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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
protocols::features::FeaturesReporter Class Referenceabstract

#include <FeaturesReporter.hh>

Inherits VirtualBase.

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

Public Member Functions

 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual std::string type_name () const
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
virtual utility::vector1
< std::string > 
features_reporter_dependencies () const
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
virtual void write_schema_to_db (utility::sql_database::sessionOP db_session) const =0
 Define the schema and write it to the database. This is most easily achieved using the schema_generator. Once everything has converted to the schema generator this should be made a pure virtual. More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual core::Size report_features (core::pose::Pose const &, utility::vector1< bool > const &, StructureID, utility::sql_database::sessionOP)=0
 collect all the feature data for the pose. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &)
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Protected Member Functions

std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 

Protected Attributes

RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::features::FeaturesReporter::FeaturesReporter ( )
inline
protocols::features::FeaturesReporter::~FeaturesReporter ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

bool protocols::features::FeaturesReporter::check_relevant_residues ( utility::vector1< bool > const &  relevant_residues,
core::Size  res1 
) const

References protocols::features::RelevantResiduesMode::Exclusive, protocols::features::RelevantResiduesMode::Inclusive, relevant_residues_mode_, and core::id::to_string().

Referenced by protocols::features::DdGFeatures::insert_ddG_rows(), protocols::features::ResidueScoresFeatures::insert_one_body_residue_score_rows(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), protocols::features::PdbDataFeatures::insert_residue_pdb_identification_rows(), protocols::features::ResidueFeatures::insert_residue_rows(), protocols::features::ResidueTotalScoresFeatures::insert_residue_total_scores_rows(), protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ResidueGridScoresFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::ResidueBurialFeatures::report_features(), protocols::features::ResidueTypesFeatures::report_features(), protocols::features::SecondaryStructureSegmentFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::RotamerBoltzmannWeightFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::InterfaceFeatures::report_interface_residue_features(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), and protocols::features::PairFeatures::report_residue_pairs().

bool protocols::features::FeaturesReporter::check_relevant_residues ( utility::vector1< bool > const &  relevant_residues,
core::Size  res1,
core::Size  res2 
) const
bool protocols::features::FeaturesReporter::check_relevant_residues ( utility::vector1< bool > const &  relevant_residues,
utility::vector1< core::Size > const &  residues 
) const
bool protocols::features::FeaturesReporter::check_relevant_residues_range ( utility::vector1< bool > const &  relevant_residues,
core::Size  res1,
core::Size  res2 
) const
virtual void protocols::features::FeaturesReporter::delete_record ( StructureID  ,
utility::sql_database::sessionOP   
)
inlinevirtual
void protocols::features::FeaturesReporter::delete_records_from_table ( std::string const &  table_name,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
protected

a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized!

Referenced by protocols::features::TrajectoryMapFeatures::delete_record(), protocols::features::ResidueFeatures::delete_record(), and protocols::features::UnrecognizedAtomFeatures::delete_record().

virtual utility::vector1<std::string> protocols::features::FeaturesReporter::features_reporter_dependencies ( ) const
inlinevirtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

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

string protocols::features::FeaturesReporter::find_tag ( core::pose::Pose const &  pose) const
protected
RelevantResiduesMode::T protocols::features::FeaturesReporter::get_relevant_residues_mode ( ) const
virtual void protocols::features::FeaturesReporter::load_into_pose ( utility::sql_database::sessionOP  ,
StructureID  ,
core::pose::Pose  
)
inlinevirtual
void protocols::features::FeaturesReporter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
virtual
core::Size protocols::features::FeaturesReporter::report_features ( core::pose::Pose const &  ,
StructureID  ,
utility::sql_database::sessionOP   
)

collect all the feature data for the pose.

virtual core::Size protocols::features::FeaturesReporter::report_features ( core::pose::Pose const &  ,
utility::vector1< bool > const &  ,
StructureID  ,
utility::sql_database::sessionOP   
)
pure virtual

collect all the feature data for the pose.

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

virtual std::string protocols::features::FeaturesReporter::schema ( ) const
inlinevirtual

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

Referenced by write_schema_to_db().

void protocols::features::FeaturesReporter::set_relevant_residues_mode ( RelevantResiduesMode::T  setting)
virtual std::string protocols::features::FeaturesReporter::type_name ( ) const
inlinevirtual

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

Referenced by write_schema_to_db().

void protocols::features::FeaturesReporter::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
pure virtual

Define the schema and write it to the database. This is most easily achieved using the schema_generator. Once everything has converted to the schema generator this should be made a pure virtual.

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

References schema(), and type_name().

Member Data Documentation

RelevantResiduesMode::T protocols::features::FeaturesReporter::relevant_residues_mode_
protected

The documentation for this class was generated from the following files: