protocols::features::OrbitalsFeatures Class Reference

#include <OrbitalsFeatures.hh>

Inheritance diagram for protocols::features::OrbitalsFeatures:

Public Member Functions
	OrbitalsFeatures ()
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_hpol_orbital_interactions (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID const struct_id, utility::sql_database::sessionOP db_session)
	get statistics based upon polar hydrogen to orbital distance/angle More...
void	report_haro_orbital_interactions (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID const struct_id, utility::sql_database::sessionOP db_session)
	get statistics based upon aromatic hydrogen to orbital distance/angle More...
void	set_OrbH_features_data (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Size const Aindex, core::Size const Hindex, core::Size const Orbindex, numeric::xyzVector< core::Real > const &Orbxyz, core::Size &resNum2, std::string &orbName1, std::string &htype2, std::string &res2name, core::Size &orbNum1, core::Size &hpolNum2, core::Real &cosAOH, core::Real &cosDHO, core::Real &chiBDHO, core::Real &chiBAOH, core::Real &AOH_angle, core::Real &DHO_angle, core::Real &chiBAHD, core::Real &cosAHD, core::Real &OrbHdist)
void	set_OrbOrb_features_data (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Size Aindex, core::Size Dindex, core::Size Orbindex1, core::Size Orbindex2, numeric::xyzVector< core::Real > const &Orbxyz1, numeric::xyzVector< core::Real > const &Orbxyz2, core::Size &resNum2, std::string &orbName1, std::string &res2name, std::string &OrbName2, core::Size &orbNum1, core::Size &OrbNum2, core::Real &cosAOO, core::Real &cosDOO, core::Real &chiBAOO, core::Real &chiBDOO, core::Real &AOO_angle, core::Real &DOO_angle, core::Real &OrbHdist, core::Real &cosAOD, core::Real &AOD_angle, core::Real &chiBAHD, core::Real &cosAHD)
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_HPOL_orbital_table_schema (utility::sql_database::sessionOP db_session) const
	generate the HPOL_orbital table schema More...
void	write_HARO_orbital_table_schema (utility::sql_database::sessionOP db_session) const
	generate the HARO_orbital table schema More...
void	write_orbital_orbital_table_schema (utility::sql_database::sessionOP db_session) const
	generate the HPOL_orbital table schema More...

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::OrbitalsFeatures::OrbitalsFeatures

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Member Function Documentation

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

static

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

utility::vector1< std::string > protocols::features::OrbitalsFeatures::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::OrbitalsFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

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

Size protocols::features::OrbitalsFeatures::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_hpol_orbital_interactions().

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

get statistics based upon aromatic hydrogen to orbital distance/angle

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

get statistics based upon polar hydrogen to orbital distance/angle

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atoms_with_orb_index(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::bonded_orbitals(), core::conformation::Residue::Haro_index(), core::conformation::Residue::Hpol_index(), core::conformation::Residue::name3(), core::conformation::Residue::orbital_xyz(), core::pose::Pose::residue(), set_OrbH_features_data(), set_OrbOrb_features_data(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by report_features().

void protocols::features::OrbitalsFeatures::set_OrbH_features_data	(	core::conformation::Residue &	res1,
		core::conformation::Residue &	res2,
		core::Size const	Aindex,
		core::Size const	Hindex,
		core::Size const	Orbindex,
		numeric::xyzVector< core::Real > const &	Orbxyz,
		core::Size &	resNum2,
		std::string &	orbName1,
		std::string &	htype2,
		std::string &	res2name,
		core::Size &	orbNum1,
		core::Size &	hpolNum2,
		core::Real &	cosAOH,
		core::Real &	cosDHO,
		core::Real &	chiBDHO,
		core::Real &	chiBAOH,
		core::Real &	AOH_angle,
		core::Real &	DHO_angle,
		core::Real &	chiBAHD,
		core::Real &	cosAHD,
		core::Real &	OrbHdist
	)

References core::conformation::Residue::actcoord(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_type(), core::conformation::Residue::bonded_neighbor(), core::chemical::orbitals::OrbitalType::name(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), core::conformation::Residue::orbital_type(), core::conformation::Residue::seqpos(), core::conformation::Residue::update_actcoord(), protocols::kinmatch::xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by report_hpol_orbital_interactions().

void protocols::features::OrbitalsFeatures::set_OrbOrb_features_data	(	core::conformation::Residue &	res1,
		core::conformation::Residue &	res2,
		core::Size	Aindex,
		core::Size	Dindex,
		core::Size	Orbindex1,
		core::Size	Orbindex2,
		numeric::xyzVector< core::Real > const &	Orbxyz1,
		numeric::xyzVector< core::Real > const &	Orbxyz2,
		core::Size &	resNum2,
		std::string &	orbName1,
		std::string &	res2name,
		std::string &	OrbName2,
		core::Size &	orbNum1,
		core::Size &	OrbNum2,
		core::Real &	cosAOO,
		core::Real &	cosDOO,
		core::Real &	chiBAOO,
		core::Real &	chiBDOO,
		core::Real &	AOO_angle,
		core::Real &	DOO_angle,
		core::Real &	OrbHdist,
		core::Real &	cosAOD,
		core::Real &	AOD_angle,
		core::Real &	chiBAHD,
		core::Real &	cosAHD
	)

References core::conformation::Residue::actcoord(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::chemical::orbitals::OrbitalType::name(), core::conformation::Residue::name3(), core::conformation::Residue::orbital_type(), core::conformation::Residue::seqpos(), core::conformation::Residue::update_actcoord(), protocols::kinmatch::xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by report_hpol_orbital_interactions().

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::OrbitalsFeatures::write_HARO_orbital_table_schema ( utility::sql_database::sessionOP  db_session ) const

private

generate the HARO_orbital table schema

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::write_HPOL_orbital_table_schema ( utility::sql_database::sessionOP  db_session ) const

private

generate the HPOL_orbital table schema

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::write_orbital_orbital_table_schema ( utility::sql_database::sessionOP  db_session ) const

private

generate the HPOL_orbital table schema

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::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_HARO_orbital_table_schema(), write_HPOL_orbital_table_schema(), and write_orbital_orbital_table_schema().

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

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