBackboneAtomAtomPairFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBackboneAtomAtomPairFeatures const >	ProteinBackboneAtomAtomPairFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBackboneTorsionAngleFeatures >	ProteinBackboneTorsionAngleFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBackboneTorsionAngleFeatures const >	ProteinBackboneTorsionAngleFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBondGeometryFeatures >	ProteinBondGeometryFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBondGeometryFeatures const >	ProteinBondGeometryFeaturesCOP

typedef utility::pointer::shared_ptr< BondAngleDatabase >	BondAngleDatabaseOP

typedef utility::pointer::shared_ptr< ProteinResidueConformationFeatures >	ProteinResidueConformationFeaturesOP

typedef utility::pointer::shared_ptr< ProteinResidueConformationFeatures const >	ProteinResidueConformationFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinRMSDFeatures >	ProteinRMSDFeaturesOP

typedef utility::pointer::shared_ptr< ProteinRMSDFeatures const >	ProteinRMSDFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinRMSDNoSuperpositionFeatures >	ProteinRMSDNoSuperpositionFeaturesOP

typedef utility::pointer::shared_ptr< ProteinRMSDNoSuperpositionFeatures const >	ProteinRMSDNoSuperpositionFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinSilentReport >	ProteinSilentReportOP

typedef utility::pointer::shared_ptr< ProteinSilentReport const >	ProteinSilentReportCOP

typedef utility::pointer::shared_ptr< ProtocolFeatures >	ProtocolFeaturesOP

typedef utility::pointer::shared_ptr< ProtocolFeatures const >	ProtocolFeaturesCOP

typedef utility::pointer::shared_ptr< RadiusOfGyrationFeatures >	RadiusOfGyrationFeaturesOP

typedef utility::pointer::shared_ptr< RadiusOfGyrationFeatures const >	RadiusOfGyrationFeaturesCOP

typedef utility::pointer::shared_ptr< Report >	ReportOP

typedef utility::pointer::shared_ptr< Report const >	ReportCOP

typedef utility::pointer::shared_ptr< ReportToDB >	ReportToDBOP

typedef utility::pointer::shared_ptr< ReportToDB const >	ReportToDBCOP

typedef utility::pointer::shared_ptr< ResidueBurialFeatures >	ResidueBurialFeaturesOP

typedef utility::pointer::shared_ptr< ResidueBurialFeatures const >	ResidueBurialFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueConformationFeatures >	ResidueConformationFeaturesOP

typedef utility::pointer::shared_ptr< ResidueConformationFeatures const >	ResidueConformationFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueFeatures >	ResidueFeaturesOP

typedef utility::pointer::shared_ptr< ResidueFeatures const >	ResidueFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueGridScoresFeatures >	ResidueGridScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueGridScoresFeatures const >	ResidueGridScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueScoresFeatures >	ResidueScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueScoresFeatures const >	ResidueScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueSecondaryStructureFeatures >	ResidueSecondaryStructureFeaturesOP

typedef utility::pointer::shared_ptr< ResidueSecondaryStructureFeatures const >	ResidueSecondaryStructureFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueTotalScoresFeatures >	ResidueTotalScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueTotalScoresFeatures const >	ResidueTotalScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueTypesFeatures >	ResidueTypesFeaturesOP

typedef utility::pointer::shared_ptr< ResidueTypesFeatures const >	ResidueTypesFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeightFeatures >	RotamerBoltzmannWeightFeaturesOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeightFeatures const >	RotamerBoltzmannWeightFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerFeatures >	RotamerFeaturesOP

typedef utility::pointer::shared_ptr< RotamerFeatures const >	RotamerFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFeatures >	RotamerRecoveryFeaturesOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFeatures const >	RotamerRecoveryFeaturesCOP

typedef utility::pointer::shared_ptr< RuntimeFeatures >	RuntimeFeaturesOP

typedef utility::pointer::shared_ptr< RuntimeFeatures const >	RuntimeFeaturesCOP

typedef utility::pointer::shared_ptr< SaltBridgeFeatures >	SaltBridgeFeaturesOP

typedef utility::pointer::shared_ptr< SaltBridgeFeatures const >	SaltBridgeFeaturesCOP

typedef utility::pointer::shared_ptr< ScoreFunctionFeatures >	ScoreFunctionFeaturesOP

typedef utility::pointer::shared_ptr< ScoreFunctionFeatures const >	ScoreFunctionFeaturesCOP

typedef utility::pointer::shared_ptr< ScoreTypeFeatures >	ScoreTypeFeaturesOP

typedef utility::pointer::shared_ptr< ScoreTypeFeatures const >	ScoreTypeFeaturesCOP

typedef utility::pointer::shared_ptr< ScreeningFeatures >	ScreeningFeaturesOP

typedef utility::pointer::shared_ptr< ScreeningFeatures const >	ScreeningFeaturesCOP

typedef utility::pointer::shared_ptr< SecondaryStructureSegmentFeatures >	SecondaryStructureSegmentFeaturesOP

typedef utility::pointer::shared_ptr< SecondaryStructureSegmentFeatures const >	SecondaryStructureSegmentFeaturesCOP

typedef utility::pointer::shared_ptr< SimpleMetricFeatures >	SimpleMetricFeaturesOP

typedef utility::pointer::shared_ptr< SimpleMetricFeatures const >	SimpleMetricFeaturesCOP

typedef utility::pointer::shared_ptr< StructureFeatures >	StructureFeaturesOP

typedef utility::pointer::shared_ptr< StructureFeatures const >	StructureFeaturesCOP

typedef utility::pointer::shared_ptr< StructureScoresFeatures >	StructureScoresFeaturesOP

typedef utility::pointer::shared_ptr< StructureScoresFeatures const >	StructureScoresFeaturesCOP

typedef utility::pointer::shared_ptr< TaskOperationFeatures >	TaskOperationFeaturesOP

typedef utility::pointer::shared_ptr< TaskOperationFeatures const >	TaskOperationFeaturesCOP

typedef utility::pointer::shared_ptr< TotalScoreFeatures >	TotalScoreFeaturesOP

typedef utility::pointer::shared_ptr< TotalScoreFeatures const >	TotalScoreFeaturesCOP

typedef utility::pointer::shared_ptr< TrajectoryMapFeatures >	TrajectoryMapFeaturesOP

typedef utility::pointer::shared_ptr< TrajectoryMapFeatures const >	TrajectoryMapFeaturesCOP

typedef utility::pointer::shared_ptr< TrajectoryReportToDB >	TrajectoryReportToDBOP

typedef utility::pointer::shared_ptr< TrajectoryReportToDB const >	TrajectoryReportToDBCOP

typedef utility::pointer::shared_ptr< UnrecognizedAtomFeatures >	UnrecognizedAtomFeaturesOP

typedef utility::pointer::shared_ptr< UnrecognizedAtomFeatures const >	UnrecognizedAtomFeaturesCOP

typedef utility::pointer::shared_ptr< WaterFeatures >	WaterFeaturesOP

typedef utility::pointer::shared_ptr< WaterFeatures const >	WaterFeaturesCOP

Enumerations
enum	RamachandranHash { A = 1 , B , L , E , number_of_ramachandran_hashes = E }

enum	HBDefType { hbdef_NONE = 1 , hbdef_ENERGY , hbdef_AHDIST , hbdef_MAX = hbdef_AHDIST }
	How a hydrogen bond should be defined See note for definition_type_ below. More...

Functions
static Tracer	TR ("protocols.features.AtomAtomPairFeatures")

static Tracer	TR ("protocols.features.AtomTypesFeatures")

static basic::Tracer	TR ("protocols.features.BatchFeatures")

static basic::Tracer	TR ("protocols.features.DatabaseFilters")

core::Real	get_current_model_score (core::pose::Pose const &pose, core::Size score_type_id)

DatabaseFilterOP	get_DB_filter_ptr ()

WriteDeletePair	get_write_delete_pair (core::pose::Pose const &pose, utility::sql_database::sessionOP db_session, core::Size const &protocol_id, core::Size const &count, std::string const &score_term, std::string current_input="")

template<class T >
T	get_something_from_database (cppdb::statement statement, T)

cppdb::statement	get_structure_count_statement (utility::sql_database::sessionOP db_session, std::string const &input_tag, core::Size const &protocol_id)

core::Size	get_score_type_id_from_score_term (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &score_term)

cppdb::statement	get_nth_lowest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)

cppdb::statement	get_nth_lowest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)

cppdb::statement	get_highest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, std::string const &input_tag, core::Size const &protocol_id)

cppdb::statement	get_highest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, std::string const &input_tag, core::Size const &protocol_id)

core::Size	get_current_structure_count (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_nth_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_nth_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_highest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)

StructureID	get_struct_id_with_highest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)

core::Real	get_score_for_struct_id_and_score_term_from_job_data (utility::sql_database::sessionOP db_session, StructureID const &struct_id, std::string const &score_term)

core::Real	get_score_for_struct_id_and_score_term_from_score_data (utility::sql_database::sessionOP db_session, StructureID const &struct_id, core::Size const &score_type_id)

static basic::Tracer	TR ("protocols.features.DdGFeatures")

std::string	complex_type_name_for_features_reporter (std::string const &features_reporter_name)

void	xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &features_reporter_type, std::string const &description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a Features_Reporter that contains no subtags but may contain any number of attributes (aka options). More...

void	xsd_type_definition_w_attributes_and_repeatable_subelements (utility::tag::XMLSchemaDefinition &xsd, std::string const &features_reporter_type, std::string const &description, utility::tag::AttributeList const &attributes, utility::tag::XMLSchemaSimpleSubelementList const &subelements)

static Tracer	TR ("protocols.features.FeaturesReporter")

static basic::Tracer	tr ("protocols.features.FeaturesReporterFactory")

static Tracer	TR ("protocols.features.HBondFeatures")

static Tracer	TR ("protocols.features.HBondParameterFeatures")

static basic::Tracer	TR ("protocols.features.LoopAnchorFeatures")

static basic::Tracer	TR ("protocols.features.PdbDataFeatures")

static basic::Tracer	TR ("protocols.features.PoseConformationFeatures")

static basic::Tracer	TR ("protocols.features.ProteinBondGeometry")

static basic::Tracer	TR ("protocols.features.ProteinResidueConformationFeatures")

static basic::Tracer	tr ("protocols.features.ProteinRMSDFeatures")

static basic::Tracer	tr ("protocols.features.ProteinRMSDNoSuperpositionFeatures")

static basic::Tracer	TR ("protocols.features.ProteinSilentReport")

static Tracer	TR ("protocols.features.ReportToDB")

static basic::Tracer	TR ("protocols.features.ResidueFeatures")

static Tracer	TR ("protocols.features.ResidueSecondaryStructureFeatures")

static basic::Tracer	TR ("protocols.features.ResidueTotalScoresFeatures")

static Tracer	TR ("protocols.features.ResidueTypesFeatures")

static basic::Tracer	TR ("protocols.features.RotamerFeatures")

static Tracer	TR ("protocols.features.RotamerRecoveryFeatures")

static basic::Tracer	TR ("protocols.features.SimpleMetricFeatures")

static basic::Tracer	TR ("protocols.features.SmotifFeatures")

static basic::Tracer	TR ("protocols.features.StructureScoresFeatures")

static Tracer	TR ("protocols.features.TaskOperationFeatures")

static basic::Tracer	TR ("protocols.features.TrajectoryMapFeatures")

static basic::Tracer	TR ("protocols.features.TrajectoryReportToDB")

static basic::Tracer	TR ("protocols.features.UnrecognizedAtomFeatures")

static Tracer	TR ("protocols.features.util")

void	set_protocol_and_batch_id (core::Size protocol_id, core::Size batch_id, string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
	write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing) More...

pair< core::Size, core::Size >	get_protocol_and_batch_id (string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
	Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info. More...

void	write_features_reporters_table (utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)

void	write_batch_reports_table (utility::vector1< FeaturesReporterOP > features_reporters, core::Size batch_id, utility::sql_database::sessionOP db_session)
	write the linking table between features reporters and batches. This happens here so that the protocol/batch id framework can be used to prevent duplicate key entries. This function gets called when the batch id is written. More...

pair< core::Size, core::Size >	deserialize_db_listener_data (string data)

string	serialize_ids (int protocol_id, string batch_name, core::Size batch_id)

Size	get_batch_id (StructureID struct_id, sessionOP db_session)

utility::vector1< StructureID >	struct_ids_from_tag (sessionOP db_session, string const &tag)

std::string	serialize_residue_xyz_coords (core::conformation::Residue const &residue)

utility::vector1< numeric::xyzVector< core::Real > >	deserialize_xyz_coords (std::string const &data, core::Size natoms)

std::string	get_question_mark_string (core::Size const n)
	Returns (?,?,?) With question marks of length n to help create database query. More...

void	set_protocol_and_batch_id (core::Size protocol_id, core::Size batch_id, std::string const &batch_name, std::string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)
	write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing) More...

std::pair< core::Size, core::Size >	get_protocol_and_batch_id (std::string const &batch_name, std::string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)
	Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info. More...

core::Size	get_batch_id (StructureID struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StructureID >	struct_ids_from_tag (utility::sql_database::sessionOP db_session, std::string const &tag)

Variables
Size	static_protocol_id_ = 0

bool	protocol_table_initialized_ = false

map< string, core::Size >	static_batch_id_map_

Typedef Documentation

◆ AtomAtomPairFeaturesCOP

typedef utility::pointer::shared_ptr< AtomAtomPairFeatures const > protocols::features::AtomAtomPairFeaturesCOP

◆ AtomAtomPairFeaturesOP

typedef utility::pointer::shared_ptr< AtomAtomPairFeatures > protocols::features::AtomAtomPairFeaturesOP

◆ AtomInResidueAtomInResiduePairFeaturesCOP

typedef utility::pointer::shared_ptr< AtomInResidueAtomInResiduePairFeatures const > protocols::features::AtomInResidueAtomInResiduePairFeaturesCOP

◆ AtomInResidueAtomInResiduePairFeaturesOP

typedef utility::pointer::shared_ptr< AtomInResidueAtomInResiduePairFeatures > protocols::features::AtomInResidueAtomInResiduePairFeaturesOP

◆ AtomTypesFeaturesCOP

typedef utility::pointer::shared_ptr< AtomTypesFeatures const > protocols::features::AtomTypesFeaturesCOP

◆ AtomTypesFeaturesOP

typedef utility::pointer::shared_ptr< AtomTypesFeatures > protocols::features::AtomTypesFeaturesOP

◆ BatchFeaturesCOP

typedef utility::pointer::shared_ptr< BatchFeatures const > protocols::features::BatchFeaturesCOP

◆ BatchFeaturesOP

typedef utility::pointer::shared_ptr< BatchFeatures > protocols::features::BatchFeaturesOP

◆ BetaTurnDetectionCOP

typedef utility::pointer::shared_ptr< BetaTurnDetection const > protocols::features::BetaTurnDetectionCOP

◆ BetaTurnDetectionFeaturesCOP

typedef utility::pointer::shared_ptr< BetaTurnDetectionFeatures const > protocols::features::BetaTurnDetectionFeaturesCOP

◆ BetaTurnDetectionFeaturesOP

typedef utility::pointer::shared_ptr< BetaTurnDetectionFeatures > protocols::features::BetaTurnDetectionFeaturesOP

◆ BetaTurnDetectionOP

typedef utility::pointer::shared_ptr< BetaTurnDetection > protocols::features::BetaTurnDetectionOP

◆ BondAngleDatabaseOP

typedef utility::pointer::shared_ptr< BondAngleDatabase > protocols::features::BondAngleDatabaseOP

◆ ChargeChargeFeaturesCOP

typedef utility::pointer::shared_ptr< ChargeChargeFeatures const > protocols::features::ChargeChargeFeaturesCOP

◆ ChargeChargeFeaturesOP

typedef utility::pointer::shared_ptr< ChargeChargeFeatures > protocols::features::ChargeChargeFeaturesOP

◆ DatabaseFilterCOP

typedef utility::pointer::shared_ptr< DatabaseFilter const > protocols::features::DatabaseFilterCOP

◆ DatabaseFilterOP

typedef utility::pointer::shared_ptr< DatabaseFilter > protocols::features::DatabaseFilterOP

◆ DatabaseJobInputterOP

typedef utility::pointer::shared_ptr< DatabaseJobInputter > protocols::features::DatabaseJobInputterOP

◆ DatabaseJobOutputterOP

typedef utility::pointer::shared_ptr< DatabaseJobOutputter > protocols::features::DatabaseJobOutputterOP

◆ DdGFeaturesCOP

typedef utility::pointer::shared_ptr< DdGFeatures const > protocols::features::DdGFeaturesCOP

◆ DdGFeaturesOP

typedef utility::pointer::shared_ptr< DdGFeatures > protocols::features::DdGFeaturesOP

◆ FeaturesReporterCOP

typedef utility::pointer::shared_ptr< FeaturesReporter const > protocols::features::FeaturesReporterCOP

◆ FeaturesReporterCreatorCOP

typedef utility::pointer::shared_ptr< FeaturesReporterCreator const > protocols::features::FeaturesReporterCreatorCOP

◆ FeaturesReporterCreatorOP

typedef utility::pointer::shared_ptr< FeaturesReporterCreator > protocols::features::FeaturesReporterCreatorOP

◆ FeaturesReporterOP

typedef utility::pointer::shared_ptr< FeaturesReporter > protocols::features::FeaturesReporterOP

◆ GeometricSolvationFeaturesCOP

typedef utility::pointer::shared_ptr< GeometricSolvationFeatures const > protocols::features::GeometricSolvationFeaturesCOP

◆ GeometricSolvationFeaturesOP

typedef utility::pointer::shared_ptr< GeometricSolvationFeatures > protocols::features::GeometricSolvationFeaturesOP

◆ HBondFeaturesCOP

typedef utility::pointer::shared_ptr< HBondFeatures const > protocols::features::HBondFeaturesCOP

◆ HBondFeaturesOP

typedef utility::pointer::shared_ptr< HBondFeatures > protocols::features::HBondFeaturesOP

◆ HBondParameterFeaturesCOP

typedef utility::pointer::shared_ptr< HBondParameterFeatures const > protocols::features::HBondParameterFeaturesCOP

◆ HBondParameterFeaturesOP

typedef utility::pointer::shared_ptr< HBondParameterFeatures > protocols::features::HBondParameterFeaturesOP

◆ InteractionEdge

typedef boost::graph_traits<SegmentGraph>::edge_descriptor protocols::features::InteractionEdge

◆ InterfaceDdGMoverCOP

typedef utility::pointer::shared_ptr< InterfaceDdGMover const > protocols::features::InterfaceDdGMoverCOP

◆ InterfaceDdGMoverOP

typedef utility::pointer::shared_ptr< InterfaceDdGMover > protocols::features::InterfaceDdGMoverOP

◆ InterfaceFeaturesCOP

typedef utility::pointer::shared_ptr< InterfaceFeatures const > protocols::features::InterfaceFeaturesCOP

◆ InterfaceFeaturesOP

typedef utility::pointer::shared_ptr< protocols::features::InterfaceFeatures > protocols::features::InterfaceFeaturesOP

◆ JobDataFeaturesCOP

typedef utility::pointer::shared_ptr<JobDataFeatures const> protocols::features::JobDataFeaturesCOP

◆ JobDataFeaturesOP

typedef utility::pointer::shared_ptr<JobDataFeatures> protocols::features::JobDataFeaturesOP

◆ LoopAnchorFeaturesCOP

typedef utility::pointer::shared_ptr< LoopAnchorFeatures const > protocols::features::LoopAnchorFeaturesCOP

◆ LoopAnchorFeaturesOP

typedef utility::pointer::shared_ptr< LoopAnchorFeatures > protocols::features::LoopAnchorFeaturesOP

◆ ModelFeaturesCOP

typedef utility::pointer::shared_ptr< ModelFeatures const > protocols::features::ModelFeaturesCOP

◆ ModelFeaturesOP

typedef utility::pointer::shared_ptr< ModelFeatures > protocols::features::ModelFeaturesOP

◆ OrbitalsFeaturesCOP

typedef utility::pointer::shared_ptr< OrbitalsFeatures const > protocols::features::OrbitalsFeaturesCOP

◆ OrbitalsFeaturesOP

typedef utility::pointer::shared_ptr< OrbitalsFeatures > protocols::features::OrbitalsFeaturesOP

◆ PairFeaturesCOP

typedef utility::pointer::shared_ptr< PairFeatures const > protocols::features::PairFeaturesCOP

◆ PairFeaturesOP

typedef utility::pointer::shared_ptr< PairFeatures > protocols::features::PairFeaturesOP

◆ PdbDataFeaturesOP

typedef utility::pointer::shared_ptr< PdbDataFeatures > protocols::features::PdbDataFeaturesOP

◆ PoseCommentsFeaturesCOP

typedef utility::pointer::shared_ptr< PoseCommentsFeatures const > protocols::features::PoseCommentsFeaturesCOP

◆ PoseCommentsFeaturesOP

typedef utility::pointer::shared_ptr< PoseCommentsFeatures > protocols::features::PoseCommentsFeaturesOP

◆ PoseConformationFeaturesCOP

typedef utility::pointer::shared_ptr< PoseConformationFeatures const > protocols::features::PoseConformationFeaturesCOP

◆ PoseConformationFeaturesOP

typedef utility::pointer::shared_ptr< PoseConformationFeatures > protocols::features::PoseConformationFeaturesOP

◆ ProteinBackboneAtomAtomPairFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBackboneAtomAtomPairFeatures const > protocols::features::ProteinBackboneAtomAtomPairFeaturesCOP

◆ ProteinBackboneAtomAtomPairFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBackboneAtomAtomPairFeatures > protocols::features::ProteinBackboneAtomAtomPairFeaturesOP

◆ ProteinBackboneTorsionAngleFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBackboneTorsionAngleFeatures const > protocols::features::ProteinBackboneTorsionAngleFeaturesCOP

◆ ProteinBackboneTorsionAngleFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBackboneTorsionAngleFeatures > protocols::features::ProteinBackboneTorsionAngleFeaturesOP

◆ ProteinBondGeometryFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinBondGeometryFeatures const > protocols::features::ProteinBondGeometryFeaturesCOP

◆ ProteinBondGeometryFeaturesOP

typedef utility::pointer::shared_ptr< ProteinBondGeometryFeatures > protocols::features::ProteinBondGeometryFeaturesOP

◆ ProteinResidueConformationFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinResidueConformationFeatures const > protocols::features::ProteinResidueConformationFeaturesCOP

◆ ProteinResidueConformationFeaturesOP

typedef utility::pointer::shared_ptr< ProteinResidueConformationFeatures > protocols::features::ProteinResidueConformationFeaturesOP

◆ ProteinRMSDFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinRMSDFeatures const > protocols::features::ProteinRMSDFeaturesCOP

◆ ProteinRMSDFeaturesOP

typedef utility::pointer::shared_ptr< ProteinRMSDFeatures > protocols::features::ProteinRMSDFeaturesOP

◆ ProteinRMSDNoSuperpositionFeaturesCOP

typedef utility::pointer::shared_ptr< ProteinRMSDNoSuperpositionFeatures const > protocols::features::ProteinRMSDNoSuperpositionFeaturesCOP

◆ ProteinRMSDNoSuperpositionFeaturesOP

typedef utility::pointer::shared_ptr< ProteinRMSDNoSuperpositionFeatures > protocols::features::ProteinRMSDNoSuperpositionFeaturesOP

◆ ProteinSilentReportCOP

typedef utility::pointer::shared_ptr< ProteinSilentReport const > protocols::features::ProteinSilentReportCOP

◆ ProteinSilentReportOP

typedef utility::pointer::shared_ptr< ProteinSilentReport > protocols::features::ProteinSilentReportOP

◆ ProtocolFeaturesCOP

typedef utility::pointer::shared_ptr< ProtocolFeatures const > protocols::features::ProtocolFeaturesCOP

◆ ProtocolFeaturesOP

typedef utility::pointer::shared_ptr< ProtocolFeatures > protocols::features::ProtocolFeaturesOP

◆ RadiusOfGyrationFeaturesCOP

typedef utility::pointer::shared_ptr< RadiusOfGyrationFeatures const > protocols::features::RadiusOfGyrationFeaturesCOP

◆ RadiusOfGyrationFeaturesOP

typedef utility::pointer::shared_ptr< RadiusOfGyrationFeatures > protocols::features::RadiusOfGyrationFeaturesOP

◆ ReportCOP

typedef utility::pointer::shared_ptr< Report const > protocols::features::ReportCOP

◆ ReportOP

typedef utility::pointer::shared_ptr< Report > protocols::features::ReportOP

◆ ReportToDBCOP

typedef utility::pointer::shared_ptr< ReportToDB const > protocols::features::ReportToDBCOP

◆ ReportToDBOP

typedef utility::pointer::shared_ptr< ReportToDB > protocols::features::ReportToDBOP

◆ ResidueBurialFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueBurialFeatures const > protocols::features::ResidueBurialFeaturesCOP

◆ ResidueBurialFeaturesOP

typedef utility::pointer::shared_ptr< ResidueBurialFeatures > protocols::features::ResidueBurialFeaturesOP

◆ ResidueConformationFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueConformationFeatures const > protocols::features::ResidueConformationFeaturesCOP

◆ ResidueConformationFeaturesOP

typedef utility::pointer::shared_ptr< ResidueConformationFeatures > protocols::features::ResidueConformationFeaturesOP

◆ ResidueFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueFeatures const > protocols::features::ResidueFeaturesCOP

◆ ResidueFeaturesOP

typedef utility::pointer::shared_ptr< ResidueFeatures > protocols::features::ResidueFeaturesOP

◆ ResidueGridScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueGridScoresFeatures const > protocols::features::ResidueGridScoresFeaturesCOP

◆ ResidueGridScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueGridScoresFeatures > protocols::features::ResidueGridScoresFeaturesOP

◆ ResidueScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueScoresFeatures const > protocols::features::ResidueScoresFeaturesCOP

◆ ResidueScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueScoresFeatures > protocols::features::ResidueScoresFeaturesOP

◆ ResidueSecondaryStructureFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueSecondaryStructureFeatures const > protocols::features::ResidueSecondaryStructureFeaturesCOP

◆ ResidueSecondaryStructureFeaturesOP

typedef utility::pointer::shared_ptr< ResidueSecondaryStructureFeatures > protocols::features::ResidueSecondaryStructureFeaturesOP

◆ ResidueTotalScoresFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueTotalScoresFeatures const > protocols::features::ResidueTotalScoresFeaturesCOP

◆ ResidueTotalScoresFeaturesOP

typedef utility::pointer::shared_ptr< ResidueTotalScoresFeatures > protocols::features::ResidueTotalScoresFeaturesOP

◆ ResidueTypesFeaturesCOP

typedef utility::pointer::shared_ptr< ResidueTypesFeatures const > protocols::features::ResidueTypesFeaturesCOP

◆ ResidueTypesFeaturesOP

typedef utility::pointer::shared_ptr< ResidueTypesFeatures > protocols::features::ResidueTypesFeaturesOP

◆ RotamerBoltzmannWeightFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeightFeatures const > protocols::features::RotamerBoltzmannWeightFeaturesCOP

◆ RotamerBoltzmannWeightFeaturesOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeightFeatures > protocols::features::RotamerBoltzmannWeightFeaturesOP

◆ RotamerFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerFeatures const > protocols::features::RotamerFeaturesCOP

◆ RotamerFeaturesOP

typedef utility::pointer::shared_ptr< RotamerFeatures > protocols::features::RotamerFeaturesOP

◆ RotamerRecoveryFeaturesCOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFeatures const > protocols::features::RotamerRecoveryFeaturesCOP

◆ RotamerRecoveryFeaturesOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFeatures > protocols::features::RotamerRecoveryFeaturesOP

◆ RuntimeFeaturesCOP

typedef utility::pointer::shared_ptr<RuntimeFeatures const> protocols::features::RuntimeFeaturesCOP

◆ RuntimeFeaturesOP

typedef utility::pointer::shared_ptr<RuntimeFeatures> protocols::features::RuntimeFeaturesOP

◆ SaltBridgeFeaturesCOP

typedef utility::pointer::shared_ptr< SaltBridgeFeatures const > protocols::features::SaltBridgeFeaturesCOP

◆ SaltBridgeFeaturesOP

typedef utility::pointer::shared_ptr< SaltBridgeFeatures > protocols::features::SaltBridgeFeaturesOP

◆ ScoreFunctionFeaturesCOP

typedef utility::pointer::shared_ptr< ScoreFunctionFeatures const > protocols::features::ScoreFunctionFeaturesCOP

◆ ScoreFunctionFeaturesOP

typedef utility::pointer::shared_ptr< ScoreFunctionFeatures > protocols::features::ScoreFunctionFeaturesOP

◆ ScoreTypeFeaturesCOP

typedef utility::pointer::shared_ptr< ScoreTypeFeatures const > protocols::features::ScoreTypeFeaturesCOP

◆ ScoreTypeFeaturesOP

typedef utility::pointer::shared_ptr< ScoreTypeFeatures > protocols::features::ScoreTypeFeaturesOP

◆ ScreeningFeaturesCOP

typedef utility::pointer::shared_ptr<ScreeningFeatures const> protocols::features::ScreeningFeaturesCOP

◆ ScreeningFeaturesOP

typedef utility::pointer::shared_ptr<ScreeningFeatures> protocols::features::ScreeningFeaturesOP

◆ SecondaryStructureSegmentFeaturesCOP

typedef utility::pointer::shared_ptr< SecondaryStructureSegmentFeatures const > protocols::features::SecondaryStructureSegmentFeaturesCOP

◆ SecondaryStructureSegmentFeaturesOP

typedef utility::pointer::shared_ptr< SecondaryStructureSegmentFeatures > protocols::features::SecondaryStructureSegmentFeaturesOP

◆ SegmentGraph

typedef boost::undirected_graph<core::Size> protocols::features::SegmentGraph

◆ SegmentVertex

typedef boost::graph_traits<SegmentGraph>::vertex_descriptor protocols::features::SegmentVertex

◆ SimpleMetricFeaturesCOP

typedef utility::pointer::shared_ptr< SimpleMetricFeatures const > protocols::features::SimpleMetricFeaturesCOP

◆ SimpleMetricFeaturesOP

typedef utility::pointer::shared_ptr< SimpleMetricFeatures > protocols::features::SimpleMetricFeaturesOP

◆ StructureFeaturesCOP

typedef utility::pointer::shared_ptr< StructureFeatures const > protocols::features::StructureFeaturesCOP

◆ StructureFeaturesOP

typedef utility::pointer::shared_ptr< StructureFeatures > protocols::features::StructureFeaturesOP

◆ StructureID

typedef std::uint64_t protocols::features::StructureID

◆ StructureScoresFeaturesCOP

typedef utility::pointer::shared_ptr< StructureScoresFeatures const > protocols::features::StructureScoresFeaturesCOP

◆ StructureScoresFeaturesOP

typedef utility::pointer::shared_ptr< StructureScoresFeatures > protocols::features::StructureScoresFeaturesOP

◆ TaskOperationFeaturesCOP

typedef utility::pointer::shared_ptr< TaskOperationFeatures const > protocols::features::TaskOperationFeaturesCOP

◆ TaskOperationFeaturesOP

typedef utility::pointer::shared_ptr< TaskOperationFeatures > protocols::features::TaskOperationFeaturesOP

◆ TotalScoreFeaturesCOP

typedef utility::pointer::shared_ptr<TotalScoreFeatures const> protocols::features::TotalScoreFeaturesCOP

◆ TotalScoreFeaturesOP

typedef utility::pointer::shared_ptr<TotalScoreFeatures> protocols::features::TotalScoreFeaturesOP

◆ TrajectoryMapFeaturesCOP

typedef utility::pointer::shared_ptr< TrajectoryMapFeatures const > protocols::features::TrajectoryMapFeaturesCOP

◆ TrajectoryMapFeaturesOP

typedef utility::pointer::shared_ptr< TrajectoryMapFeatures > protocols::features::TrajectoryMapFeaturesOP

◆ TrajectoryReportToDBCOP

typedef utility::pointer::shared_ptr< TrajectoryReportToDB const > protocols::features::TrajectoryReportToDBCOP

◆ TrajectoryReportToDBOP

typedef utility::pointer::shared_ptr< TrajectoryReportToDB > protocols::features::TrajectoryReportToDBOP

◆ UnrecognizedAtomFeaturesCOP

typedef utility::pointer::shared_ptr< UnrecognizedAtomFeatures const > protocols::features::UnrecognizedAtomFeaturesCOP

◆ UnrecognizedAtomFeaturesOP

typedef utility::pointer::shared_ptr< UnrecognizedAtomFeatures > protocols::features::UnrecognizedAtomFeaturesOP

◆ WaterFeaturesCOP

typedef utility::pointer::shared_ptr< WaterFeatures const > protocols::features::WaterFeaturesCOP

◆ WaterFeaturesOP

typedef utility::pointer::shared_ptr< WaterFeatures > protocols::features::WaterFeaturesOP

◆ WriteDeletePair

typedef std::pair<bool, utility::vector1<StructureID> > protocols::features::WriteDeletePair

Enumeration Type Documentation

◆ HBDefType

enum protocols::features::HBDefType

How a hydrogen bond should be defined See note for definition_type_ below.

Enumerator
hbdef_NONE
hbdef_ENERGY
hbdef_AHDIST
hbdef_MAX

◆ RamachandranHash

enum protocols::features::RamachandranHash

Enumerator
A
B
L
E
number_of_ramachandran_hashes

Function Documentation

◆ complex_type_name_for_features_reporter()

std::string protocols::features::complex_type_name_for_features_reporter ( std::string const & features_reporter_name )

Referenced by protocols::features::FeaturesReporterFactory::define_features_reporter_xml_schema_group(), xsd_type_definition_w_attributes(), and xsd_type_definition_w_attributes_and_repeatable_subelements().

◆ deserialize_db_listener_data()

std::pair< core::Size, core::Size > protocols::features::deserialize_db_listener_data ( string data )

References protocols::sparta::split().

