protocols::features::FeaturesReporter Class Reference

#include <FeaturesReporter.hh>

Public Member Functions
	FeaturesReporter ()
virtual	~FeaturesReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
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 ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Member Function Documentation

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

Referenced by 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::ResidueGridScoresFeatures::report_features(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueTypesFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ResidueBurialFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::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

References protocols::features::RelevantResiduesMode::Exclusive, protocols::features::RelevantResiduesMode::Inclusive, relevant_residues_mode_, and utility_exit_with_message.

Referenced by protocols::features::BetaTurnDetectionFeatures::report_features().

virtual void protocols::features::FeaturesReporter::delete_record ( StructureID  , utility::sql_database::sessionOP    )

inlinevirtual

Reimplemented in protocols::features::RotamerFeatures, protocols::features::UnrecognizedAtomFeatures, protocols::features::StructureFeatures, protocols::features::StructureScoresFeatures, protocols::features::ScoreFunctionFeatures, protocols::features::ScoreTypeFeatures, protocols::features::ResidueFeatures, protocols::features::PoseCommentsFeatures, protocols::features::PoseConformationFeatures, protocols::features::ProteinResidueConformationFeatures, protocols::features::ResidueConformationFeatures, protocols::features::PdbDataFeatures, protocols::features::JobDataFeatures, and protocols::features::TrajectoryMapFeatures.

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!

References safely_prepare_statement(), and safely_write_to_database().

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

string protocols::features::FeaturesReporter::find_tag ( core::pose::Pose const &  pose ) const

protected

References protocols::jd2::JobDistributor::current_output_name(), core::pose::Pose::data(), basic::datacache::BasicDataCache::get(), protocols::jd2::JobDistributor::get_instance(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, core::pose::Pose::pdb_info(), and protocols::kinmatch::str().

Referenced by protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().

RelevantResiduesMode::T protocols::features::FeaturesReporter::get_relevant_residues_mode

(

)

const

References relevant_residues_mode_.

virtual void protocols::features::FeaturesReporter::load_into_pose ( utility::sql_database::sessionOP  , StructureID  , core::pose::Pose &    )

inlinevirtual

Reimplemented in protocols::features::StructureFeatures, protocols::features::PoseCommentsFeatures, protocols::features::ResidueConformationFeatures, protocols::features::PdbDataFeatures, and protocols::features::JobDataFeatures.

void protocols::features::FeaturesReporter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  , protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented in protocols::features::HBondFeatures, protocols::features::ProteinRMSDNoSuperpositionFeatures, protocols::features::ProteinRMSDFeatures, protocols::features::ResidueScoresFeatures, protocols::features::ResidueTotalScoresFeatures, protocols::features::UnrecognizedAtomFeatures, protocols::features::RotamerBoltzmannWeightFeatures, protocols::antibody::AntibodyFeatures, protocols::features::helixAssembly::HelixBundleFeatures, protocols::features::RotamerRecoveryFeatures, protocols::features::LoopAnchorFeatures, protocols::features::SmotifFeatures, protocols::features::ScoreFunctionFeatures, protocols::features::WaterFeatures, protocols::features::AtomAtomPairFeatures, protocols::features::HBondParameterFeatures, protocols::features::StructureScoresFeatures, protocols::features::InterfaceFeatures, protocols::features::SecondaryStructureSegmentFeatures, protocols::features::ResidueGridScoresFeatures, protocols::antibody::clusters::CDRClusterFeatures, protocols::features::ScreeningFeatures, and protocols::features::strand_assembly::SandwichFeatures.

References runtime_assert.

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::ProteinRMSDNoSuperpositionFeatures, protocols::features::helixAssembly::HelixBundleFeatures, protocols::features::ProteinRMSDFeatures, protocols::features::ResidueScoresFeatures, protocols::features::ResidueTotalScoresFeatures, protocols::features::UnrecognizedAtomFeatures, protocols::features::WaterFeatures, protocols::features::ProteinBondGeometryFeatures, protocols::features::SmotifFeatures, protocols::features::RotamerRecoveryFeatures, protocols::features::RotamerBoltzmannWeightFeatures, protocols::antibody::AntibodyFeatures, protocols::features::StructureScoresFeatures, protocols::features::LoopAnchorFeatures, protocols::features::TaskOperationFeatures, protocols::features::OrbitalsFeatures, protocols::features::BetaTurnDetectionFeatures, protocols::features::ScoreFunctionFeatures, protocols::features::AtomAtomPairFeatures, protocols::features::HBondParameterFeatures, protocols::features::InterfaceFeatures, protocols::features::SaltBridgeFeatures, protocols::features::HelixCapFeatures, protocols::features::SecondaryStructureSegmentFeatures, protocols::features::helixAssembly::ConcurrencyTest, protocols::features::AtomInResidueAtomInResiduePairFeatures, protocols::features::GeometricSolvationFeatures, protocols::features::RadiusOfGyrationFeatures, protocols::features::ProteinBackboneAtomAtomPairFeatures, protocols::features::ProteinBackboneTorsionAngleFeatures, protocols::features::ResidueBurialFeatures, protocols::features::PairFeatures, protocols::features::ChargeChargeFeatures, protocols::features::strand_assembly::StrandBundleFeatures, protocols::features::PoseCommentsFeatures, protocols::features::ResidueTypesFeatures, protocols::features::PoseConformationFeatures, protocols::features::ProteinResidueConformationFeatures, protocols::features::ResidueConformationFeatures, protocols::features::ResidueSecondaryStructureFeatures, protocols::features::ScoreTypeFeatures, protocols::features::strand_assembly::SandwichFeatures, protocols::features::PdbDataFeatures, protocols::features::StructureFeatures, protocols::features::AtomTypesFeatures, protocols::features::ResidueFeatures, protocols::features::TrajectoryMapFeatures, protocols::features::ResidueGridScoresFeatures, 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

)

References relevant_residues_mode_.

virtual std::string protocols::features::FeaturesReporter::type_name ( ) const

inlinevirtual

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

References schema(), type_name(), utility_exit_with_message, and basic::database::write_schema_to_database().

Member Data Documentation

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

protected

Referenced by check_relevant_residues_range(), protocols::features::StructureScoresFeatures::compute_energies(), get_relevant_residues_mode(), and set_relevant_residues_mode().

---

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

• src/protocols/features/FeaturesReporter.hh
• src/protocols/features/FeaturesReporter.cc