#include <ProteinBondGeometryFeatures.hh>

Public Member Functions
	ProteinBondGeometryFeatures ()

	ProteinBondGeometryFeatures (ProteinBondGeometryFeatures const &src)

virtual	~ProteinBondGeometryFeatures ()

std::string	type_name () const
	return string with class name More...

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

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...

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

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

virtual	~FeaturesReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 &, 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

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::scoring::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_, basic::options::OptionKeys::score::linear_bonded_potential, linear_bonded_potential_, and basic::options::option.

protocols::features::ProteinBondGeometryFeatures::ProteinBondGeometryFeatures ( ProteinBondGeometryFeatures const & src )

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

virtual

Member Function Documentation

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

virtual

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.

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
	)

virtual

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::ResidueType::aa(), core::chemical::aa_vrt, angle, numeric::angle_radians(), 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(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), core::pose::Pose::total_residue(), 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::ResidueType::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), protocols::features::FeaturesReporter::check_relevant_residues(), db_, core::conformation::Residue::is_protein(), j, length, linear_bonded_potential_, core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), core::pose::Pose::total_residue(), 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 angle, core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), protocols::features::FeaturesReporter::check_relevant_residues(), db_, core::chemical::ResidueType::dihedral(), numeric::dihedral_radians(), core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::ResidueType::ndihe(), basic::periodic_range(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), basic::subtract_radian_angles(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by report_features().

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

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

virtual

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().