core::simple_metrics Namespace Reference

Namespaces
	composite_metrics
	metrics
	per_residue_metrics

Classes
class	CompositeRealMetric
	A class that is derived to calculate a set of core::Real values. Apply(pose) method calculates this metric and adds it to the pose score for output. More...
class	CompositeStringMetric
	A class that is derived to calculate a set of string values. Apply(pose) method calculates this metric and adds it to the pose score for output. More...
class	PerResidueProbabilitiesMetric
	A class that is derived to calculate probabilities for different residue types for each Residue. Apply(pose) method calculates this metric and adds it to the pose score for output. More...
class	PerResidueRealMetric
	A class that is derived to calculate a set of core::Real values for each Residue. Apply(pose) method calculates this metric and adds it to the pose score for output. More...
class	PerResidueStringMetric
	A class that is derived to calculate a set of string values. Apply(pose) method calculates this metric and adds it to the pose score for output. More...
class	RealMetric
	A class that is derived to calculate a Real (float) value. More...
class	SimpleMetric
	The base class for Metrics in the Metric/Filter/Reporter system. More...
class	SimpleMetricCreator
class	MetricKey
	The key needed to set data in our SimpleMetricData. This allows only SimpleMetrics to set data. More...
class	SimpleMetricData
	A container class for all Simple Metrics stored in the pose. More...
class	SimpleMetricFactory
class	SimpleMetricRegistrator
	This templated class will register an instance of an SimpleMetricCreator (class T) with the SimpleMetricFactory. It will ensure that no SimpleMetric creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
struct	SimpleMetricStruct
	Structure for all SimpleMetric Data. Used for mmTF IO and multistage protocols. More...
class	StringMetric
	A class that is derived to calculate a string value. More...
class	TestStringMetric
	Create subclasses for each type of metric. More...
class	TestRealMetric
class	TestCompositeStringMetric
class	TestCompositeRealMetric
class	TestPerResidueRealMetric
class	TestPerResidueProbabilitiesMetric
class	TestPerResidueStringMetric
class	TestStringMetricCreator
class	TestRealMetricCreator
class	TestCompositeStringMetricCreator
class	TestCompositeRealMetricCreator
class	TestPerResidueRealMetricCreator
class	TestPerResidueProbabilitiesMetricCreator
class	TestPerResidueStringMetricCreator

Typedefs
typedef utility::pointer::shared_ptr< CompositeRealMetric >	CompositeRealMetricOP
typedef utility::pointer::shared_ptr< CompositeRealMetric const >	CompositeRealMetricCOP
typedef utility::pointer::shared_ptr< CompositeRealMetricCreator >	CompositeRealMetricCreatorOP
typedef utility::pointer::shared_ptr< CompositeRealMetricCreator const >	CompositeRealMetricCreatorCOP
typedef utility::pointer::shared_ptr< CompositeStringMetric >	CompositeStringMetricOP
typedef utility::pointer::shared_ptr< CompositeStringMetric const >	CompositeStringMetricCOP
typedef utility::pointer::shared_ptr< CompositeStringMetricCreator >	CompositeStringMetricCreatorOP
typedef utility::pointer::shared_ptr< CompositeStringMetricCreator const >	CompositeStringMetricCreatorCOP
typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetric >	PerResidueProbabilitiesMetricOP
typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetric const >	PerResidueProbabilitiesMetricCOP
typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetricCreator >	PerResidueProbabilitiesMetricCreatorOP
typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetricCreator const >	PerResidueProbabilitiesMetricCreatorCOP
typedef utility::pointer::shared_ptr< PerResidueRealMetric >	PerResidueRealMetricOP
typedef utility::pointer::shared_ptr< PerResidueRealMetric const >	PerResidueRealMetricCOP
typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator >	PerResidueRealMetricCreatorOP
typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator const >	PerResidueRealMetricCreatorCOP
typedef utility::pointer::shared_ptr< PerResidueStringMetric >	PerResidueStringMetricOP
typedef utility::pointer::shared_ptr< PerResidueStringMetric const >	PerResidueStringMetricCOP
typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator >	PerResidueStringMetricCreatorOP
typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator const >	PerResidueStringMetricCreatorCOP
typedef utility::pointer::shared_ptr< RealMetric >	RealMetricOP
typedef utility::pointer::shared_ptr< RealMetric const >	RealMetricCOP
typedef utility::pointer::shared_ptr< RealMetricCreator >	RealMetricCreatorOP
typedef utility::pointer::shared_ptr< RealMetricCreator const >	RealMetricCreatorCOP
typedef utility::pointer::shared_ptr< SimpleMetric >	SimpleMetricOP
typedef utility::pointer::shared_ptr< SimpleMetric const >	SimpleMetricCOP
typedef utility::pointer::shared_ptr< SimpleMetricCreator >	SimpleMetricCreatorOP
typedef utility::pointer::shared_ptr< SimpleMetricCreator const >	SimpleMetricCreatorCOP
typedef utility::pointer::shared_ptr< SimpleMetricData >	SimpleMetricDataOP
typedef utility::pointer::shared_ptr< SimpleMetricData const >	SimpleMetricDataCOP
typedef utility::pointer::weak_ptr< SimpleMetricData >	SimpleMetricDataAP
typedef utility::pointer::weak_ptr< SimpleMetricData const >	SimpleMetricDataCAP
typedef utility::pointer::shared_ptr< StringMetric >	StringMetricOP
typedef utility::pointer::shared_ptr< StringMetric const >	StringMetricCOP
typedef utility::pointer::shared_ptr< StringMetricCreator >	StringMetricCreatorOP
typedef utility::pointer::shared_ptr< StringMetricCreator const >	StringMetricCreatorCOP
typedef utility::pointer::shared_ptr< TestStringMetric >	TestStringMetricOP
typedef utility::pointer::shared_ptr< TestStringMetric const >	TestStringMetricCOP
typedef utility::pointer::shared_ptr< TestRealMetric >	TestRealMetricOP
typedef utility::pointer::shared_ptr< TestRealMetric const >	TestRealMetricCOP
typedef utility::pointer::shared_ptr< TestCompositeStringMetric >	TestCompositeStringMetricOP
typedef utility::pointer::shared_ptr< TestCompositeStringMetric const >	TestCompositeStringMetricCOP
typedef utility::pointer::shared_ptr< TestCompositeRealMetric >	TestCompositeRealMetricOP
typedef utility::pointer::shared_ptr< TestCompositeRealMetric const >	TestCompositeRealMetricCOP
typedef utility::pointer::shared_ptr< TestPerResidueRealMetric >	TestPerResidueRealMetricOP
typedef utility::pointer::shared_ptr< TestPerResidueRealMetric const >	TestPerResidueRealMetricCOP
typedef utility::pointer::shared_ptr< TestPerResidueProbabilitiesMetric >	TestPerResidueProbabilitiesMetricOP
typedef utility::pointer::shared_ptr< TestPerResidueProbabilitiesMetric const >	TestPerResidueProbabilitiesMetricCOP
typedef utility::pointer::shared_ptr< TestPerResidueStringMetric >	TestPerResidueStringMetricOP
typedef utility::pointer::shared_ptr< TestPerResidueStringMetric const >	TestPerResidueStringMetricCOP

Functions
void	run_metrics (core::pose::Pose &pose, utility::vector1< SimpleMetricCOP > const &metrics, std::string prefix="", std::string suffix="")
	Apply a set of SimpleMetrics. More...
SimpleMetricDataOP	get_sm_data (pose::Pose &pose)
	Get a modifiable SM data. Use with caution. Create it in the pose if it does not exist yet. Not for general use. More...
SimpleMetricDataCOP	get_sm_data (pose::Pose const &pose)
	Get a SM Data cache if present. Otherwise, returns a nullptr. More...
std::string	complex_type_name_for_simple_metric (std::string const &simple_metric_name)
bool	has_sm_data (pose::Pose const &pose)
	Does the pose have a SMCache? More...
void	clear_sm_data (pose::Pose &pose)
	Clear the SM data stored in the pose. More...
void	xsd_simple_metric_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &simple_metric_name, std::string const &description, utility::tag::AttributeList const &attributes)
	Generate the ComplexTypeGenerator from the SimpleMetric base class. Add any additional schema options from sub-derived classes. More...
void	xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements (utility::tag::XMLSchemaDefinition &xsd, std::string const &rs_type, std::string const &description, utility::tag::AttributeList const &attributes, utility::tag::XMLSchemaSimpleSubelementList const &subelements)
void	xsd_per_residue_real_metric_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &simple_metric_name, std::string const &description, utility::tag::AttributeList const &attributes)
	Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueRealMetric base classes. Add any additional schema options from sub-derived classes. More...
void	xsd_per_residue_probabilities_metric_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &simple_metric_name, std::string const &description, utility::tag::AttributeList const &attributes)
	Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueProbabilitiesMetric base classes. Add any additional schema options from sub-derived classes. More...
void	xsd_per_residue_string_metric_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &simple_metric_name, std::string const &description, utility::tag::AttributeList const &attributes)
	Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueStringMetric base classes. Add any additional schema options from sub-derived classes. More...
utility::vector1< SimpleMetricCOP >	get_metrics_from_datamap_and_subtags (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap, std::string tag_name)
SimpleMetricCOP	get_metric_from_datamap_and_subtags (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap, std::string tag_name)
void	add_per_residue_simple_metric_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP ct_gen)
	Add options to the schema from this base class. More...
void	throw_sm_override_error (std::string const &out_tag, std::string const &metric_name)
	Get an informative error message if the SM data already exists and is not overriden. Throws. More...

Typedef Documentation

CompositeRealMetricCOP

typedef utility::pointer::shared_ptr< CompositeRealMetric const > core::simple_metrics::CompositeRealMetricCOP

CompositeRealMetricCreatorCOP

typedef utility::pointer::shared_ptr< CompositeRealMetricCreator const > core::simple_metrics::CompositeRealMetricCreatorCOP

CompositeRealMetricCreatorOP

typedef utility::pointer::shared_ptr< CompositeRealMetricCreator > core::simple_metrics::CompositeRealMetricCreatorOP

CompositeRealMetricOP

typedef utility::pointer::shared_ptr< CompositeRealMetric > core::simple_metrics::CompositeRealMetricOP

CompositeStringMetricCOP

typedef utility::pointer::shared_ptr< CompositeStringMetric const > core::simple_metrics::CompositeStringMetricCOP

CompositeStringMetricCreatorCOP

typedef utility::pointer::shared_ptr< CompositeStringMetricCreator const > core::simple_metrics::CompositeStringMetricCreatorCOP

CompositeStringMetricCreatorOP

typedef utility::pointer::shared_ptr< CompositeStringMetricCreator > core::simple_metrics::CompositeStringMetricCreatorOP

CompositeStringMetricOP

typedef utility::pointer::shared_ptr< CompositeStringMetric > core::simple_metrics::CompositeStringMetricOP

PerResidueProbabilitiesMetricCOP

typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetric const > core::simple_metrics::PerResidueProbabilitiesMetricCOP

PerResidueProbabilitiesMetricCreatorCOP

typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetricCreator const > core::simple_metrics::PerResidueProbabilitiesMetricCreatorCOP

PerResidueProbabilitiesMetricCreatorOP

typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetricCreator > core::simple_metrics::PerResidueProbabilitiesMetricCreatorOP

PerResidueProbabilitiesMetricOP

typedef utility::pointer::shared_ptr< PerResidueProbabilitiesMetric > core::simple_metrics::PerResidueProbabilitiesMetricOP

PerResidueRealMetricCOP

typedef utility::pointer::shared_ptr< PerResidueRealMetric const > core::simple_metrics::PerResidueRealMetricCOP

PerResidueRealMetricCreatorCOP

typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator const > core::simple_metrics::PerResidueRealMetricCreatorCOP

PerResidueRealMetricCreatorOP

typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator > core::simple_metrics::PerResidueRealMetricCreatorOP

PerResidueRealMetricOP

typedef utility::pointer::shared_ptr< PerResidueRealMetric > core::simple_metrics::PerResidueRealMetricOP

PerResidueStringMetricCOP

typedef utility::pointer::shared_ptr< PerResidueStringMetric const > core::simple_metrics::PerResidueStringMetricCOP

PerResidueStringMetricCreatorCOP

typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator const > core::simple_metrics::PerResidueStringMetricCreatorCOP

PerResidueStringMetricCreatorOP

typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator > core::simple_metrics::PerResidueStringMetricCreatorOP

PerResidueStringMetricOP

typedef utility::pointer::shared_ptr< PerResidueStringMetric > core::simple_metrics::PerResidueStringMetricOP

RealMetricCOP

typedef utility::pointer::shared_ptr< RealMetric const > core::simple_metrics::RealMetricCOP

RealMetricCreatorCOP

typedef utility::pointer::shared_ptr< RealMetricCreator const > core::simple_metrics::RealMetricCreatorCOP

RealMetricCreatorOP

typedef utility::pointer::shared_ptr< RealMetricCreator > core::simple_metrics::RealMetricCreatorOP

RealMetricOP

typedef utility::pointer::shared_ptr< RealMetric > core::simple_metrics::RealMetricOP

SimpleMetricCOP

typedef utility::pointer::shared_ptr< SimpleMetric const > core::simple_metrics::SimpleMetricCOP

SimpleMetricCreatorCOP

typedef utility::pointer::shared_ptr< SimpleMetricCreator const > core::simple_metrics::SimpleMetricCreatorCOP

SimpleMetricCreatorOP

typedef utility::pointer::shared_ptr< SimpleMetricCreator > core::simple_metrics::SimpleMetricCreatorOP

SimpleMetricDataAP

typedef utility::pointer::weak_ptr< SimpleMetricData > core::simple_metrics::SimpleMetricDataAP

SimpleMetricDataCAP

typedef utility::pointer::weak_ptr< SimpleMetricData const > core::simple_metrics::SimpleMetricDataCAP

SimpleMetricDataCOP

typedef utility::pointer::shared_ptr< SimpleMetricData const > core::simple_metrics::SimpleMetricDataCOP

SimpleMetricDataOP

typedef utility::pointer::shared_ptr< SimpleMetricData > core::simple_metrics::SimpleMetricDataOP

SimpleMetricOP

typedef utility::pointer::shared_ptr< SimpleMetric > core::simple_metrics::SimpleMetricOP

StringMetricCOP

typedef utility::pointer::shared_ptr< StringMetric const > core::simple_metrics::StringMetricCOP

StringMetricCreatorCOP

typedef utility::pointer::shared_ptr< StringMetricCreator const > core::simple_metrics::StringMetricCreatorCOP

StringMetricCreatorOP

typedef utility::pointer::shared_ptr< StringMetricCreator > core::simple_metrics::StringMetricCreatorOP

StringMetricOP

typedef utility::pointer::shared_ptr< StringMetric > core::simple_metrics::StringMetricOP

TestCompositeRealMetricCOP

typedef utility::pointer::shared_ptr< TestCompositeRealMetric const > core::simple_metrics::TestCompositeRealMetricCOP

TestCompositeRealMetricOP

typedef utility::pointer::shared_ptr< TestCompositeRealMetric > core::simple_metrics::TestCompositeRealMetricOP

TestCompositeStringMetricCOP

typedef utility::pointer::shared_ptr< TestCompositeStringMetric const > core::simple_metrics::TestCompositeStringMetricCOP

TestCompositeStringMetricOP

typedef utility::pointer::shared_ptr< TestCompositeStringMetric > core::simple_metrics::TestCompositeStringMetricOP

TestPerResidueProbabilitiesMetricCOP

typedef utility::pointer::shared_ptr< TestPerResidueProbabilitiesMetric const > core::simple_metrics::TestPerResidueProbabilitiesMetricCOP

TestPerResidueProbabilitiesMetricOP

typedef utility::pointer::shared_ptr< TestPerResidueProbabilitiesMetric > core::simple_metrics::TestPerResidueProbabilitiesMetricOP

TestPerResidueRealMetricCOP

typedef utility::pointer::shared_ptr< TestPerResidueRealMetric const > core::simple_metrics::TestPerResidueRealMetricCOP

TestPerResidueRealMetricOP

typedef utility::pointer::shared_ptr< TestPerResidueRealMetric > core::simple_metrics::TestPerResidueRealMetricOP

TestPerResidueStringMetricCOP

typedef utility::pointer::shared_ptr< TestPerResidueStringMetric const > core::simple_metrics::TestPerResidueStringMetricCOP

TestPerResidueStringMetricOP

typedef utility::pointer::shared_ptr< TestPerResidueStringMetric > core::simple_metrics::TestPerResidueStringMetricOP

TestRealMetricCOP

typedef utility::pointer::shared_ptr< TestRealMetric const > core::simple_metrics::TestRealMetricCOP

TestRealMetricOP

typedef utility::pointer::shared_ptr< TestRealMetric > core::simple_metrics::TestRealMetricOP

TestStringMetricCOP

typedef utility::pointer::shared_ptr< TestStringMetric const > core::simple_metrics::TestStringMetricCOP

TestStringMetricOP

typedef utility::pointer::shared_ptr< TestStringMetric > core::simple_metrics::TestStringMetricOP

Function Documentation

add_per_residue_simple_metric_schema()

void core::simple_metrics::add_per_residue_simple_metric_schema

(

utility::tag::XMLSchemaComplexTypeGeneratorOP

ct_gen

)

Add options to the schema from this base class.

Add the schema for per-residue simple metrics. This is to reduce code dup.

References core::select::residue_selector::attributes_for_parse_residue_selector(), and complex_type_name_for_simple_metric().

Referenced by core::simple_metrics::PerResidueProbabilitiesMetric::add_schema(), core::simple_metrics::PerResidueRealMetric::add_schema(), and core::simple_metrics::PerResidueStringMetric::add_schema().

clear_sm_data()

void core::simple_metrics::clear_sm_data

(

core::pose::Pose &

pose

)

Clear the SM data stored in the pose.

References core::pose::Pose::data(), has_sm_data(), and core::pose::datacache::CacheableDataType::SIMPLE_METRIC_DATA.

complex_type_name_for_simple_metric()

std::string core::simple_metrics::complex_type_name_for_simple_metric

(

std::string const &

simple_metric_name

)

Referenced by add_per_residue_simple_metric_schema(), core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), core::simple_metrics::SimpleMetricFactory::define_simple_metric_xml_schema(), xsd_per_residue_probabilities_metric_type_definition_w_attributes(), xsd_per_residue_real_metric_type_definition_w_attributes(), xsd_per_residue_string_metric_type_definition_w_attributes(), xsd_simple_metric_type_definition_w_attributes(), and xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements().

get_metric_from_datamap_and_subtags()

SimpleMetricCOP core::simple_metrics::get_metric_from_datamap_and_subtags	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap,
		std::string	tag_name
	)

References TR().

Referenced by core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::parse_my_tag(), core::simple_metrics::metrics::CalculatorMetric::parse_my_tag(), core::simple_metrics::metrics::ResidueSummaryMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::ProbabilityConservationMetric::parse_my_tag(), protocols::esm_perplexity::PseudoPerplexityMetric::parse_my_tag(), protocols::simple_filters::SimpleMetricFilter::parse_my_tag(), protocols::simple_moves::SampleSequenceFromProbabilities::parse_my_tag(), protocols::simple_moves::SaveProbabilitiesMetricMover::parse_my_tag(), core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(), core::select::residue_selector::SimpleMetricSelector::parse_my_tag(), and protocols::task_operations::RestrictAAsFromProbabilities::parse_tag().

get_metrics_from_datamap_and_subtags()

utility::vector1< SimpleMetricCOP > core::simple_metrics::get_metrics_from_datamap_and_subtags	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap,
		std::string	tag_name
	)

References TR().

Referenced by core::simple_metrics::metrics::AverageProbabilitiesMetric::parse_my_tag(), protocols::analysis::simple_metrics::RunSimpleMetricsMover::parse_my_tag(), protocols::features::SimpleMetricFeatures::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), and protocols::rosetta_scripts::ParsedProtocol::parse_my_tag().

get_sm_data() [1/2]

SimpleMetricDataOP core::simple_metrics::get_sm_data

(

core::pose::Pose &

pose

)

Get a modifiable SM data. Use with caution. Create it in the pose if it does not exist yet. Not for general use.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SIMPLE_METRIC_DATA.

Referenced by core::simple_metrics::CompositeRealMetric::apply(), core::simple_metrics::CompositeStringMetric::apply(), core::simple_metrics::PerResidueProbabilitiesMetric::apply(), core::simple_metrics::PerResidueRealMetric::apply(), core::simple_metrics::PerResidueStringMetric::apply(), core::simple_metrics::RealMetric::apply(), core::simple_metrics::StringMetric::apply(), core::simple_metrics::PerResidueProbabilitiesMetric::cached_calculate(), core::simple_metrics::CompositeRealMetric::cached_calculate(), core::simple_metrics::CompositeStringMetric::cached_calculate(), core::simple_metrics::RealMetric::cached_calculate(), core::simple_metrics::StringMetric::cached_calculate(), core::simple_metrics::PerResidueRealMetric::cached_calculate(), core::simple_metrics::PerResidueStringMetric::cached_calculate(), protocols::jd3::job_summaries::StandardPoseJobSummary::extract_simple_metric_data(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_simple_metric_data(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_metric_to_bfactor().

get_sm_data() [2/2]

SimpleMetricDataCOP core::simple_metrics::get_sm_data

(

core::pose::Pose const &

pose

)

Get a SM Data cache if present. Otherwise, returns a nullptr.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SIMPLE_METRIC_DATA.

has_sm_data()

bool core::simple_metrics::has_sm_data

(

core::pose::Pose const &

pose

)

Does the pose have a SMCache?

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SIMPLE_METRIC_DATA.

Referenced by core::simple_metrics::PerResidueProbabilitiesMetric::cached_calculate(), core::simple_metrics::CompositeRealMetric::cached_calculate(), core::simple_metrics::CompositeStringMetric::cached_calculate(), core::simple_metrics::RealMetric::cached_calculate(), core::simple_metrics::StringMetric::cached_calculate(), core::simple_metrics::PerResidueRealMetric::cached_calculate(), core::simple_metrics::PerResidueStringMetric::cached_calculate(), clear_sm_data(), protocols::jd3::job_summaries::StandardPoseJobSummary::extract_simple_metric_data(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_simple_metric_data(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose().

run_metrics()

void core::simple_metrics::run_metrics	(	core::pose::Pose &	pose,
		utility::vector1< SimpleMetricCOP > const &	metrics,
		std::string	prefix,
		std::string	suffix
	)

Apply a set of SimpleMetrics.

References core::simple_metrics::SimpleMetric::metric().

Referenced by protocols::jd3::jobs::MoverJob::run().

throw_sm_override_error()

void core::simple_metrics::throw_sm_override_error	(	std::string const &	out_tag,
		std::string const &	metric_name
	)

Get an informative error message if the SM data already exists and is not overriden. Throws.

Referenced by core::simple_metrics::CompositeRealMetric::apply(), core::simple_metrics::CompositeStringMetric::apply(), core::simple_metrics::PerResidueProbabilitiesMetric::apply(), core::simple_metrics::PerResidueRealMetric::apply(), core::simple_metrics::PerResidueStringMetric::apply(), core::simple_metrics::RealMetric::apply(), and core::simple_metrics::StringMetric::apply().

xsd_per_residue_probabilities_metric_type_definition_w_attributes()

void core::simple_metrics::xsd_per_residue_probabilities_metric_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueProbabilitiesMetric base classes. Add any additional schema options from sub-derived classes.

References core::simple_metrics::PerResidueProbabilitiesMetric::add_schema(), core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), and complex_type_name_for_simple_metric().

Referenced by core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::provide_xml_schema().

xsd_per_residue_real_metric_type_definition_w_attributes()

void core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueRealMetric base classes. Add any additional schema options from sub-derived classes.

References core::simple_metrics::PerResidueRealMetric::add_schema(), core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), and complex_type_name_for_simple_metric().

Referenced by core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::HbondMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::provide_xml_schema(), and core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::provide_xml_schema().

xsd_per_residue_string_metric_type_definition_w_attributes()

void core::simple_metrics::xsd_per_residue_string_metric_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueStringMetric base classes. Add any additional schema options from sub-derived classes.

References core::simple_metrics::PerResidueStringMetric::add_schema(), core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), and complex_type_name_for_simple_metric().

xsd_simple_metric_type_definition_w_attributes()

void core::simple_metrics::xsd_simple_metric_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Generate the ComplexTypeGenerator from the SimpleMetric base class. Add any additional schema options from sub-derived classes.

References core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), and complex_type_name_for_simple_metric().

Referenced by core::pack::guidance_scoreterms::sap::SapScoreMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ProtocolSettingsMetric::provide_xml_schema(), core::simple_metrics::metrics::AverageProbabilitiesMetric::provide_xml_schema(), core::simple_metrics::metrics::CustomRealValueMetric::provide_xml_schema(), core::simple_metrics::metrics::CustomStringValueMetric::provide_xml_schema(), core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(), core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), core::simple_metrics::metrics::SasaMetric::provide_xml_schema(), core::simple_metrics::metrics::SecondaryStructureMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResidueCountMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema(), core::simple_metrics::metrics::ShapeSimilarityMetric::provide_xml_schema(), core::simple_metrics::metrics::TimingProfileMetric::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::ProbabilityConservationMetric::provide_xml_schema(), core::simple_metrics::TestStringMetric::provide_xml_schema(), core::simple_metrics::TestRealMetric::provide_xml_schema(), core::simple_metrics::TestCompositeStringMetric::provide_xml_schema(), core::simple_metrics::TestCompositeRealMetric::provide_xml_schema(), core::simple_metrics::TestPerResidueRealMetric::provide_xml_schema(), core::simple_metrics::TestPerResidueProbabilitiesMetric::provide_xml_schema(), core::simple_metrics::TestPerResidueStringMetric::provide_xml_schema(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema(), protocols::analysis::simple_metrics::ConstraintsMetric::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_xml_schema(), protocols::drug_design::RDKitMetric::provide_xml_schema(), protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::provide_xml_schema(), protocols::esm_perplexity::PseudoPerplexityMetric::provide_xml_schema(), protocols::filters::FilterValueMetric::provide_xml_schema(), protocols::inverse_folding::MIFSTProbabilitiesMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::provide_xml_schema(), protocols::ptm_prediction::PTMPredictionMetric::provide_xml_schema(), and protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema().

xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements()

void core::simple_metrics::xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes,
		utility::tag::XMLSchemaSimpleSubelementList const &	subelements
	)

References core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(), and complex_type_name_for_simple_metric().

Referenced by core::simple_metrics::metrics::CalculatorMetric::provide_xml_schema(), and protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::provide_xml_schema().