Namespaces
	helixAssembly

	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	BatchFeaturesCreator
	creator for the BatchFeatures class More...

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	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	JobDataFeatures

class	JobDataFeaturesCreator
	creator for the JobDataFeatures class More...

class	LoopAnchorFeatures

class	LoopAnchorFeaturesCreator
	creator for the LoopAnchorFeatures 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	ProteinSilentReport

class	ProtocolFeatures

class	ProtocolFeaturesCreator
	creator for the ProtocolFeatures class More...

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	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	SecondaryStructureSegmentFeatures

class	SecondaryStructureSegmentFeaturesCreator
	creator for the SecondaryStructureSegmentFeaturesCreator 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	UnrecognizedAtomFeatures

class	UnrecognizedAtomFeaturesCreator
	creator for the UnrecognizedAtomFeatures class More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef std::pair< bool, utility::vector1 < boost::uuids::uuid > >	WriteDeletePair

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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")

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)

boost::uuids::uuid	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)

boost::uuids::uuid	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)

boost::uuids::uuid	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)

boost::uuids::uuid	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)

boost::uuids::uuid	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)

boost::uuids::uuid	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, boost::uuids::uuid 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, boost::uuids::uuid const &struct_id, core::Size const &score_type_id)

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.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.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.SmotifFeatures")

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

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

pair< Size, Size >	get_protocol_and_batch_id (string identifier, 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...

pair< Size, Size >	deserialize_db_listener_data (string data)

string	serialize_ids (int protocol_id, string identifier, Size batch_id)

Size	get_batch_id (boost::uuids::uuid struct_id, sessionOP db_session)

std::pair< core::Size, core::Size >	get_protocol_and_batch_id (std::string identifier, utility::sql_database::sessionOP db_session)

std::string	serialize_ids (int protocol_id, std::string identifier, core::Size batch_id)

core::Size	get_batch_id (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

Variables
Size	static_protocol_id_ = 0

bool	protocol_table_initialized_ = false

map< string, Size >	static_batch_id_map_

Typedef Documentation

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

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

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

Definition at line 23 of file AtomAtomPairFeatures.fwd.hh.

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

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

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

Definition at line 23 of file AtomInResidueAtomInResiduePairFeatures.fwd.hh.

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

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

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

Definition at line 23 of file AtomTypesFeatures.fwd.hh.

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

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

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

Definition at line 24 of file BatchFeatures.fwd.hh.

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

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

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

Definition at line 23 of file BetaTurnDetectionFeatures.fwd.hh.

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

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

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

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

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

Definition at line 23 of file ChargeChargeFeatures.fwd.hh.

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

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

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

Definition at line 23 of file DatabaseFilters.fwd.hh.

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

Definition at line 22 of file DatabaseJobInputter.fwd.hh.

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

Definition at line 22 of file DatabaseJobOutputter.fwd.hh.

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

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

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

Definition at line 28 of file FeaturesReporterCreator.fwd.hh.

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

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

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

Definition at line 23 of file FeaturesReporter.fwd.hh.

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

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

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

Definition at line 23 of file GeometricSolvationFeatures.fwd.hh.

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

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

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

Definition at line 23 of file HBondFeatures.fwd.hh.

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

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

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

Definition at line 23 of file HBondParameterFeatures.fwd.hh.

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

Definition at line 23 of file JobDataFeatures.fwd.hh.

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

Definition at line 21 of file JobDataFeatures.fwd.hh.

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

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

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

Definition at line 23 of file LoopAnchorFeatures.fwd.hh.

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

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

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

Definition at line 23 of file OrbitalsFeatures.fwd.hh.

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

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

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

Definition at line 23 of file PairFeatures.fwd.hh.

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

Definition at line 22 of file PdbDataFeatures.fwd.hh.

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

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

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

Definition at line 23 of file PoseCommentsFeatures.fwd.hh.

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

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

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

Definition at line 23 of file PoseConformationFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ProteinBackboneAtomAtomPairFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ProteinBackboneTorsionAngleFeatures.fwd.hh.

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

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

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

Definition at line 24 of file ProteinBondGeometryFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ProteinResidueConformationFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ProteinRMSDFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ProteinSilentReport.fwd.hh.

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

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

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

Definition at line 23 of file ProtocolFeatures.fwd.hh.

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

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

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

Definition at line 23 of file RadiusOfGyrationFeatures.fwd.hh.

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

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

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

Definition at line 23 of file Report.fwd.hh.

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

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

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

Definition at line 23 of file ReportToDB.fwd.hh.

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

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

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

Definition at line 23 of file ResidueBurialFeatures.fwd.hh.

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

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

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

Definition at line 24 of file ResidueConformationFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ResidueFeatures.fwd.hh.

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

Definition at line 24 of file ResidueGridScoresFeatures.fwd.hh.

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

Definition at line 22 of file ResidueGridScoresFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ResidueScoresFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ResidueSecondaryStructureFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ResidueTotalScoresFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ResidueTypesFeatures.fwd.hh.

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

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

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

Definition at line 23 of file RotamerBoltzmannWeightFeatures.fwd.hh.

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

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

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

Definition at line 23 of file RotamerFeatures.fwd.hh.

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

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

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

Definition at line 23 of file RotamerRecoveryFeatures.fwd.hh.

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

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

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

Definition at line 23 of file SaltBridgeFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ScoreFunctionFeatures.fwd.hh.

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

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

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

Definition at line 23 of file ScoreTypeFeatures.fwd.hh.

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

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

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

Definition at line 23 of file StructureFeatures.fwd.hh.

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

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

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

Definition at line 23 of file StructureScoresFeatures.fwd.hh.

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

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

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

Definition at line 23 of file UnrecognizedAtomFeatures.fwd.hh.

typedef std::pair<bool, utility::vector1<boost::uuids::uuid> > protocols::features::WriteDeletePair

Definition at line 39 of file DatabaseFilters.hh.

Enumeration Type Documentation

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

Definition at line 48 of file HBondFeatures.hh.

enum protocols::features::RamachandranHash

Enumerator
A
B
L
E
number_of_ramachandran_hashes

Definition at line 41 of file BetaTurnDetectionFeatures.hh.

Function Documentation

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

Definition at line 260 of file util.cc.

References core::io::pdb::split().

Referenced by get_protocol_and_batch_id().

core::Size protocols::features::get_batch_id	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Size protocols::features::get_batch_id	(	boost::uuids::uuid	struct_id,
		sessionOP	db_session
	)

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.

Definition at line 288 of file util.cc.

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

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

Definition at line 54 of file DatabaseFilters.cc.

References core::pose::Pose::energies(), core::scoring::getScoreFunction(), and core::pose::Pose::total_residue().

Referenced by get_write_delete_pair().

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

Definition at line 346 of file DatabaseStatements.cc.

References get_something_from_database(), and get_structure_count_statement().

Referenced by get_write_delete_pair().

DatabaseFilterOP protocols::features::get_DB_filter_ptr ( )

Definition at line 65 of file DatabaseFilters.cc.

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

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
	)

Definition at line 234 of file DatabaseStatements.cc.

Referenced by get_struct_id_with_highest_score_from_job_data().

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
	)

Definition at line 289 of file DatabaseStatements.cc.

Referenced by get_struct_id_with_highest_score_from_score_data().

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
	)

Definition at line 119 of file DatabaseStatements.cc.

Referenced by get_struct_id_with_nth_lowest_score_from_job_data().

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
	)

Definition at line 176 of file DatabaseStatements.cc.

Referenced by get_struct_id_with_nth_lowest_score_from_score_data().

std::pair<core::Size, core::Size> protocols::features::get_protocol_and_batch_id	(	std::string	identifier,
		utility::sql_database::sessionOP	db_session
	)

pair<Size, Size> protocols::features::get_protocol_and_batch_id	(	string	identifier,
		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.

Definition at line 87 of file util.cc.

References deserialize_db_listener_data(), protocol_table_initialized_, serialize_ids(), static_batch_id_map_, static_protocol_id_, and TR().

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

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

Definition at line 450 of file DatabaseStatements.cc.

References get_something_from_database().

Referenced by get_write_delete_pair().

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

Definition at line 480 of file DatabaseStatements.cc.

References get_something_from_database().

Referenced by get_write_delete_pair().

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
	)

Definition at line 89 of file DatabaseStatements.cc.

References get_something_from_database().

Referenced by get_write_delete_pair().

template<class T >

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

Definition at line 37 of file DatabaseStatements.cc.

References core::pack::interaction_graph::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().

boost::uuids::uuid 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
	)

Definition at line 413 of file DatabaseStatements.cc.

References get_highest_score_from_job_data_statement(), and get_something_from_database().

Referenced by get_write_delete_pair().

boost::uuids::uuid 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
	)

Definition at line 431 of file DatabaseStatements.cc.

References get_highest_score_from_score_data_statement(), and get_something_from_database().

Referenced by get_write_delete_pair().

boost::uuids::uuid 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
	)

Definition at line 395 of file DatabaseStatements.cc.

References get_struct_id_with_nth_lowest_score_from_job_data().

boost::uuids::uuid 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
	)

Definition at line 404 of file DatabaseStatements.cc.

References get_struct_id_with_nth_lowest_score_from_score_data().

boost::uuids::uuid 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
	)

Definition at line 356 of file DatabaseStatements.cc.

References get_nth_lowest_score_from_job_data_statement(), and get_something_from_database().

Referenced by get_struct_id_with_lowest_score_from_job_data(), and get_write_delete_pair().

boost::uuids::uuid 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
	)

Definition at line 376 of file DatabaseStatements.cc.

References get_nth_lowest_score_from_score_data_statement(), and get_something_from_database().

Referenced by get_struct_id_with_lowest_score_from_score_data(), and get_write_delete_pair().

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

Definition at line 52 of file DatabaseStatements.cc.

Referenced by get_current_structure_count().

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 = `""`
	)

Definition at line 85 of file DatabaseFilters.cc.

References protocols::nonlocal::current_job(), get_current_model_score(), get_current_structure_count(), protocols::jd2::JobDistributor::get_instance(), 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(), get_struct_id_with_nth_lowest_score_from_score_data(), and TR().

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

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

string protocols::features::serialize_ids	(	int	protocol_id,
		string	identifier,
		Size	batch_id
	)

Definition at line 273 of file util.cc.

Referenced by get_protocol_and_batch_id().

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

static

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

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

static

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

static

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

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

Variable Documentation

bool protocols::features::protocol_table_initialized_ = false

Definition at line 75 of file util.cc.

Referenced by get_protocol_and_batch_id().

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

Definition at line 76 of file util.cc.

Referenced by get_protocol_and_batch_id().

Size protocols::features::static_protocol_id_ = 0

Definition at line 74 of file util.cc.

Referenced by get_protocol_and_batch_id().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation