#include <AtomAtomPairFeatures.hh>

Inheritance diagram for protocols::features::AtomAtomPairFeatures:

Public Member Functions
	AtomAtomPairFeatures ()

	AtomAtomPairFeatures (AtomAtomPairFeatures const &src)

	~AtomAtomPairFeatures () override

void	write_schema_to_db (utility::sql_database::sessionOP db_session) const override
	return string with class name 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...

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

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	report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

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 Member Functions
void	write_atom_pairs_table_schema (utility::sql_database::sessionOP db_session) const
	generate the atom_in_residue_pairs table schema More...

Private Attributes
core::Real	min_dist_

core::Real	max_dist_

core::Size	nbins_

utility::vector1< std::string >	relevant_atom_names_

std::map< core::Size, core::Size >	atom_index_to_relevant_atom_index_

std::map< std::string, core::Size >	relevant_elements_

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::AtomAtomPairFeatures::AtomAtomPairFeatures ( )

References atom_index_to_relevant_atom_index_, relevant_atom_names_, and relevant_elements_.

protocols::features::AtomAtomPairFeatures::AtomAtomPairFeatures ( AtomAtomPairFeatures const & src )

default

protocols::features::AtomAtomPairFeatures::~AtomAtomPairFeatures ( )

overridedefault

Member Function Documentation

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

static

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

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

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References max_dist_, min_dist_, and nbins_.

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

static

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

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

void protocols::features::AtomAtomPairFeatures::report_atom_pairs	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References atom_index_to_relevant_atom_index_, core::chemical::ResidueTypeBase::atom_type_set(), protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::conformation(), core::pose::Pose::energies(), max_dist_, min_dist_, core::chemical::AtomTypeSet::name(), nbins_, relevant_atom_names_, relevant_elements_, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), core::conformation::Conformation::structure_moved(), and core::conformation::Residue::type().

Referenced by report_features().

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