#include <PdbDataFeatures.hh>

Inheritance diagram for protocols::features::PdbDataFeatures:

Collaboration diagram for protocols::features::PdbDataFeatures:

Public Member Functions
	PdbDataFeatures ()

	PdbDataFeatures (PdbDataFeatures const &src)

virtual	~PdbDataFeatures ()

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

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

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

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 &)

Private Member Functions
void	load_residue_pdb_identification (utility::sql_database::sessionOP db_session, boost::uuids::uuid struct_id, core::pose::Pose &pose)

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

void	load_residue_pdb_confidence (utility::sql_database::sessionOP db_session, boost::uuids::uuid 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, boost::uuids::uuid 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, 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 38 of file PdbDataFeatures.hh.

Constructor & Destructor Documentation

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

Definition at line 76 of file PdbDataFeatures.cc.

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

Definition at line 81 of file PdbDataFeatures.cc.

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

virtual

Definition at line 86 of file PdbDataFeatures.cc.

Member Function Documentation

void protocols::features::PdbDataFeatures::delete_record	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

virtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 177 of file PdbDataFeatures.cc.

utility::vector1< std::string > protocols::features::PdbDataFeatures::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 157 of file PdbDataFeatures.cc.

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

private

Definition at line 358 of file PdbDataFeatures.cc.

References core::pose::Pose::n_residue(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

Referenced by report_features().

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

private

Definition at line 253 of file PdbDataFeatures.cc.

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

Referenced by report_features().

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 193 of file PdbDataFeatures.cc.

References load_residue_pdb_confidence(), and load_residue_pdb_identification().

void protocols::features::PdbDataFeatures::load_residue_pdb_confidence	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid	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.

Definition at line 290 of file PdbDataFeatures.cc.

References core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by load_into_pose().

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

private

Definition at line 203 of file PdbDataFeatures.cc.

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

Referenced by load_into_pose().

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