protocols::features::SmotifFeatures Class Reference

#include <SmotifFeatures.hh>

Inheritance diagram for protocols::features::SmotifFeatures:

Collaboration diagram for protocols::features::SmotifFeatures:

Public Member Functions
	SmotifFeatures ()
	SmotifFeatures (core::scoring::ScoreFunctionOP scfxn)
	SmotifFeatures (SmotifFeatures const &src)
virtual	~SmotifFeatures ()
std::string	type_name () const
	return string with class name More...
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...
void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
utility::vector1 < SecondaryStructureSegment >	get_ss_segments (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
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...
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	load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)
virtual void	delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)

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...

Constructor & Destructor Documentation

protocols::features::SmotifFeatures::SmotifFeatures

(

)

protocols::features::SmotifFeatures::SmotifFeatures

(

core::scoring::ScoreFunctionOP

scfxn)

protocols::features::SmotifFeatures::SmotifFeatures

(

SmotifFeatures const &

src)

protocols::features::SmotifFeatures::~SmotifFeatures ( )

virtual

Member Function Documentation

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

utility::vector1< SecondaryStructureSegment > protocols::features::SmotifFeatures::get_ss_segments	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References protocols::features::SecondaryStructureSegment::dssp, protocols::features::SecondaryStructureSegment::residue_begin, protocols::features::SecondaryStructureSegment::residue_end, and protocols::features::SecondaryStructureSegment::segment_id.

Referenced by report_features().

void protocols::features::SmotifFeatures::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented from protocols::features::FeaturesReporter.

core::Size protocols::features::SmotifFeatures::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.

References core::conformation::Residue::atom(), protocols::geometry::center_of_mass(), core::kinematics::distance(), protocols::features::SecondaryStructureSegment::dssp, get_ss_segments(), core::pose::Pose::residue(), protocols::features::SecondaryStructureSegment::residue_begin, protocols::features::SecondaryStructureSegment::residue_end, protocols::features::SecondaryStructureSegment::segment_id, and core::conformation::Atom::xyz().

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

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::SmotifFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const

virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References core::kinematics::distance().

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

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