#include <PoseConformationFeatures.hh>

Inheritance diagram for protocols::features::PoseConformationFeatures:

Public Member Functions
	PoseConformationFeatures ()

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, bool &ideal)
	Load information from pose_conformations into pose. More...

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 &)

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
bool	load_sequence (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)

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

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

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

core::Size	report_features_implementation (core::pose::Pose const &pose_orig, 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

◆ PoseConformationFeatures()

protocols::features::PoseConformationFeatures::PoseConformationFeatures ( )

inline

Member Function Documentation

◆ class_name()

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

static

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

◆ delete_record()

void protocols::features::PoseConformationFeatures::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::PoseConformationFeatures::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.

◆ load_chain_endings()

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

private

References core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), and protocols::features::TR().

Referenced by load_into_pose().

◆ load_fold_tree()

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

private

References core::pose::Pose::fold_tree(), protocols::hybridization::t, and protocols::features::TR().

Referenced by load_into_pose().

◆ load_into_pose()

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

Load information from pose_conformations into pose.

Parameters

[in,out] ideal - true if structure is ideal, false if not

References load_chain_endings(), load_fold_tree(), load_jumps(), and load_sequence().

◆ load_jumps()

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

private

References core::pose::Pose::set_jump(), protocols::hybridization::t, and protocols::features::TR().

Referenced by load_into_pose().

◆ load_sequence()

bool protocols::features::PoseConformationFeatures::load_sequence	(	utility::sql_database::sessionOP	db_session,
		StructureID	struct_id,
		core::pose::Pose &	pose
	)

private

Returns: true if structure is ideal, false if not

References core::chemical::CENTROID, protocols::pack_daemon::error_message, core::chemical::FA_STANDARD, core::pose::make_pose_from_sequence(), core::pose::Pose::size(), and protocols::features::TR().

Referenced by load_into_pose().

◆ provide_xml_schema()

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

static

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

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

◆ report_features()

Size protocols::features::PoseConformationFeatures::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 core::io::pose_from_pose(), report_features_implementation(), and core::pose::Pose::size().

◆ report_features_implementation()

Size protocols::features::PoseConformationFeatures::report_features_implementation	(	core::pose::Pose const &	pose_orig,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)