#include <SimpleMetricFeatures.hh>

Inheritance diagram for protocols::features::SimpleMetricFeatures:

Public Member Functions
	SimpleMetricFeatures ()

	SimpleMetricFeatures (utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics)

utility::vector1< std::string >	features_reporter_dependencies () const override
	return string with class name 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...

void	add_simple_metric (core::simple_metrics::SimpleMetricCOP metric)
	Add a simple_metric. More...

void	set_use_cached_data (bool use_cache)
	Set this FeaturesReporter to use cached data from the pose matching the metric if possible. Default false. More...

void	set_fail_on_missing_cache (bool fail_on_missing)
	If use_cache is set to false, do we fail if no data is found in the pose? Default True. More...

void	set_simple_metrics (utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics)
	Set the simple metrics we will run. More...

void	set_prefix_suffix (std::string prefix="", std::string suffix="")
	Set extra columns, prefix and suffix, for each data added to the database. Used for multiple runs of the features. Also used for matching cached data from the pose. More...

void	set_table_name (std::string="simple_metrics")

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

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 Member Functions
void	write_general_schema_to_db (utility::sql_database::sessionOP db_session) const

void	write_per_residue_schema_to_db (utility::sql_database::sessionOP db_session) const

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

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

void	write_per_residue_data_row (StructureID struct_id, core::Size resnum, utility::vector1< std::string > const &data_names, std::map< std::string, std::map< core::Size, std::string > > const &string_data, std::map< std::string, std::map< core::Size, core::Real > > const &real_data, utility::sql_database::sessionOP db_session)

Private Attributes
utility::vector1 < core::simple_metrics::SimpleMetricCOP >	metrics_

std::string	prefix_ =""

std::string	suffix_ =""

std::string	table_name_ ="simple_metrics"

bool	use_cache_ = false

bool	fail_on_missing_cache_ = true

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::SimpleMetricFeatures::SimpleMetricFeatures ( )

protocols::features::SimpleMetricFeatures::SimpleMetricFeatures ( utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics )

References set_simple_metrics().

Member Function Documentation

void protocols::features::SimpleMetricFeatures::add_simple_metric ( core::simple_metrics::SimpleMetricCOP metric )

Add a simple_metric.

References metrics_.

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

static

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

utility::vector1< std::string > protocols::features::SimpleMetricFeatures::features_reporter_dependencies ( ) const

overridevirtual

return string with class name

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References fail_on_missing_cache_, core::simple_metrics::get_metrics_from_datamap_and_subtags(), prefix_, set_fail_on_missing_cache(), set_prefix_suffix(), set_simple_metrics(), set_table_name(), set_use_cached_data(), suffix_, table_name_, type_name(), and use_cache_.

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

static

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

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

core::Size protocols::features::SimpleMetricFeatures::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 report_general_features(), and report_per_residue_features().

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

private

collect all the feature data for the pose

References core::simple_metrics::StringMetric::cached_calculate(), core::simple_metrics::RealMetric::cached_calculate(), core::simple_metrics::CompositeStringMetric::cached_calculate(), core::simple_metrics::CompositeRealMetric::cached_calculate(), fail_on_missing_cache_, protocols::features::get_question_mark_string(), core::simple_metrics::StringMetric::metric(), core::simple_metrics::RealMetric::metric(), core::simple_metrics::CompositeStringMetric::metric(), core::simple_metrics::CompositeRealMetric::metric(), metrics_, prefix_, suffix_, table_name_, protocols::features::TR(), and use_cache_.

Referenced by report_features().

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

private

References core::simple_metrics::PerResidueStringMetric::cached_calculate(), core::simple_metrics::PerResidueRealMetric::cached_calculate(), fail_on_missing_cache_, core::simple_metrics::PerResidueStringMetric::metric(), core::simple_metrics::PerResidueRealMetric::metric(), metrics_, prefix_, core::simple_metrics::PerResidueRealMetric::set_residue_selector(), core::simple_metrics::PerResidueStringMetric::set_residue_selector(), core::pose::Pose::size(), suffix_, use_cache_, and write_per_residue_data_row().

Referenced by report_features().

void protocols::features::SimpleMetricFeatures::set_fail_on_missing_cache ( bool fail_on_missing )

If use_cache is set to false, do we fail if no data is found in the pose? Default True.

References fail_on_missing_cache_.

Referenced by parse_my_tag().

void protocols::features::SimpleMetricFeatures::set_prefix_suffix	(	std::string	prefix = `""`,
		std::string	suffix = `""`
	)

Set extra columns, prefix and suffix, for each data added to the database. Used for multiple runs of the features. Also used for matching cached data from the pose.

References prefix_, and suffix_.

Referenced by parse_my_tag().

void protocols::features::SimpleMetricFeatures::set_simple_metrics ( utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics )

Set the simple metrics we will run.

References metrics_.

Referenced by parse_my_tag(), and SimpleMetricFeatures().

void protocols::features::SimpleMetricFeatures::set_table_name ( std::string table_name = "simple_metrics" )

References table_name_.

Referenced by parse_my_tag().

void protocols::features::SimpleMetricFeatures::set_use_cached_data ( bool use_cache )

Set this FeaturesReporter to use cached data from the pose matching the metric if possible. Default false.

See Also: set_prefix_suffix() for matching on prefix/suffix set for the metric.

References use_cache_.

Referenced by parse_my_tag().

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

Referenced by parse_my_tag().

void protocols::features::SimpleMetricFeatures::write_general_schema_to_db ( utility::sql_database::sessionOP db_session ) const

private

References metrics_, and table_name_.

Referenced by write_schema_to_db().

void protocols::features::SimpleMetricFeatures::write_per_residue_data_row	(	StructureID	struct_id,
		core::Size	resnum,
		utility::vector1< std::string > const &	data_names,
		std::map< std::string, std::map< core::Size, std::string > > const &	string_data,
		std::map< std::string, std::map< core::Size, core::Real > > const &	real_data,
		utility::sql_database::sessionOP	db_session
	)