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	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	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...

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	RotamerFeatures

class	RotamerFeaturesCreator
	creator for the RotamerFeatures class More...

class	RotamerInitializer

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...

struct	SecondaryStructureSegment

class	SecondaryStructureSegmentFeatures

class	SecondaryStructureSegmentFeaturesCreator
	creator for the SecondaryStructureSegmentFeaturesCreator class More...

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	TopCountOfAllInputs

class	TopCountOfEachInput

class	TopPercentOfAllInputs

class	TopPercentOfEachInput

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 boost::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 < 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 < 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 < 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 { , 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 thread_local basic::Tracer	TR ("protocols.features.BatchFeatures")

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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< Size, 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< Size, Size >	deserialize_db_listener_data (string data)

string	serialize_ids (int protocol_id, string batch_name, 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...

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

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

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

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

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

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

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

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

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

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

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

Size	static_protocol_id_ = 0

bool	protocol_table_initialized_ = false

map< string, Size >	static_batch_id_map_

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

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef boost::uint64_t protocols::features::StructureID

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

enum protocols::features::RamachandranHash

Enumerator
B
L
E
number_of_ramachandran_hashes

Function Documentation

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

References utility::split(), utility::string2int(), and utility_exit_with_message.

Referenced by get_protocol_and_batch_id().

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

References utility::decode6bit().

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

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

Size protocols::features::get_batch_id	(	StructureID	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.

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and utility_exit_with_message.

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
	)

References core::pose::Pose::energies(), core::scoring::get_score_function(), core::pose::symmetry::make_score_function_consistent_with_symmetric_state_of_pose(), 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
	)

References get_something_from_database(), and get_structure_count_statement().

Referenced by get_write_delete_pair().

DatabaseFilterOP protocols::features::get_DB_filter_ptr ( )

References begin, basic::options::option, user, and utility_exit_with_message.

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
	)

References basic::database::safely_prepare_statement().

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
	)

References basic::database::safely_prepare_statement().

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
	)

References basic::database::safely_prepare_statement().

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
	)

References basic::database::safely_prepare_statement().

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 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.

pair<Size, 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 DATABASE_PROTOCOL_AND_BATCH_ID_TAG, deserialize_db_listener_data(), request_data_from_head_node(), runtime_assert, send_data_to_head_node(), serialize_ids(), TR, utility_exit_with_message, write_batch_reports_table(), and write_features_reporters_table().

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

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::InterfaceFeatures::report_interface_features(), protocols::features::InterfaceFeatures::report_interface_side_features(), and protocols::features::InterfaceFeatures::write_interface_residue_data_row_to_db().

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(), basic::database::safely_prepare_statement(), and utility_exit_with_message.

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,
		StructureID const &	struct_id,
		core::Size const &	score_type_id
	)

References get_something_from_database(), basic::database::safely_prepare_statement(), and utility_exit_with_message.

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
	)

References get_something_from_database(), and basic::database::safely_prepare_statement().

Referenced by get_write_delete_pair().

template<class T >

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

References basic::database::safely_read_from_database().

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().

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(), get_something_from_database(), and utility_exit_with_message.

Referenced by get_write_delete_pair().

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(), utility::to_string(), and utility_exit_with_message.

Referenced by get_write_delete_pair().

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().

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().

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(), utility::to_string(), and utility_exit_with_message.

Referenced by get_struct_id_with_lowest_score_from_job_data(), and get_write_delete_pair().

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(), utility::to_string(), and utility_exit_with_message.

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
	)

References basic::database::safely_prepare_statement().

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 = `""`
	)

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	batch_name,
		core::Size	batch_id
	)

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

References utility::to_string().

Referenced by get_protocol_and_batch_id().

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

References utility::encode6bit(), core::conformation::Residue::natoms(), protocols::stepwise::modeler::rna::output_data(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

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)

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().

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

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

References basic::database::safely_prepare_statement().

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

static

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

static

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

static

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

static

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

static

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

static

static thread_local 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(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::DatabaseJobInputter::pose_from_job(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose_from_options().

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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.

References basic::database::schema_generator::Schema::add_constraint(), basic::database::schema_generator::Schema::add_foreign_key(), safely_prepare_statement(), safely_read_from_database(), safely_write_to_database(), and basic::database::schema_generator::Schema::write().

Referenced by get_protocol_and_batch_id(), and set_protocol_and_batch_id().

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

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.

References insert_or_ignore(), and basic::database::schema_generator::Schema::write().

Referenced by get_protocol_and_batch_id(), and set_protocol_and_batch_id().

Variable Documentation

bool protocols::features::protocol_table_initialized_ = false

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

Size protocols::features::static_protocol_id_ = 0

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

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation