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protocols::features Namespace Reference

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...
 
struct  clique_saver
 
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  InterfaceDdGMover
 Calculates ddG of binding. More...
 
class  InterfaceDdGMoverCreator
 
class  InterfaceFeatures
 Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS. More...
 
class  InterfaceFeaturesCreator
 creator for the HBondParameterFeatures class More...
 
class  JobDataFeatures
 
class  JobDataFeaturesCreator
 creator for the JobDataFeatures class More...
 
class  LoopAnchorFeatures
 
class  LoopAnchorFeaturesCreator
 creator for the LoopAnchorFeatures class More...
 
struct  MetricData
 
class  ModelFeatures
 
class  ModelFeaturesCreator
 creator for the ModelFeatures class More...
 
class  OrbitalsFeatures
 
class  OrbitalsFeaturesCreator
 creator for the OrbitalsFeatures class More...
 
class  PairFeatures
 
class  PairFeaturesCreator
 creator for the PairFeatures class More...
 
class  PdbDataFeatures
 
class  PdbDataFeaturesCreator
 creator for the PdbDataFeatures class More...
 
class  PoseCommentsFeatures
 
class  PoseCommentsFeaturesCreator
 creator for the PoseCommentsFeatures class More...
 
class  PoseConformationFeatures
 
class  PoseConformationFeaturesCreator
 creator for the PoseConformationFeatures class More...
 
class  ProteinBackboneAtomAtomPairFeatures
 
class  ProteinBackboneAtomAtomPairFeaturesCreator
 creator for the ProteinBackboneAtomAtomPairFeatures class More...
 
class  ProteinBackboneTorsionAngleFeatures
 
class  ProteinBackboneTorsionAngleFeaturesCreator
 creator for the ProteinBackboneTorsionAngleFeatures class More...
 
class  ProteinBondGeometryFeatures
 
class  ProteinBondGeometryFeaturesCreator
 creator for the ProteinBondGeometryFeatures class More...
 
class  ProteinResidueConformationFeatures
 
class  ProteinResidueConformationFeaturesCreator
 creator for the ProteinResidueConformationFeatures class More...
 
class  ProteinRMSDFeatures
 
class  ProteinRMSDFeaturesCreator
 creator for the ProteinRMSDFeatures class More...
 
class  ProteinRMSDNoSuperpositionFeatures
 
class  ProteinRMSDNoSuperpositionFeaturesCreator
 creator for the ProteinRMSDNoSuperpositionFeatures class More...
 
class  ProteinSilentReport
 
class  ProtocolFeatures
 
class  RadiusOfGyrationFeatures
 
class  RadiusOfGyrationFeaturesCreator
 creator for the RadiusOfGyrationFeatures class More...
 
class  Report
 
class  ReportToDB
 
class  ReportToDBCreator
 
class  ResidueBurialFeatures
 
class  ResidueBurialFeaturesCreator
 creator for the ResidueBurialFeatures class More...
 
class  ResidueConformationFeatures
 
class  ResidueConformationFeaturesCreator
 creator for the ResidueConformationFeatures class More...
 
class  ResidueFeatures
 
class  ResidueFeaturesCreator
 creator for the ResidueFeatures class More...
 
class  ResidueGridScoresFeatures
 
class  ResidueGridScoresFeaturesCreator
 creator for the ResidueGridScoresFeatures class More...
 
class  ResidueScoresFeatures
 
class  ResidueScoresFeaturesCreator
 creator for the ResidueScoresFeatures class More...
 
class  ResidueSecondaryStructureFeatures
 
class  ResidueSecondaryStructureFeaturesCreator
 creator for the ResidueSecondaryStructureFeatures class More...
 
class  ResidueTotalScoresFeatures
 
class  ResidueTotalScoresFeaturesCreator
 creator for the ResidueTotalScoresFeatures class More...
 
class  ResidueTypesFeatures
 
class  ResidueTypesFeaturesCreator
 creator for the ResidueTypesFeatures class More...
 
class  RotamerBoltzmannWeightFeatures
 
class  RotamerBoltzmannWeightFeaturesCreator
 creator for the RotamerBoltzmannWeightFeatures class More...
 
class  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...
 
struct  Segment
 
class  SimpleMetricFeatures
 
class  SimpleMetricFeaturesCreator
 creator for the SimpleMetricFeatures 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 std::uint64_t StructureID
 
typedef
utility::pointer::shared_ptr
< FeaturesReporterCreator
FeaturesReporterCreatorOP
 
typedef
utility::pointer::shared_ptr
< FeaturesReporterCreator
const > 
FeaturesReporterCreatorCOP
 
typedef
utility::pointer::shared_ptr
< GeometricSolvationFeatures
GeometricSolvationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< GeometricSolvationFeatures
const > 
GeometricSolvationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< HBondFeatures
HBondFeaturesOP
 
typedef
utility::pointer::shared_ptr
< HBondFeatures const > 
HBondFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< HBondParameterFeatures
HBondParameterFeaturesOP
 
typedef
utility::pointer::shared_ptr
< HBondParameterFeatures const > 
HBondParameterFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< InterfaceDdGMover
InterfaceDdGMoverOP
 
typedef
utility::pointer::shared_ptr
< InterfaceDdGMover const > 
InterfaceDdGMoverCOP
 
typedef
utility::pointer::shared_ptr
< protocols::features::InterfaceFeatures
InterfaceFeaturesOP
 
typedef
utility::pointer::shared_ptr
< InterfaceFeatures const > 
InterfaceFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< JobDataFeatures
JobDataFeaturesOP
 
typedef
utility::pointer::shared_ptr
< JobDataFeatures const > 
JobDataFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< LoopAnchorFeatures
LoopAnchorFeaturesOP
 
typedef
utility::pointer::shared_ptr
< LoopAnchorFeatures const > 
LoopAnchorFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ModelFeatures
ModelFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ModelFeatures const > 
ModelFeaturesCOP
 
typedef
boost::undirected_graph
< core::Size
SegmentGraph
 
typedef boost::graph_traits
< SegmentGraph >
::vertex_descriptor 
SegmentVertex
 
typedef boost::graph_traits
< SegmentGraph >
::edge_descriptor 
InteractionEdge
 
typedef
utility::pointer::shared_ptr
< OrbitalsFeatures
OrbitalsFeaturesOP
 
typedef
utility::pointer::shared_ptr
< OrbitalsFeatures const > 
OrbitalsFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< PairFeatures
PairFeaturesOP
 
typedef
utility::pointer::shared_ptr
< PairFeatures const > 
PairFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< PdbDataFeatures
PdbDataFeaturesOP
 
typedef
utility::pointer::shared_ptr
< PoseCommentsFeatures
PoseCommentsFeaturesOP
 
typedef
utility::pointer::shared_ptr
< PoseCommentsFeatures const > 
PoseCommentsFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< PoseConformationFeatures
PoseConformationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< PoseConformationFeatures
const > 
PoseConformationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinBackboneAtomAtomPairFeatures
ProteinBackboneAtomAtomPairFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinBackboneAtomAtomPairFeatures
const > 
ProteinBackboneAtomAtomPairFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinBackboneTorsionAngleFeatures
ProteinBackboneTorsionAngleFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinBackboneTorsionAngleFeatures
const > 
ProteinBackboneTorsionAngleFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinBondGeometryFeatures
ProteinBondGeometryFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinBondGeometryFeatures
const > 
ProteinBondGeometryFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< BondAngleDatabase > 
BondAngleDatabaseOP
 
typedef
utility::pointer::shared_ptr
< ProteinResidueConformationFeatures
ProteinResidueConformationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinResidueConformationFeatures
const > 
ProteinResidueConformationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinRMSDFeatures
ProteinRMSDFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinRMSDFeatures const > 
ProteinRMSDFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinRMSDNoSuperpositionFeatures
ProteinRMSDNoSuperpositionFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProteinRMSDNoSuperpositionFeatures
const > 
ProteinRMSDNoSuperpositionFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ProteinSilentReport
ProteinSilentReportOP
 
typedef
utility::pointer::shared_ptr
< ProteinSilentReport const > 
ProteinSilentReportCOP
 
typedef
utility::pointer::shared_ptr
< ProtocolFeatures
ProtocolFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ProtocolFeatures const > 
ProtocolFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< RadiusOfGyrationFeatures
RadiusOfGyrationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< RadiusOfGyrationFeatures
const > 
RadiusOfGyrationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< Report
ReportOP
 
typedef
utility::pointer::shared_ptr
< Report const > 
ReportCOP
 
typedef
utility::pointer::shared_ptr
< ReportToDB
ReportToDBOP
 
typedef
utility::pointer::shared_ptr
< ReportToDB const > 
ReportToDBCOP
 
typedef
utility::pointer::shared_ptr
< ResidueBurialFeatures
ResidueBurialFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueBurialFeatures const > 
ResidueBurialFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueConformationFeatures
ResidueConformationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueConformationFeatures
const > 
ResidueConformationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueFeatures
ResidueFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueFeatures const > 
ResidueFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueGridScoresFeatures
ResidueGridScoresFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueGridScoresFeatures
const > 
ResidueGridScoresFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueScoresFeatures
ResidueScoresFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueScoresFeatures const > 
ResidueScoresFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueSecondaryStructureFeatures
ResidueSecondaryStructureFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueSecondaryStructureFeatures
const > 
ResidueSecondaryStructureFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueTotalScoresFeatures
ResidueTotalScoresFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueTotalScoresFeatures
const > 
ResidueTotalScoresFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ResidueTypesFeatures
ResidueTypesFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ResidueTypesFeatures const > 
ResidueTypesFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< RotamerBoltzmannWeightFeatures
RotamerBoltzmannWeightFeaturesOP
 
typedef
utility::pointer::shared_ptr
< RotamerBoltzmannWeightFeatures
const > 
RotamerBoltzmannWeightFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< RotamerFeatures
RotamerFeaturesOP
 
typedef
utility::pointer::shared_ptr
< RotamerFeatures const > 
RotamerFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< RotamerRecoveryFeatures
RotamerRecoveryFeaturesOP
 
typedef
utility::pointer::shared_ptr
< RotamerRecoveryFeatures
const > 
RotamerRecoveryFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< RuntimeFeatures
RuntimeFeaturesOP
 
typedef
utility::pointer::shared_ptr
< RuntimeFeatures const > 
RuntimeFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< SaltBridgeFeatures
SaltBridgeFeaturesOP
 
typedef
utility::pointer::shared_ptr
< SaltBridgeFeatures const > 
SaltBridgeFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ScoreFunctionFeatures
ScoreFunctionFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ScoreFunctionFeatures const > 
ScoreFunctionFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ScoreTypeFeatures
ScoreTypeFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ScoreTypeFeatures const > 
ScoreTypeFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< ScreeningFeatures
ScreeningFeaturesOP
 
typedef
utility::pointer::shared_ptr
< ScreeningFeatures const > 
ScreeningFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< SecondaryStructureSegmentFeatures
SecondaryStructureSegmentFeaturesOP
 
typedef
utility::pointer::shared_ptr
< SecondaryStructureSegmentFeatures
const > 
SecondaryStructureSegmentFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< SimpleMetricFeatures
SimpleMetricFeaturesOP
 
typedef
utility::pointer::shared_ptr
< SimpleMetricFeatures const > 
SimpleMetricFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< StructureFeatures
StructureFeaturesOP
 
typedef
utility::pointer::shared_ptr
< StructureFeatures const > 
StructureFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< StructureScoresFeatures
StructureScoresFeaturesOP
 
typedef
utility::pointer::shared_ptr
< StructureScoresFeatures
const > 
StructureScoresFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationFeatures
TaskOperationFeaturesOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationFeatures const > 
TaskOperationFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< TotalScoreFeatures
TotalScoreFeaturesOP
 
typedef
utility::pointer::shared_ptr
< TotalScoreFeatures const > 
TotalScoreFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< TrajectoryMapFeatures
TrajectoryMapFeaturesOP
 
typedef
utility::pointer::shared_ptr
< TrajectoryMapFeatures const > 
TrajectoryMapFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< TrajectoryReportToDB
TrajectoryReportToDBOP
 
typedef
utility::pointer::shared_ptr
< TrajectoryReportToDB const > 
TrajectoryReportToDBCOP
 
typedef
utility::pointer::shared_ptr
< UnrecognizedAtomFeatures
UnrecognizedAtomFeaturesOP
 
typedef
utility::pointer::shared_ptr
< UnrecognizedAtomFeatures
const > 
UnrecognizedAtomFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< WaterFeatures
WaterFeaturesOP
 
typedef
utility::pointer::shared_ptr
< WaterFeatures const > 
WaterFeaturesCOP
 

Enumerations

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

Functions

static Tracer TR ("protocols.features.AtomAtomPairFeatures")
 
static Tracer TR ("protocols.features.AtomTypesFeatures")
 
static basic::Tracer TR ("protocols.features.BatchFeatures")
 
static basic::Tracer TR ("protocols.features.DatabaseFilters")
 
core::Real get_current_model_score (core::pose::Pose const &pose, core::Size score_type_id)
 
DatabaseFilterOP get_DB_filter_ptr ()
 
WriteDeletePair get_write_delete_pair (core::pose::Pose const &pose, utility::sql_database::sessionOP db_session, core::Size const &protocol_id, core::Size const &count, std::string const &score_term, std::string current_input="")
 
template<class T >
get_something_from_database (cppdb::statement statement, T)
 
cppdb::statement get_structure_count_statement (utility::sql_database::sessionOP db_session, std::string const &input_tag, core::Size const &protocol_id)
 
core::Size get_score_type_id_from_score_term (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &score_term)
 
cppdb::statement get_nth_lowest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)
 
cppdb::statement get_nth_lowest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)
 
cppdb::statement get_highest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, std::string const &input_tag, core::Size const &protocol_id)
 
cppdb::statement get_highest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, std::string const &input_tag, core::Size const &protocol_id)
 
core::Size get_current_structure_count (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_nth_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_nth_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_highest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)
 
StructureID get_struct_id_with_highest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)
 
core::Real get_score_for_struct_id_and_score_term_from_job_data (utility::sql_database::sessionOP db_session, StructureID const &struct_id, std::string const &score_term)
 
core::Real get_score_for_struct_id_and_score_term_from_score_data (utility::sql_database::sessionOP db_session, StructureID const &struct_id, core::Size const &score_type_id)
 
static basic::Tracer TR ("protocols.features.DdGFeatures")
 
std::string complex_type_name_for_features_reporter (std::string const &features_reporter_name)
 
void xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &features_reporter_type, std::string const &description, utility::tag::AttributeList const &attributes)
 Define the XML schema definition for a Features_Reporter that contains no subtags but may contain any number of attributes (aka options). More...
 
void xsd_type_definition_w_attributes_and_repeatable_subelements (utility::tag::XMLSchemaDefinition &xsd, std::string const &features_reporter_type, std::string const &description, utility::tag::AttributeList const &attributes, utility::tag::XMLSchemaSimpleSubelementList const &subelements)
 
static Tracer TR ("protocols.features.FeaturesReporter")
 
static basic::Tracer tr ("protocols.features.FeaturesReporterFactory")
 
static Tracer TR ("protocols.features.HBondFeatures")
 
static Tracer TR ("protocols.features.HBondParameterFeatures")
 
static basic::Tracer TR ("protocols.features.LoopAnchorFeatures")
 
static basic::Tracer TR ("protocols.features.PdbDataFeatures")
 
static basic::Tracer TR ("protocols.features.PoseConformationFeatures")
 
static basic::Tracer TR ("protocols.features.ProteinBondGeometry")
 
static basic::Tracer TR ("protocols.features.ProteinResidueConformationFeatures")
 
static basic::Tracer tr ("protocols.features.ProteinRMSDFeatures")
 
static basic::Tracer tr ("protocols.features.ProteinRMSDNoSuperpositionFeatures")
 
static basic::Tracer TR ("protocols.features.ProteinSilentReport")
 
static Tracer TR ("protocols.features.ReportToDB")
 
static basic::Tracer TR ("protocols.features.ResidueFeatures")
 
static Tracer TR ("protocols.features.ResidueSecondaryStructureFeatures")
 
static basic::Tracer TR ("protocols.features.ResidueTotalScoresFeatures")
 
static Tracer TR ("protocols.features.ResidueTypesFeatures")
 
static basic::Tracer TR ("protocols.features.RotamerFeatures")
 
static Tracer TR ("protocols.features.RotamerRecoveryFeatures")
 
static basic::Tracer TR ("protocols.features.SimpleMetricFeatures")
 
static basic::Tracer TR ("protocols.features.SmotifFeatures")
 
static basic::Tracer TR ("protocols.features.StructureScoresFeatures")
 
static Tracer TR ("protocols.features.TaskOperationFeatures")
 
static basic::Tracer TR ("protocols.features.TrajectoryMapFeatures")
 
static basic::Tracer TR ("protocols.features.TrajectoryReportToDB")
 
static basic::Tracer TR ("protocols.features.UnrecognizedAtomFeatures")
 
static Tracer TR ("protocols.features.util")
 
void set_protocol_and_batch_id (core::Size protocol_id, core::Size batch_id, string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
 write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing) More...
 
pair< core::Size, core::Sizeget_protocol_and_batch_id (string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
 Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info. More...
 
void write_features_reporters_table (utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)
 
void write_batch_reports_table (utility::vector1< FeaturesReporterOP > features_reporters, core::Size batch_id, utility::sql_database::sessionOP db_session)
 write the linking table between features reporters and batches. This happens here so that the protocol/batch id framework can be used to prevent duplicate key entries. This function gets called when the batch id is written. More...
 
pair< core::Size, core::Sizedeserialize_db_listener_data (string data)
 
string serialize_ids (int protocol_id, string batch_name, core::Size batch_id)
 
Size get_batch_id (StructureID struct_id, sessionOP db_session)
 
utility::vector1< StructureIDstruct_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::Sizeget_protocol_and_batch_id (std::string const &batch_name, std::string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)
 Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info. More...
 
core::Size get_batch_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StructureIDstruct_ids_from_tag (utility::sql_database::sessionOP db_session, std::string const &tag)
 

Variables

Size static_protocol_id_ = 0
 
bool protocol_table_initialized_ = false
 
map< string, core::Sizestatic_batch_id_map_
 

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< 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< 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< FeaturesReporter > protocols::features::FeaturesReporterOP
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 boost::graph_traits<SegmentGraph>::edge_descriptor protocols::features::InteractionEdge
typedef utility::pointer::shared_ptr< InterfaceDdGMover const > protocols::features::InterfaceDdGMoverCOP
typedef utility::pointer::shared_ptr< InterfaceDdGMover > protocols::features::InterfaceDdGMoverOP
typedef utility::pointer::shared_ptr< InterfaceFeatures const > protocols::features::InterfaceFeaturesCOP
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< ModelFeatures const > protocols::features::ModelFeaturesCOP
typedef utility::pointer::shared_ptr< ModelFeatures > protocols::features::ModelFeaturesOP
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< ProteinRMSDFeatures const > protocols::features::ProteinRMSDFeaturesCOP
typedef utility::pointer::shared_ptr< ProteinRMSDFeatures > protocols::features::ProteinRMSDFeaturesOP
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< 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< ResidueFeatures const > protocols::features::ResidueFeaturesCOP
typedef utility::pointer::shared_ptr< ResidueFeatures > protocols::features::ResidueFeaturesOP
typedef utility::pointer::shared_ptr< ResidueScoresFeatures const > protocols::features::ResidueScoresFeaturesCOP
typedef utility::pointer::shared_ptr< ResidueTypesFeatures const > protocols::features::ResidueTypesFeaturesCOP
typedef utility::pointer::shared_ptr< ResidueTypesFeatures > protocols::features::ResidueTypesFeaturesOP
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<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< 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 boost::undirected_graph<core::Size> protocols::features::SegmentGraph
typedef boost::graph_traits<SegmentGraph>::vertex_descriptor protocols::features::SegmentVertex
typedef utility::pointer::shared_ptr< SimpleMetricFeatures const > protocols::features::SimpleMetricFeaturesCOP
typedef utility::pointer::shared_ptr< SimpleMetricFeatures > protocols::features::SimpleMetricFeaturesOP
typedef utility::pointer::shared_ptr< StructureFeatures const > protocols::features::StructureFeaturesCOP
typedef utility::pointer::shared_ptr< StructureFeatures > protocols::features::StructureFeaturesOP
typedef std::uint64_t protocols::features::StructureID
typedef utility::pointer::shared_ptr< StructureScoresFeatures const > protocols::features::StructureScoresFeaturesCOP
typedef utility::pointer::shared_ptr< TaskOperationFeatures const > protocols::features::TaskOperationFeaturesCOP
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< 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< 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

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

Enumerator
hbdef_NONE 
hbdef_ENERGY 
hbdef_AHDIST 
hbdef_MAX 
Enumerator
number_of_ramachandran_hashes 

Function Documentation

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

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

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

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

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

std::string protocols::features::get_question_mark_string ( core::Size const  n)
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 
)
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 
)
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 
)
template<class T >
T protocols::features::get_something_from_database ( cppdb::statement  statement,
 
)
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 
)
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 
)
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 
)
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 
)
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 
)
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 
)
cppdb::statement protocols::features::get_structure_count_statement ( utility::sql_database::sessionOP  db_session,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
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 = "" 
)
std::string protocols::features::serialize_ids ( int  protocol_id,
string  batch_name,
core::Size  batch_id 
)
std::string protocols::features::serialize_residue_xyz_coords ( core::conformation::Residue const &  residue)
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 
)
static basic::Tracer protocols::features::tr ( "protocols.features.FeaturesReporterFactory"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.BatchFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.DatabaseFilters"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.PdbDataFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.AtomTypesFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.ResidueTypesFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.SmotifFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.ResidueFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.ResidueSecondaryStructureFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.TrajectoryMapFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.ProteinSilentReport"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.UnrecognizedAtomFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.ProteinBondGeometry"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.ProteinResidueConformationFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.FeaturesReporter"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.LoopAnchorFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.StructureScoresFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.HBondParameterFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.PoseConformationFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.ResidueTotalScoresFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.DdGFeatures"  )
static
static basic::Tracer protocols::features::tr ( "protocols.features.ProteinRMSDNoSuperpositionFeatures"  )
static
static basic::Tracer protocols::features::tr ( "protocols.features.ProteinRMSDFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.TaskOperationFeatures"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.RotamerFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.AtomAtomPairFeatures"  )
static

Referenced by protocols::features::ReportToDB::apply(), protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms(), protocols::features::InterfaceDdGMover::compute(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::features::ModelFeatures::find_segments(), protocols::features::InterfaceFeatures::get_all_pose_chains(), protocols::features::helixAssembly::HelixBundleFeatures::get_helices(), protocols::features::InterfaceDdGMover::get_movable_jumps(), get_protocol_and_batch_id(), get_write_delete_pair(), protocols::features::ReportToDB::initialize_pose(), protocols::features::ReportToDB::initialize_relevant_residues(), protocols::features::DdGFeatures::insert_ddG_rows(), protocols::features::ResidueTotalScoresFeatures::insert_residue_total_scores_rows(), protocols::features::TaskOperationFeatures::insert_task_operation_residue_effects_row(), protocols::features::TaskOperationFeatures::insert_task_operations_row(), protocols::features::PoseConformationFeatures::load_chain_endings(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::features::PoseConformationFeatures::load_jumps(), protocols::features::PdbDataFeatures::load_residue_pdb_confidence(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::features::InterfaceFeatures::make_interface_combos(), protocols::features::InterfaceDdGMover::mutation_list(), protocols::features::ReportToDB::parse_batch_name_tag_item(), protocols::features::InterfaceDdGMover::parse_my_tag(), protocols::features::WaterFeatures::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), protocols::features::InterfaceFeatures::report_all_interface_features(), protocols::features::ProtocolFeatures::report_features(), protocols::features::BatchFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::WaterFeatures::report_features(), protocols::features::helixAssembly::HelixBundleFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::ReportToDB::report_features(), protocols::features::SimpleMetricFeatures::report_general_features(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residues(), protocols::features::UnrecognizedAtomFeatures::UnrecognizedAtomFeatures(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), protocols::features::ProteinSilentReport::write_full_report(), protocols::features::SimpleMetricFeatures::write_per_residue_data_row(), protocols::features::StructureFeatures::write_schema_to_db(), protocols::features::TaskOperationFeatures::write_schema_to_db(), protocols::features::TaskOperationFeatures::write_task_operation_residue_effects_table_schema(), and protocols::features::TaskOperationFeatures::write_task_operations_table_schema().

static Tracer protocols::features::TR ( "protocols.features.util"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.SimpleMetricFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.RotamerRecoveryFeatures"  )
static
static Tracer protocols::features::TR ( "protocols.features.ReportToDB"  )
static
static basic::Tracer protocols::features::TR ( "protocols.features.TrajectoryReportToDB"  )
static
static Tracer protocols::features::TR ( "protocols.features.HBondFeatures"  )
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.

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.

Referenced by get_protocol_and_batch_id(), and set_protocol_and_batch_id().

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

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

References complex_type_name_for_features_reporter().

Referenced by protocols::features::ResidueSecondaryStructureFeatures::provide_xml_schema(), protocols::features::AtomTypesFeatures::provide_xml_schema(), protocols::features::ChargeChargeFeatures::provide_xml_schema(), protocols::features::JobDataFeatures::provide_xml_schema(), protocols::features::RuntimeFeatures::provide_xml_schema(), protocols::features::ProteinBackboneAtomAtomPairFeatures::provide_xml_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::provide_xml_schema(), protocols::features::ResidueGridScoresFeatures::provide_xml_schema(), protocols::features::ResidueFeatures::provide_xml_schema(), protocols::features::ResidueBurialFeatures::provide_xml_schema(), protocols::features::PoseCommentsFeatures::provide_xml_schema(), protocols::features::TrajectoryMapFeatures::provide_xml_schema(), protocols::features::GeometricSolvationFeatures::provide_xml_schema(), protocols::features::ResidueTypesFeatures::provide_xml_schema(), protocols::features::PdbDataFeatures::provide_xml_schema(), protocols::features::TotalScoreFeatures::provide_xml_schema(), protocols::features::BetaTurnDetectionFeatures::provide_xml_schema(), protocols::features::RadiusOfGyrationFeatures::provide_xml_schema(), protocols::antibody::clusters::CDRClusterFeatures::provide_xml_schema(), protocols::features::ScoreTypeFeatures::provide_xml_schema(), protocols::features::SecondaryStructureSegmentFeatures::provide_xml_schema(), protocols::features::HelixCapFeatures::provide_xml_schema(), protocols::features::HBondParameterFeatures::provide_xml_schema(), protocols::features::PairFeatures::provide_xml_schema(), protocols::features::helixAssembly::ConcurrencyTest::provide_xml_schema(), protocols::features::SaltBridgeFeatures::provide_xml_schema(), protocols::features::PoseConformationFeatures::provide_xml_schema(), protocols::features::ResidueConformationFeatures::provide_xml_schema(), protocols::features::RotamerBoltzmannWeightFeatures::provide_xml_schema(), protocols::features::AtomInResidueAtomInResiduePairFeatures::provide_xml_schema(), protocols::features::RotamerRecoveryFeatures::provide_xml_schema(), protocols::features::strand_assembly::SandwichFeatures::provide_xml_schema(), protocols::features::LoopAnchorFeatures::provide_xml_schema(), protocols::features::ProteinResidueConformationFeatures::provide_xml_schema(), protocols::features::ScoreFunctionFeatures::provide_xml_schema(), protocols::features::AtomAtomPairFeatures::provide_xml_schema(), protocols::features::WaterFeatures::provide_xml_schema(), protocols::features::ProteinRMSDFeatures::provide_xml_schema(), protocols::features::ResidueTotalScoresFeatures::provide_xml_schema(), protocols::features::ProteinRMSDNoSuperpositionFeatures::provide_xml_schema(), protocols::features::StructureScoresFeatures::provide_xml_schema(), protocols::features::TaskOperationFeatures::provide_xml_schema(), protocols::features::SmotifFeatures::provide_xml_schema(), protocols::features::ResidueScoresFeatures::provide_xml_schema(), protocols::features::DdGFeatures::provide_xml_schema(), protocols::features::StructureFeatures::provide_xml_schema(), protocols::features::UnrecognizedAtomFeatures::provide_xml_schema(), protocols::features::helixAssembly::HelixBundleFeatures::provide_xml_schema(), protocols::features::ProteinBondGeometryFeatures::provide_xml_schema(), protocols::antibody::AntibodyFeatures::provide_xml_schema(), protocols::features::ModelFeatures::provide_xml_schema(), protocols::features::RotamerFeatures::provide_xml_schema(), protocols::features::OrbitalsFeatures::provide_xml_schema(), protocols::features::InterfaceFeatures::provide_xml_schema(), protocols::features::strand_assembly::StrandBundleFeatures::provide_xml_schema(), and protocols::features::HBondFeatures::provide_xml_schema().

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

Variable Documentation

bool protocols::features::protocol_table_initialized_ = false
map<string, core::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