Referenced by get_protocol_and_batch_id().

◆ deserialize_xyz_coords()

utility::vector1< numeric::xyzVector< core::Real > > protocols::features::deserialize_xyz_coords	(	std::string const &	data,
		core::Size	natoms
	)

Note: This function uses new and delete, but cleans up its own heap data.

Referenced by protocols::features::ProteinResidueConformationFeatures::set_coords_for_residue_from_compact_schema(), and protocols::features::ResidueConformationFeatures::set_coords_for_residue_from_compact_schema().

◆ get_batch_id() [1/2]

Size protocols::features::get_batch_id	(	StructureID	struct_id,
		sessionOP	db_session
	)

@detail look up the batch id given a struct id. Note this should only be used once the structure's table has been created, eg in an average features reporter's report_features function.

Referenced by protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), protocols::features::StructureScoresFeatures::insert_structure_score_rows(), and protocols::features::ScoreFunctionFeatures::report_features().

◆ get_batch_id() [2/2]

core::Size protocols::features::get_batch_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

◆ get_current_model_score()

core::Real protocols::features::get_current_model_score	(	core::pose::Pose const &	pose,
		core::Size	score_type_id
	)

References core::pose::Pose::energies(), core::scoring::get_score_function(), core::pose::Pose::size(), and core::scoring::Energies::weights().

Referenced by get_write_delete_pair().

◆ get_current_structure_count()

core::Size protocols::features::get_current_structure_count	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_something_from_database(), and get_structure_count_statement().

Referenced by get_write_delete_pair().

◆ get_DB_filter_ptr()

DatabaseFilterOP protocols::features::get_DB_filter_ptr ( )

Referenced by protocols::features::ProteinSilentReport::ProteinSilentReport().

◆ get_highest_score_from_job_data_statement()

cppdb::statement protocols::features::get_highest_score_from_job_data_statement	(	utility::sql_database::sessionOP	db_session,
		std::string const &	score_term,
		std::string const &	input_tag,
		core::Size const &	protocol_id
	)

Referenced by get_struct_id_with_highest_score_from_job_data().

◆ get_highest_score_from_score_data_statement()

cppdb::statement protocols::features::get_highest_score_from_score_data_statement	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	score_type_id,
		std::string const &	input_tag,
		core::Size const &	protocol_id
	)

Referenced by get_struct_id_with_highest_score_from_score_data().

◆ get_nth_lowest_score_from_job_data_statement()

cppdb::statement protocols::features::get_nth_lowest_score_from_job_data_statement	(	utility::sql_database::sessionOP	db_session,
		std::string const &	score_term,
		core::Size const &	cutoff_index,
		std::string const &	input_tag,
		core::Size const &	protocol_id
	)

Referenced by get_struct_id_with_nth_lowest_score_from_job_data().

◆ get_nth_lowest_score_from_score_data_statement()

cppdb::statement protocols::features::get_nth_lowest_score_from_score_data_statement	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	score_type_id,
		core::Size const &	cutoff_index,
		std::string const &	input_tag,
		core::Size const &	protocol_id
	)

Referenced by get_struct_id_with_nth_lowest_score_from_score_data().

◆ get_protocol_and_batch_id() [1/2]

std::pair<core::Size, core::Size> protocols::features::get_protocol_and_batch_id	(	std::string const &	batch_name,
		std::string const &	batch_description,
		utility::vector1< FeaturesReporterOP >	features_reporters,
		utility::sql_database::sessionOP	db_session
	)

Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info.

◆ get_protocol_and_batch_id() [2/2]

pair<core::Size, core::Size> protocols::features::get_protocol_and_batch_id	(	string const &	batch_name,
		string const &	batch_description,
		utility::vector1< FeaturesReporterOP >	features_reporters,
		sessionOP	db_session
	)

Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info.

References deserialize_db_listener_data(), serialize_ids(), TR(), write_batch_reports_table(), and write_features_reporters_table().

Referenced by protocols::features::ReportToDB::apply(), and protocols::features::ProteinSilentReport::write_protocol_report().

◆ get_question_mark_string()

std::string protocols::features::get_question_mark_string ( core::Size const n )

Returns (?,?,?) With question marks of length n to help create database query.

Referenced by protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features(), protocols::antibody::AntibodyFeatures::report_ab_metrics_features(), protocols::antibody::AntibodyFeatures::report_cdr_metrics_features(), protocols::antibody::AntibodyFeatures::report_cdr_residue_features_row(), protocols::features::SimpleMetricFeatures::report_general_features(), protocols::features::InterfaceFeatures::report_interface_features(), protocols::features::InterfaceFeatures::report_interface_side_features(), protocols::features::InterfaceFeatures::write_interface_residue_data_row_to_db(), and protocols::features::SimpleMetricFeatures::write_per_residue_data_row().

◆ get_score_for_struct_id_and_score_term_from_job_data()

core::Real protocols::features::get_score_for_struct_id_and_score_term_from_job_data	(	utility::sql_database::sessionOP	db_session,
		StructureID const &	struct_id,
		std::string const &	score_term
	)

References get_something_from_database().

Referenced by get_write_delete_pair().

◆ get_score_for_struct_id_and_score_term_from_score_data()

core::Real protocols::features::get_score_for_struct_id_and_score_term_from_score_data	(	utility::sql_database::sessionOP	db_session,
		StructureID const &	struct_id,
		core::Size const &	score_type_id
	)

References get_something_from_database().

Referenced by get_write_delete_pair().

◆ get_score_type_id_from_score_term()

core::Size protocols::features::get_score_type_id_from_score_term	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	protocol_id,
		std::string const &	score_term
	)

References get_something_from_database().

Referenced by get_write_delete_pair().

◆ get_something_from_database()

template<class T >

T protocols::features::get_something_from_database	(	cppdb::statement	statement,
		T
	)

Referenced by get_current_structure_count(), get_score_for_struct_id_and_score_term_from_job_data(), get_score_for_struct_id_and_score_term_from_score_data(), get_score_type_id_from_score_term(), get_struct_id_with_highest_score_from_job_data(), get_struct_id_with_highest_score_from_score_data(), get_struct_id_with_nth_lowest_score_from_job_data(), and get_struct_id_with_nth_lowest_score_from_score_data().

◆ get_struct_id_with_highest_score_from_job_data()

StructureID protocols::features::get_struct_id_with_highest_score_from_job_data	(	utility::sql_database::sessionOP	db_session,
		std::string const &	score_term,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_highest_score_from_job_data_statement(), and get_something_from_database().

Referenced by get_write_delete_pair().

◆ get_struct_id_with_highest_score_from_score_data()

StructureID protocols::features::get_struct_id_with_highest_score_from_score_data	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	score_type_id,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_highest_score_from_score_data_statement(), get_something_from_database(), and core::id::to_string().

Referenced by get_write_delete_pair().

◆ get_struct_id_with_lowest_score_from_job_data()

StructureID protocols::features::get_struct_id_with_lowest_score_from_job_data	(	utility::sql_database::sessionOP	db_session,
		std::string const &	score_term,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_struct_id_with_nth_lowest_score_from_job_data().

◆ get_struct_id_with_lowest_score_from_score_data()

StructureID protocols::features::get_struct_id_with_lowest_score_from_score_data	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	score_type_id,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_struct_id_with_nth_lowest_score_from_score_data().

◆ get_struct_id_with_nth_lowest_score_from_job_data()

StructureID protocols::features::get_struct_id_with_nth_lowest_score_from_job_data	(	utility::sql_database::sessionOP	db_session,
		std::string const &	score_term,
		core::Size const &	cutoff_index,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_nth_lowest_score_from_job_data_statement(), get_something_from_database(), and core::id::to_string().

Referenced by get_struct_id_with_lowest_score_from_job_data(), and get_write_delete_pair().

◆ get_struct_id_with_nth_lowest_score_from_score_data()

StructureID protocols::features::get_struct_id_with_nth_lowest_score_from_score_data	(	utility::sql_database::sessionOP	db_session,
		core::Size const &	score_type_id,
		core::Size const &	cutoff_index,
		core::Size const &	protocol_id,
		std::string const &	input_tag
	)

References get_nth_lowest_score_from_score_data_statement(), get_something_from_database(), and core::id::to_string().

Referenced by get_struct_id_with_lowest_score_from_score_data(), and get_write_delete_pair().

◆ get_structure_count_statement()

cppdb::statement protocols::features::get_structure_count_statement	(	utility::sql_database::sessionOP	db_session,
		std::string const &	input_tag,
		core::Size const &	protocol_id
	)

Referenced by get_current_structure_count().

◆ get_write_delete_pair()

WriteDeletePair protocols::features::get_write_delete_pair	(	core::pose::Pose const &	pose,
		utility::sql_database::sessionOP	db_session,
		core::Size const &	protocol_id,
		core::Size const &	count,
		std::string const &	score_term,
		std::string	current_input = `""`
	)

References get_current_model_score(), get_current_structure_count(), get_score_for_struct_id_and_score_term_from_job_data(), get_score_for_struct_id_and_score_term_from_score_data(), get_score_type_id_from_score_term(), protocols::jd2::get_string_real_pairs_from_current_job(), get_struct_id_with_highest_score_from_job_data(), get_struct_id_with_highest_score_from_score_data(), get_struct_id_with_nth_lowest_score_from_job_data(), get_struct_id_with_nth_lowest_score_from_score_data(), and TR().

Referenced by protocols::features::TopCountOfEachInput::operator()(), and protocols::features::TopCountOfAllInputs::operator()().

◆ serialize_ids()

std::string protocols::features::serialize_ids	(	int	protocol_id,
		string	batch_name,
		core::Size	batch_id
	)

References core::id::to_string().

Referenced by get_protocol_and_batch_id().

◆ serialize_residue_xyz_coords()

std::string protocols::features::serialize_residue_xyz_coords ( core::conformation::Residue const & residue )

References core::conformation::Residue::natoms(), protocols::stepwise::modeler::rna::output_data(), and core::conformation::Residue::xyz().

Referenced by protocols::features::ProteinResidueConformationFeatures::report_features(), and protocols::features::ResidueConformationFeatures::report_features().

◆ set_protocol_and_batch_id() [1/2]

void protocols::features::set_protocol_and_batch_id	(	core::Size	protocol_id,
		core::Size	batch_id,
		std::string const &	batch_name,
		std::string const &	batch_description,
		utility::vector1< FeaturesReporterOP >	features_reporters,
		utility::sql_database::sessionOP	db_session
	)

write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing)

◆ set_protocol_and_batch_id() [2/2]

void protocols::features::set_protocol_and_batch_id	(	core::Size	protocol_id,
		core::Size	batch_id,
		string const &	batch_name,
		string const &	batch_description,
		utility::vector1< FeaturesReporterOP >	features_reporters,
		sessionOP	db_session
	)

write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing)

References write_batch_reports_table(), and write_features_reporters_table().

Referenced by protocols::features::ReportToDB::apply().

◆ struct_ids_from_tag() [1/2]

utility::vector1<StructureID> protocols::features::struct_ids_from_tag	(	sessionOP	db_session,
		string const &	tag
	)

◆ struct_ids_from_tag() [2/2]

utility::vector1<StructureID> protocols::features::struct_ids_from_tag	(	utility::sql_database::sessionOP	db_session,
		std::string const &	tag
	)

◆ TR() [1/29]

static Tracer protocols::features::TR ( "protocols.features.AtomAtomPairFeatures" )

static

◆ TR() [2/29]

static Tracer protocols::features::TR ( "protocols.features.AtomTypesFeatures" )

static

◆ TR() [3/29]

static basic::Tracer protocols::features::TR ( "protocols.features.BatchFeatures" )

static

◆ TR() [4/29]

static basic::Tracer protocols::features::TR ( "protocols.features.DatabaseFilters" )

static

◆ TR() [5/29]

static basic::Tracer protocols::features::TR ( "protocols.features.DdGFeatures" )

static

◆ TR() [6/29]

static Tracer protocols::features::TR ( "protocols.features.FeaturesReporter" )

static

◆ tr() [1/3]

static basic::Tracer protocols::features::tr ( "protocols.features.FeaturesReporterFactory" )

static

Referenced by protocols::features::DatabaseJobInputter::DatabaseJobInputter(), protocols::features::DatabaseJobInputter::fill_jobs(), protocols::features::FeaturesReporterFactory::get_features_reporter(), and protocols::features::DatabaseJobInputter::pose_from_job().

◆ TR() [7/29]

static Tracer protocols::features::TR ( "protocols.features.HBondFeatures" )

static

◆ TR() [8/29]

static Tracer protocols::features::TR ( "protocols.features.HBondParameterFeatures" )

static

◆ TR() [9/29]

static basic::Tracer protocols::features::TR ( "protocols.features.LoopAnchorFeatures" )

static

◆ TR() [10/29]

static basic::Tracer protocols::features::TR ( "protocols.features.PdbDataFeatures" )

static

◆ TR() [11/29]

static basic::Tracer protocols::features::TR ( "protocols.features.PoseConformationFeatures" )

static

◆ TR() [12/29]

static basic::Tracer protocols::features::TR ( "protocols.features.ProteinBondGeometry" )

static

◆ TR() [13/29]

static basic::Tracer protocols::features::TR ( "protocols.features.ProteinResidueConformationFeatures" )

static

◆ tr() [2/3]

static basic::Tracer protocols::features::tr ( "protocols.features.ProteinRMSDFeatures" )

static

◆ tr() [3/3]

static basic::Tracer protocols::features::tr ( "protocols.features.ProteinRMSDNoSuperpositionFeatures" )

static

◆ TR() [14/29]

static basic::Tracer protocols::features::TR ( "protocols.features.ProteinSilentReport" )

static

◆ TR() [15/29]

static Tracer protocols::features::TR ( "protocols.features.ReportToDB" )

static

◆ TR() [16/29]

static basic::Tracer protocols::features::TR ( "protocols.features.ResidueFeatures" )

static

◆ TR() [17/29]

static Tracer protocols::features::TR ( "protocols.features.ResidueSecondaryStructureFeatures" )

static

◆ TR() [18/29]

static basic::Tracer protocols::features::TR ( "protocols.features.ResidueTotalScoresFeatures" )

static

◆ TR() [19/29]

static Tracer protocols::features::TR ( "protocols.features.ResidueTypesFeatures" )

static

◆ TR() [20/29]

static basic::Tracer protocols::features::TR ( "protocols.features.RotamerFeatures" )

static

◆ TR() [21/29]

static Tracer protocols::features::TR ( "protocols.features.RotamerRecoveryFeatures" )

static

◆ TR() [22/29]

static basic::Tracer protocols::features::TR ( "protocols.features.SimpleMetricFeatures" )

static

◆ TR() [23/29]

static basic::Tracer protocols::features::TR ( "protocols.features.SmotifFeatures" )

static

◆ TR() [24/29]

static basic::Tracer protocols::features::TR ( "protocols.features.StructureScoresFeatures" )

static

◆ TR() [25/29]

static Tracer protocols::features::TR ( "protocols.features.TaskOperationFeatures" )

static

◆ TR() [26/29]

static basic::Tracer protocols::features::TR ( "protocols.features.TrajectoryMapFeatures" )

static

◆ TR() [27/29]

static basic::Tracer protocols::features::TR ( "protocols.features.TrajectoryReportToDB" )

static

◆ TR() [28/29]

static basic::Tracer protocols::features::TR ( "protocols.features.UnrecognizedAtomFeatures" )

static

◆ TR() [29/29]

static Tracer protocols::features::TR ( "protocols.features.util" )

static

◆ write_batch_reports_table()

void protocols::features::write_batch_reports_table	(	utility::vector1< FeaturesReporterOP >	features_reporters,
		core::Size	batch_id,
		utility::sql_database::sessionOP	db_session
	)

write the linking table between features reporters and batches. This happens here so that the protocol/batch id framework can be used to prevent duplicate key entries. This function gets called when the batch id is written.

Referenced by get_protocol_and_batch_id(), and set_protocol_and_batch_id().

◆ write_features_reporters_table()

void protocols::features::write_features_reporters_table	(	utility::vector1< FeaturesReporterOP >	features_reporters,
		utility::sql_database::sessionOP	db_session
	)

@detail The 'features_reporters' table lists the type_names of the all defined features reporters. The 'batch_reports' table link the features reporters with each batch defined in the 'batches' table.

Referenced by get_protocol_and_batch_id(), and set_protocol_and_batch_id().

◆ xsd_type_definition_w_attributes()

void protocols::features::xsd_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	features_reporter_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Define the XML schema definition for a Features_Reporter that contains no subtags but may contain any number of attributes (aka options).

References complex_type_name_for_features_reporter().

◆ xsd_type_definition_w_attributes_and_repeatable_subelements()

void protocols::features::xsd_type_definition_w_attributes_and_repeatable_subelements	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	features_reporter_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes,
		utility::tag::XMLSchemaSimpleSubelementList const &	subelements
	)

References complex_type_name_for_features_reporter().

Referenced by protocols::features::ScreeningFeatures::provide_xml_schema(), and protocols::features::SimpleMetricFeatures::provide_xml_schema().

Variable Documentation

◆ protocol_table_initialized_

bool protocols::features::protocol_table_initialized_ = false

◆ static_batch_id_map_

map<string, core::Size> protocols::features::static_batch_id_map_

◆ static_protocol_id_

Size protocols::features::static_protocol_id_ = 0

Macros are not properly caught and passed along by my #inclusion cleanup script

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ AtomAtomPairFeaturesCOP

◆ AtomAtomPairFeaturesOP

◆ AtomInResidueAtomInResiduePairFeaturesCOP

◆ AtomInResidueAtomInResiduePairFeaturesOP

◆ AtomTypesFeaturesCOP

◆ AtomTypesFeaturesOP

◆ BatchFeaturesCOP

◆ BatchFeaturesOP

◆ BetaTurnDetectionCOP

◆ BetaTurnDetectionFeaturesCOP

◆ BetaTurnDetectionFeaturesOP

◆ BetaTurnDetectionOP

◆ BondAngleDatabaseOP

◆ ChargeChargeFeaturesCOP

◆ ChargeChargeFeaturesOP

◆ DatabaseFilterCOP

◆ DatabaseFilterOP

◆ DatabaseJobInputterOP

◆ DatabaseJobOutputterOP

◆ DdGFeaturesCOP

◆ DdGFeaturesOP

◆ FeaturesReporterCOP

◆ FeaturesReporterCreatorCOP

◆ FeaturesReporterCreatorOP

◆ FeaturesReporterOP

◆ GeometricSolvationFeaturesCOP

◆ GeometricSolvationFeaturesOP

◆ HBondFeaturesCOP

◆ HBondFeaturesOP

◆ HBondParameterFeaturesCOP

◆ HBondParameterFeaturesOP

◆ InteractionEdge

◆ InterfaceDdGMoverCOP

◆ InterfaceDdGMoverOP

◆ InterfaceFeaturesCOP

◆ InterfaceFeaturesOP

◆ JobDataFeaturesCOP

◆ JobDataFeaturesOP

◆ LoopAnchorFeaturesCOP

◆ LoopAnchorFeaturesOP

◆ ModelFeaturesCOP

◆ ModelFeaturesOP

◆ OrbitalsFeaturesCOP

◆ OrbitalsFeaturesOP

◆ PairFeaturesCOP

◆ PairFeaturesOP

◆ PdbDataFeaturesOP

◆ PoseCommentsFeaturesCOP

◆ PoseCommentsFeaturesOP

◆ PoseConformationFeaturesCOP

◆ PoseConformationFeaturesOP

◆ ProteinBackboneAtomAtomPairFeaturesCOP

◆ ProteinBackboneAtomAtomPairFeaturesOP

◆ ProteinBackboneTorsionAngleFeaturesCOP

◆ ProteinBackboneTorsionAngleFeaturesOP

◆ ProteinBondGeometryFeaturesCOP

◆ ProteinBondGeometryFeaturesOP

◆ ProteinResidueConformationFeaturesCOP

◆ ProteinResidueConformationFeaturesOP

◆ ProteinRMSDFeaturesCOP

◆ ProteinRMSDFeaturesOP

◆ ProteinRMSDNoSuperpositionFeaturesCOP

◆ ProteinRMSDNoSuperpositionFeaturesOP

◆ ProteinSilentReportCOP

◆ ProteinSilentReportOP

◆ ProtocolFeaturesCOP

◆ ProtocolFeaturesOP

◆ RadiusOfGyrationFeaturesCOP

◆ RadiusOfGyrationFeaturesOP

◆ ReportCOP

◆ ReportOP

◆ ReportToDBCOP

◆ ReportToDBOP