#include <PoseConformationFeatures.hh>

Inheritance diagram for protocols::features::PoseConformationFeatures:

Collaboration diagram for protocols::features::PoseConformationFeatures:

Public Member Functions
	PoseConformationFeatures ()

	PoseConformationFeatures (PoseConformationFeatures const &)

virtual	~PoseConformationFeatures ()

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

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

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

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

Size	report_features_implementation (core::pose::Pose const &pose_orig, 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 PoseConformationFeatures.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 40 of file PoseConformationFeatures.hh.

protocols::features::PoseConformationFeatures::PoseConformationFeatures ( PoseConformationFeatures const & )

inline

Definition at line 42 of file PoseConformationFeatures.hh.

virtual protocols::features::PoseConformationFeatures::~PoseConformationFeatures ( )

inlinevirtual

Definition at line 48 of file PoseConformationFeatures.hh.

Member Function Documentation

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 312 of file PoseConformationFeatures.cc.

utility::vector1< std::string > protocols::features::PoseConformationFeatures::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 167 of file PoseConformationFeatures.cc.

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

private

Definition at line 485 of file PoseConformationFeatures.cc.

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

Referenced by load_into_pose().

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

private

Definition at line 389 of file PoseConformationFeatures.cc.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::fold_tree(), and core::scoring::hbonds::t().

Referenced by load_into_pose().

void protocols::features::PoseConformationFeatures::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 335 of file PoseConformationFeatures.cc.

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

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

private

Definition at line 435 of file PoseConformationFeatures.cc.

References core::pose::Pose::set_jump(), and core::scoring::hbonds::t().

Referenced by load_into_pose().

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

private

Definition at line 347 of file PoseConformationFeatures.cc.

References core::chemical::CENTROID, protocols::pack_daemon::error_message, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), and core::pose::Pose::total_residue().

Referenced by load_into_pose().

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

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

Definition at line 174 of file PoseConformationFeatures.cc.

References core::pose::Pose::n_residue(), core::io::pdb::pose_from_pose(), and report_features_implementation().

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