#include <HelixBundleFeatures.hh>

Inheritance diagram for protocols::features::helixAssembly::HelixBundleFeatures:

Public Member Functions
	HelixBundleFeatures ()

void	write_schema_to_db (utility::sql_database::sessionOP db_session) const override
	generate the table schemas and write them to the database More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &pose) override
	calculate the shared fa_attr for each pair of helices in the bundle 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...

utility::vector1 < HelicalFragmentOP >	get_helices (StructureID struct_id, utility::sql_database::sessionOP db_session)

bool	validate_bundle (core::pose::Pose const &pose, utility::vector1< HelicalFragment > const &helices)

void	write_bundle_to_db (protocols::features::StructureID const &struct_id, utility::sql_database::sessionOP db_session, utility::vector1< HelicalFragment > const &bundle)

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 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	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::Real	helix_cap_dist_cutoff_

core::Size	num_helices_per_bundle_

core::Size	min_helix_size_

core::Real	min_per_residue_fa_attr_

core::Real	min_interacting_set_fraction_

protocols::simple_filters::InterfaceSasaFilter	sasa_filter_

core::scoring::ScoreFunctionOP	scorefxn_

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::helixAssembly::HelixBundleFeatures::HelixBundleFeatures ( )

References core::scoring::get_score_function(), and scorefxn_.

Member Function Documentation

std::string protocols::features::helixAssembly::HelixBundleFeatures::class_name ( )

static

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

utility::vector1< std::string > protocols::features::helixAssembly::HelixBundleFeatures::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.

utility::vector1< HelicalFragmentOP > protocols::features::helixAssembly::HelixBundleFeatures::get_helices	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References min_helix_size_, and protocols::features::TR().

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)

overridevirtual

calculate the shared fa_attr for each pair of helices in the bundle

Reimplemented from protocols::features::FeaturesReporter.

References helix_cap_dist_cutoff_, min_helix_size_, min_interacting_set_fraction_, min_per_residue_fa_attr_, num_helices_per_bundle_, and type_name().

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

static

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

Referenced by protocols::features::helixAssembly::HelixBundleFeaturesCreator::provide_xml_schema().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::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 get_helices(), min_helix_size_, num_helices_per_bundle_, protocols::features::helixAssembly::HelicalFragment::size(), protocols::features::TR(), validate_bundle(), and write_bundle_to_db().

std::string protocols::features::helixAssembly::HelixBundleFeatures::type_name ( ) const

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

Referenced by parse_my_tag().

bool protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle	(	core::pose::Pose const &	pose,
		utility::vector1< HelicalFragment > const &	helices
	)

validate that the bundle fits all the requirements. Currently, the only requirement is that each helix in the bundle has a c-alpha, c-alpha distance less than the specified cutoff with at least 2 other helices in the same bundle

References core::conformation::Residue::atom(), core::sequence::end, helix_cap_dist_cutoff_, num_helices_per_bundle_, core::pose::Pose::residue(), protocols::loops::start, protocols::features::TR(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::write_bundle_to_db	(	protocols::features::StructureID const &	struct_id,
		utility::sql_database::sessionOP	db_session,
		utility::vector1< HelicalFragment > const &	bundle
	)

Write the given bundle to the database. This involves writing to three tables: helix_bundles - the top-level table. Has a unique bundle_id. FK to the structure bundle_helices - the individual helical segments that make up the bundle. FK to the bundle table bundle_pairs - the pairs of helices that make up the bundle. FKs to the bundle table and the bundle_helices table

References num_helices_per_bundle_.

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::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

core::Real protocols::features::helixAssembly::HelixBundleFeatures::helix_cap_dist_cutoff_

private

Referenced by parse_my_tag(), and validate_bundle().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::min_helix_size_

private

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

core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_interacting_set_fraction_

private

Referenced by parse_my_tag().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_per_residue_fa_attr_

private

Referenced by parse_my_tag().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::num_helices_per_bundle_

private

Referenced by parse_my_tag(), report_features(), validate_bundle(), and write_bundle_to_db().

protocols::simple_filters::InterfaceSasaFilter protocols::features::helixAssembly::HelixBundleFeatures::sasa_filter_

private

core::scoring::ScoreFunctionOP protocols::features::helixAssembly::HelixBundleFeatures::scorefxn_

private

Referenced by HelixBundleFeatures().

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

src/protocols/features/helixAssembly/HelixBundleFeatures.hh
src/protocols/features/helixAssembly/HelixBundleFeatures.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation