#include <ModelFeatures.hh>

Inheritance diagram for protocols::features::ModelFeatures:

Public Member Functions
	ModelFeatures ()

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...

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< Segment >	find_segments (protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session)
	get the vector of beginnings/ends of secondary structure segments More...

void	trim_pose (core::pose::Pose &pose, std::set< core::Size > resnums) const
	for testing purposes only More...

core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session) override
	collect all the feature data for the pose More...

void	write_clique_to_db (std::set< core::Size > const &clique, protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session) const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override

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

virtual void	delete_record (StructureID, utility::sql_database::sessionOP)

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 Attributes
core::Size	min_helix_size_

core::Size	min_strand_size_

core::Size	min_ss_cluster_size_

core::Size	max_ss_cluster_size_

core::Real	distance_cutoff_

core::Real	angle_cutoff_

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

◆ ModelFeatures()

protocols::features::ModelFeatures::ModelFeatures ( )

Member Function Documentation

◆ class_name()

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

static

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

◆ features_reporter_dependencies()

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

◆ find_segments()

utility::vector1< Segment > protocols::features::ModelFeatures::find_segments	(	protocols::features::StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get the vector of beginnings/ends of secondary structure segments

References protocols::features::Segment::begin, protocols::features::Segment::dssp, protocols::simple_filters::dssp(), protocols::features::Segment::end, protocols::features::Segment::id, min_helix_size_, min_strand_size_, and protocols::features::TR().

Referenced by report_features().

◆ parse_my_tag()

void protocols::features::ModelFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References angle_cutoff_, distance_cutoff_, max_ss_cluster_size_, min_helix_size_, min_ss_cluster_size_, min_strand_size_, and type_name().

◆ provide_xml_schema()

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

static

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

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

◆ report_features()

core::Size protocols::features::ModelFeatures::report_features	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		protocols::features::StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References angle_cutoff_, core::conformation::Residue::atom(), distance_cutoff_, core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::fa_atr, find_segments(), core::pose::metrics::CalculatorFactory::Instance(), protocols::mean_field::max(), max_ss_cluster_size_, core::pose::Pose::metric(), protocols::mean_field::min(), min_helix_size_, min_ss_cluster_size_, min_strand_size_, core::pose::Pose::pdb_info(), core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::metrics::CalculatorFactory::remove_calculator(), core::pose::Pose::residue(), core::pose::Pose::size(), core::id::to_string(), protocols::features::TR(), write_clique_to_db(), and core::conformation::Atom::xyz().

◆ trim_pose()

void protocols::features::ModelFeatures::trim_pose	(	core::pose::Pose &	pose,
		std::set< core::Size >	resnums
	)		const

for testing purposes only

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

◆ type_name()

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

Referenced by parse_my_tag().

◆ write_clique_to_db()

void protocols::features::ModelFeatures::write_clique_to_db	(	std::set< core::Size > const &	clique,
		protocols::features::StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)		const

Referenced by report_features().

◆ write_schema_to_db()

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

overridevirtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Member Data Documentation

◆ angle_cutoff_

core::Real protocols::features::ModelFeatures::angle_cutoff_

private

Referenced by parse_my_tag(), and report_features().

◆ distance_cutoff_

core::Real protocols::features::ModelFeatures::distance_cutoff_

private

Referenced by parse_my_tag(), and report_features().

◆ max_ss_cluster_size_

core::Size protocols::features::ModelFeatures::max_ss_cluster_size_

private

Referenced by parse_my_tag(), and report_features().

◆ min_helix_size_

core::Size protocols::features::ModelFeatures::min_helix_size_

private

Referenced by find_segments(), parse_my_tag(), and report_features().

◆ min_ss_cluster_size_

core::Size protocols::features::ModelFeatures::min_ss_cluster_size_

private

Referenced by parse_my_tag(), and report_features().

◆ min_strand_size_

core::Size protocols::features::ModelFeatures::min_strand_size_

private

Referenced by find_segments(), parse_my_tag(), and report_features().

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

src/protocols/features/ModelFeatures.hh
src/protocols/features/ModelFeatures.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ModelFeatures()

Member Function Documentation

◆ class_name()

◆ features_reporter_dependencies()

◆ find_segments()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_features()

◆ trim_pose()

◆ type_name()

◆ write_clique_to_db()

◆ write_schema_to_db()

Member Data Documentation

◆ angle_cutoff_

◆ distance_cutoff_

◆ max_ss_cluster_size_

◆ min_helix_size_

◆ min_ss_cluster_size_

◆ min_strand_size_