protocols::features::PdbDataFeatures Class Reference

#include <PdbDataFeatures.hh>

Inheritance diagram for protocols::features::PdbDataFeatures:

Public Member Functions
	PdbDataFeatures ()
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	delete_record (StructureID struct_id, utility::sql_database::sessionOP db_session) override
void	load_into_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose) override
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 &)
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	load_residue_pdb_identification (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
void	insert_residue_pdb_identification_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
void	load_residue_pdb_confidence (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
	load the temperature and occupancy information into the PDBInfo object. Backbone atoms are assigned max_bb_temperature and min_bb_occupancy while sidechain atoms are assigned max_sc_temperature and min_sc_occupancy. More...
void	insert_residue_pdb_confidence_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

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

PdbDataFeatures()

protocols::features::PdbDataFeatures::PdbDataFeatures ( )

default

Member Function Documentation

class_name()

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

static

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

delete_record()

void protocols::features::PdbDataFeatures::delete_record ( StructureID  struct_id, utility::sql_database::sessionOP  db_session  )

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

features_reporter_dependencies()

utility::vector1< std::string > protocols::features::PdbDataFeatures::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.

insert_residue_pdb_confidence_rows()

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

private

References protocols::features::FeaturesReporter::check_relevant_residues(), core::chemical::ResidueType::mainchain_atoms(), protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by report_features().

insert_residue_pdb_identification_rows()

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

private

References protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by report_features().

load_into_pose()

void protocols::features::PdbDataFeatures::load_into_pose ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::pose::Pose &  pose  )

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References load_residue_pdb_confidence(), and load_residue_pdb_identification().

load_residue_pdb_confidence()

void protocols::features::PdbDataFeatures::load_residue_pdb_confidence ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::pose::Pose &  pose  )

private

load the temperature and occupancy information into the PDBInfo object. Backbone atoms are assigned max_bb_temperature and min_bb_occupancy while sidechain atoms are assigned max_sc_temperature and min_sc_occupancy.

Note: The information stored in the residue_pdb_confidence table is at the residue level not atom level. Since the temperature and occupancy is usually at the atom level, writing data to the database and reading it back in will result in a loss of information.

References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::last_backbone_atom(), core::chemical::ResidueType::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and protocols::features::TR().

Referenced by load_into_pose().

load_residue_pdb_identification()

void protocols::features::PdbDataFeatures::load_residue_pdb_identification ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::pose::Pose &  pose  )

private

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by load_into_pose().

provide_xml_schema()

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

static

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

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

report_features()

Size protocols::features::PdbDataFeatures::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 insert_residue_pdb_confidence_rows(), and insert_residue_pdb_identification_rows().

type_name()

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

write_schema_to_db()

void protocols::features::PdbDataFeatures::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.

---

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

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