#include <PdbDataFeatures.hh>

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, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

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

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

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 &)

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	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

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

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

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

virtual

Member Function Documentation

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

References safely_prepare_statement(), and safely_write_to_database().

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.

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 basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), protocols::features::FeaturesReporter::check_relevant_residues(), utility::tools::make_vector(), max(), min, core::pose::Pose::n_residue(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

Referenced by report_features().

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 basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), protocols::features::FeaturesReporter::check_relevant_residues(), utility::tools::make_vector(), core::pose::Pose::n_residue(), core::pose::Pose::pdb_info(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

Referenced by report_features().

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

References load_residue_pdb_confidence(), and load_residue_pdb_identification().

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::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), safely_prepare_statement(), safely_read_from_database(), table_exists(), core::pose::Pose::total_residue(), and protocols::features::TR.

Referenced by load_into_pose().

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(), safely_prepare_statement(), safely_read_from_database(), table_exists(), 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,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)