#include <ProteinBondGeometryFeatures.hh>

Inheritance diagram for protocols::features::ProteinBondGeometryFeatures:

Collaboration diagram for protocols::features::ProteinBondGeometryFeatures:

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, boost::uuids::uuid 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, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

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

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

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

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

Public Member Functions inherited from protocols::features::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 &, boost::uuids::uuid, utility::sql_database::sessionOP)
	collect all the feature data for the pose. More...

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

virtual void	load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)

virtual void	delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)

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, boost::uuids::uuid 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...

Detailed Description

Definition at line 39 of file ProteinBondGeometryFeatures.hh.

Constructor & Destructor Documentation

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

Definition at line 62 of file ProteinBondGeometryFeatures.cc.

References db_, and linear_bonded_potential_.

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

Definition at line 71 of file ProteinBondGeometryFeatures.cc.

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

virtual

Definition at line 76 of file ProteinBondGeometryFeatures.cc.

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.

Definition at line 342 of file ProteinBondGeometryFeatures.cc.

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

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

Definition at line 349 of file ProteinBondGeometryFeatures.cc.

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,
		boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 445 of file ProteinBondGeometryFeatures.cc.

Referenced by report_features().

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

Definition at line 364 of file ProteinBondGeometryFeatures.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::chemical::ResidueType::bondangle(), db_, core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::AtomType::name(), core::chemical::ResidueType::num_bondangles(), core::pose::Pose::residue(), 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,
		boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 579 of file ProteinBondGeometryFeatures.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), db_, core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::AtomType::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::pose::Pose::residue(), 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,
		boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 719 of file ProteinBondGeometryFeatures.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), db_, core::chemical::ResidueType::dihedral(), core::conformation::Residue::is_protein(), linear_bonded_potential_, core::chemical::AtomType::name(), core::chemical::ResidueType::ndihe(), core::pose::Pose::residue(), 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.

Definition at line 79 of file ProteinBondGeometryFeatures.cc.

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

Definition at line 141 of file ProteinBondGeometryFeatures.cc.

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

Definition at line 235 of file ProteinBondGeometryFeatures.cc.

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

Definition at line 93 of file ProteinBondGeometryFeatures.cc.

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

Definition at line 191 of file ProteinBondGeometryFeatures.cc.

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

Definition at line 290 of file ProteinBondGeometryFeatures.cc.

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.

Definition at line 82 of file ProteinBondGeometryFeatures.cc.

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().