#include <ProteinBondGeometryFeatures.hh>

Inheritance diagram for protocols::features::ProteinBondGeometryFeatures:

Public Member Functions
	ProteinBondGeometryFeatures ()

void	write_schema_to_db (utility::sql_database::sessionOP db_session) const override
	generate the table schemas and write them to the database More...

utility::vector1< std::string >	features_reporter_dependencies () const override
	return the set of features reporters that are required to also already be extracted by the time this one is used. More...

core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) override
	collect all the feature data for the pose More...

void	report_intrares_angles (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	report_interres_angles (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	report_intrares_lengths (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	report_interres_lengths (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	report_intrares_torsions (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

std::string	type_name () const override

Public Member Functions inherited from protocols::features::FeaturesReporter
	FeaturesReporter ()

	~FeaturesReporter () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

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...

core::Size	report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
	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

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	write_bond_intrares_angles_table_schema (utility::sql_database::sessionOP db_session) const
	generate the bond_intrares_angles table schema More...

void	write_bond_interres_angles_table_schema (utility::sql_database::sessionOP db_session) const
	generate the bond_interres_angles table schema More...

void	write_bond_intrares_lengths_table_schema (utility::sql_database::sessionOP db_session) const
	generate the bond_intrares_lengths table schema More...

void	write_bond_interres_lengths_table_schema (utility::sql_database::sessionOP db_session) const
	generate the bond_interres_lengths table schema More...

void	write_bond_intrares_torsions_table_schema (utility::sql_database::sessionOP db_session) const
	generate the bond_intrares_torsions table schema More...

Private Attributes
core::energy_methods::IdealParametersDatabaseOP	db_

bool	linear_bonded_potential_

Additional Inherited Members
Protected Member Functions inherited from protocols::features::FeaturesReporter
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 inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T	relevant_residues_mode_

Constructor & Destructor Documentation

protocols::features::ProteinBondGeometryFeatures::ProteinBondGeometryFeatures ( )

References db_, and linear_bonded_potential_.

Member Function Documentation

std::string protocols::features::ProteinBondGeometryFeatures::class_name ( )

static

Referenced by provide_xml_schema(), protocols::features::ProteinBondGeometryFeaturesCreator::type_name(), and type_name().

utility::vector1< std::string > protocols::features::ProteinBondGeometryFeatures::features_reporter_dependencies ( ) const

overridevirtual

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

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::ProteinBondGeometryFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::features::xsd_type_definition_w_attributes().

Referenced by protocols::features::ProteinBondGeometryFeaturesCreator::provide_xml_schema().

Size protocols::features::ProteinBondGeometryFeatures::report_features	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References report_interres_angles(), report_interres_lengths(), report_intrares_angles(), report_intrares_lengths(), and report_intrares_torsions().

void protocols::features::ProteinBondGeometryFeatures::report_interres_angles	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Referenced by report_features().

void protocols::features::ProteinBondGeometryFeatures::report_interres_lengths	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

void protocols::features::ProteinBondGeometryFeatures::report_intrares_angles	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::bondangle(), protocols::features::FeaturesReporter::check_relevant_residues(), db_, core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::ResidueType::num_bondangles(), core::pose::Pose::residue(), core::pose::Pose::size(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by report_features().

void protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), protocols::features::FeaturesReporter::check_relevant_residues(), protocols::hybridization::d0, db_, core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::pose::Pose::residue(), core::pose::Pose::size(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by report_features().

void protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), protocols::features::FeaturesReporter::check_relevant_residues(), db_, core::chemical::ResidueType::dihedral(), core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::ResidueType::ndihe(), core::pose::Pose::residue(), core::pose::Pose::size(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by report_features().

std::string protocols::features::ProteinBondGeometryFeatures::type_name ( ) const

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::ProteinBondGeometryFeatures::write_bond_interres_angles_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the bond_interres_angles table schema

References protocols::buns::energy.

Referenced by write_schema_to_db().

void protocols::features::ProteinBondGeometryFeatures::write_bond_interres_lengths_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the bond_interres_lengths table schema

References protocols::buns::energy.

Referenced by write_schema_to_db().

void protocols::features::ProteinBondGeometryFeatures::write_bond_intrares_angles_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the bond_intrares_angles table schema

References protocols::buns::energy.

Referenced by write_schema_to_db().

void protocols::features::ProteinBondGeometryFeatures::write_bond_intrares_lengths_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the bond_intrares_lengths table schema

References protocols::buns::energy.

Referenced by write_schema_to_db().

void protocols::features::ProteinBondGeometryFeatures::write_bond_intrares_torsions_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the bond_intrares_torsions table schema

References protocols::buns::energy.

Referenced by write_schema_to_db().

void protocols::features::ProteinBondGeometryFeatures::write_schema_to_db ( utility::sql_database::sessionOP db_session ) const

overridevirtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_bond_interres_angles_table_schema(), write_bond_interres_lengths_table_schema(), write_bond_intrares_angles_table_schema(), write_bond_intrares_lengths_table_schema(), and write_bond_intrares_torsions_table_schema().