core::simple_metrics::SimpleMetric Class Reference

The base class for Metrics in the Metric/Filter/Reporter system. More...

#include <SimpleMetric.hh>

Inheritance diagram for core::simple_metrics::SimpleMetric:

Public Member Functions
	SimpleMetric (std::string const &simple_metric_type)
	~SimpleMetric () override
	SimpleMetric (SimpleMetric const &other)
SimpleMetric &	operator= (SimpleMetric const &)
virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const =0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as label Must be implemented by derived classes. More...
void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...
virtual std::string	name () const =0
	Get the name of SimpleMetric class. More...
virtual std::string	metric () const =0
	Get the name of the Metric. More...
virtual SimpleMetricOP	clone () const =0
virtual utility::vector1 < std::string >	get_metric_names () const =0
	Get the metric name(s) that this Metric will calculate. More...
void	set_custom_type (std::string const &custom_type)
std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...
virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)=0
virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...
std::string	simple_metric_type () const
std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
std::string	simple_metric_type_
	Type of SimpleMetric. AKA RealMetric, StringMetric, etc. More...
std::string	custom_type_ = ""
std::string	tag_name_ = ""

Detailed Description

The base class for Metrics in the Metric/Filter/Reporter system.

The non-templated base class allows us to build one from a factory and interact with it through RosettaScripts.

You should derive from RealMetric, StringMetric, etc. when making a new SimpleMetric. NOT this class!

Constructor & Destructor Documentation

core::simple_metrics::SimpleMetric::SimpleMetric

(

std::string const &

simple_metric_type

)

core::simple_metrics::SimpleMetric::~SimpleMetric ( )

override

core::simple_metrics::SimpleMetric::SimpleMetric

(

SimpleMetric const &

other

)

Member Function Documentation

virtual void core::simple_metrics::SimpleMetric::apply ( std::string const &  out_label, pose::Pose &  pose, bool  override_existing_data = false  ) const

pure virtual

Calculate the metric and add it to the Score, which is output into a scorefile - labeled as label Must be implemented by derived classes.

Implemented in core::simple_metrics::PerResidueRealMetric, core::simple_metrics::PerResidueStringMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::RealMetric, and core::simple_metrics::StringMetric.

Referenced by apply().

void core::simple_metrics::SimpleMetric::apply	(	pose::Pose &	pose,
		std::string const &	prefix = "",
		std::string const &	suffix = "",
		bool	override_existing_data = false
	)		const

Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix.

References apply(), and get_final_sm_type().

virtual SimpleMetricOP core::simple_metrics::SimpleMetric::clone ( ) const

pure virtual

Implemented in core::simple_metrics::TestPerResidueStringMetric, core::simple_metrics::TestPerResidueRealMetric, core::simple_metrics::TestCompositeRealMetric, core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric, core::simple_metrics::metrics::ResidueSummaryMetric, core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric, core::simple_metrics::TestCompositeStringMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::metrics::SequenceMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric, core::simple_metrics::metrics::DihedralDistanceMetric, core::simple_metrics::per_residue_metrics::HbondMetric, protocols::analysis::simple_metrics::SequenceRecoveryMetric, core::simple_metrics::PerResidueStringMetric, core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric, core::simple_metrics::metrics::TotalEnergyMetric, protocols::quantum_annealing::InteractionGraphSummaryMetric, core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric, core::simple_metrics::composite_metrics::ProtocolSettingsMetric, core::simple_metrics::composite_metrics::CompositeEnergyMetric, core::pack::guidance_scoreterms::sap::SapScoreMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::TestRealMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::metrics::CalculatorMetric, core::simple_metrics::RealMetric, core::simple_metrics::metrics::SequenceSimilarityMetric, core::simple_metrics::per_residue_metrics::PerResidueSasaMetric, core::simple_metrics::metrics::SasaMetric, core::simple_metrics::StringMetric, core::simple_metrics::metrics::SelectedResiduesMetric, core::simple_metrics::metrics::TimingProfileMetric, core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric, core::simple_metrics::metrics::SecondaryStructureMetric, core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric, protocols::drug_design::RDKitMetric, core::simple_metrics::metrics::SelectedResiduesPyMOLMetric, protocols::filters::FilterValueMetric, protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric, core::simple_metrics::metrics::SelectedResidueCountMetric, core::simple_metrics::TestStringMetric, protocols::cyclic_peptide::PeptideInternalHbondsMetric, core::simple_metrics::metrics::ShapeSimilarityMetric, core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric, and core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric.

utility::tag::XMLSchemaComplexTypeGeneratorOP core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric ( utility::tag::XMLSchemaDefinition &  )

static

References core::simple_metrics::complex_type_name_for_simple_metric().

Referenced by core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes(), core::simple_metrics::xsd_per_residue_string_metric_type_definition_w_attributes(), core::simple_metrics::xsd_simple_metric_type_definition_w_attributes(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements().

std::string core::simple_metrics::SimpleMetric::get_custom_type

(

)

const

Additional setting to prefix/suffix.

Output data name will be prefix+custom_type+type+suffix

References custom_type_.

Referenced by core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(), get_final_sm_type(), and core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag().

std::string core::simple_metrics::SimpleMetric::get_final_sm_type

(

)

const

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

References get_custom_type(), metric(), and tag_name_.

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

virtual utility::vector1< std::string > core::simple_metrics::SimpleMetric::get_metric_names ( ) const

pure virtual

Get the metric name(s) that this Metric will calculate.

Implemented in core::simple_metrics::TestCompositeRealMetric, core::simple_metrics::TestCompositeStringMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::PerResidueStringMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::composite_metrics::ProtocolSettingsMetric, core::simple_metrics::RealMetric, core::simple_metrics::StringMetric, core::simple_metrics::composite_metrics::CompositeEnergyMetric, core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric, and core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric.

virtual std::string core::simple_metrics::SimpleMetric::metric ( ) const

pure virtual

Get the name of the Metric.

Implemented in core::simple_metrics::TestPerResidueStringMetric, core::simple_metrics::TestPerResidueRealMetric, core::simple_metrics::TestCompositeRealMetric, core::simple_metrics::metrics::ResidueSummaryMetric, core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric, core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric, core::simple_metrics::TestCompositeStringMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::metrics::DihedralDistanceMetric, core::simple_metrics::per_residue_metrics::HbondMetric, core::simple_metrics::PerResidueStringMetric, protocols::analysis::simple_metrics::SequenceRecoveryMetric, core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric, core::simple_metrics::metrics::TotalEnergyMetric, core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric, core::simple_metrics::metrics::SequenceMetric, core::pack::guidance_scoreterms::sap::SapScoreMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::TestRealMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::composite_metrics::ProtocolSettingsMetric, core::simple_metrics::RealMetric, core::simple_metrics::metrics::SequenceSimilarityMetric, core::simple_metrics::metrics::CalculatorMetric, core::simple_metrics::per_residue_metrics::PerResidueSasaMetric, core::simple_metrics::StringMetric, core::simple_metrics::metrics::TimingProfileMetric, protocols::cyclic_peptide::PeptideInternalHbondsMetric, core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric, core::simple_metrics::metrics::SecondaryStructureMetric, core::simple_metrics::metrics::SelectedResiduesMetric, core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric, core::simple_metrics::composite_metrics::CompositeEnergyMetric, protocols::drug_design::RDKitMetric, core::simple_metrics::metrics::SelectedResiduesPyMOLMetric, protocols::filters::FilterValueMetric, protocols::quantum_annealing::InteractionGraphSummaryMetric, core::simple_metrics::metrics::SasaMetric, protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric, core::simple_metrics::metrics::SelectedResidueCountMetric, core::simple_metrics::metrics::ShapeSimilarityMetric, core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric, core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric, and core::simple_metrics::TestStringMetric.

Referenced by get_final_sm_type(), and core::simple_metrics::run_metrics().

virtual std::string core::simple_metrics::SimpleMetric::name ( ) const

pure virtual

Get the name of SimpleMetric class.

Implemented in core::simple_metrics::TestPerResidueStringMetric, core::simple_metrics::TestPerResidueRealMetric, core::simple_metrics::TestCompositeRealMetric, core::simple_metrics::TestCompositeStringMetric, core::simple_metrics::metrics::ResidueSummaryMetric, core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric, core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric, core::simple_metrics::PerResidueStringMetric, core::simple_metrics::metrics::DihedralDistanceMetric, core::simple_metrics::per_residue_metrics::HbondMetric, protocols::analysis::simple_metrics::SequenceRecoveryMetric, core::simple_metrics::TestRealMetric, core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric, core::simple_metrics::metrics::TotalEnergyMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric, core::simple_metrics::metrics::SequenceMetric, core::pack::guidance_scoreterms::sap::SapScoreMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::RealMetric, core::simple_metrics::StringMetric, core::simple_metrics::composite_metrics::ProtocolSettingsMetric, core::simple_metrics::metrics::SequenceSimilarityMetric, core::simple_metrics::metrics::CalculatorMetric, core::simple_metrics::per_residue_metrics::PerResidueSasaMetric, core::simple_metrics::metrics::TimingProfileMetric, protocols::cyclic_peptide::PeptideInternalHbondsMetric, core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric, core::simple_metrics::metrics::SecondaryStructureMetric, core::simple_metrics::metrics::SelectedResiduesMetric, core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric, core::simple_metrics::composite_metrics::CompositeEnergyMetric, protocols::drug_design::RDKitMetric, core::simple_metrics::metrics::SelectedResiduesPyMOLMetric, protocols::filters::FilterValueMetric, protocols::quantum_annealing::InteractionGraphSummaryMetric, core::simple_metrics::metrics::SasaMetric, protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric, core::simple_metrics::metrics::SelectedResidueCountMetric, core::simple_metrics::metrics::ShapeSimilarityMetric, core::simple_metrics::TestStringMetric, core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric, and core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric.

SimpleMetric & core::simple_metrics::SimpleMetric::operator=

(

SimpleMetric const &

ot

)

References custom_type_, and simple_metric_type_.

Referenced by core::simple_metrics::RealMetric::operator=(), and core::simple_metrics::PerResidueRealMetric::operator=().

void core::simple_metrics::SimpleMetric::parse_base_tag ( utility::tag::TagCOP  tag )

virtual

Parse the base class tag. Keep required interface for parse_my_tag.

References custom_type_, set_custom_type(), and tag_name_.

Referenced by core::simple_metrics::metrics::ShapeSimilarityMetric::parse_my_tag(), core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::parse_my_tag(), core::simple_metrics::TestStringMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResidueCountMetric::parse_my_tag(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::parse_my_tag(), core::simple_metrics::metrics::SecondaryStructureMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::parse_my_tag(), core::simple_metrics::metrics::TimingProfileMetric::parse_my_tag(), core::simple_metrics::metrics::SasaMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::parse_my_tag(), core::simple_metrics::metrics::CalculatorMetric::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), core::simple_metrics::composite_metrics::ProtocolSettingsMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::HbondMetric::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), core::simple_metrics::TestRealMetric::parse_my_tag(), core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::parse_my_tag(), core::simple_metrics::metrics::SequenceMetric::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::parse_my_tag(), core::simple_metrics::metrics::RMSDMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag(), core::simple_metrics::metrics::ResidueSummaryMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::parse_my_tag(), core::simple_metrics::TestCompositeStringMetric::parse_my_tag(), core::simple_metrics::TestCompositeRealMetric::parse_my_tag(), core::simple_metrics::TestPerResidueRealMetric::parse_my_tag(), and core::simple_metrics::TestPerResidueStringMetric::parse_my_tag().

virtual void core::simple_metrics::SimpleMetric::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

pure virtual

Implemented in core::simple_metrics::TestPerResidueStringMetric, core::simple_metrics::TestPerResidueRealMetric, core::simple_metrics::TestCompositeRealMetric, core::simple_metrics::TestCompositeStringMetric, core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric, core::simple_metrics::metrics::ResidueSummaryMetric, core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::metrics::SequenceMetric, core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric, core::simple_metrics::metrics::DihedralDistanceMetric, core::simple_metrics::PerResidueStringMetric, core::simple_metrics::TestRealMetric, core::simple_metrics::per_residue_metrics::HbondMetric, protocols::analysis::simple_metrics::SequenceRecoveryMetric, core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric, core::simple_metrics::metrics::TotalEnergyMetric, protocols::quantum_annealing::InteractionGraphSummaryMetric, core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric, core::simple_metrics::CompositeRealMetric, core::simple_metrics::composite_metrics::ProtocolSettingsMetric, core::simple_metrics::composite_metrics::CompositeEnergyMetric, core::pack::guidance_scoreterms::sap::SapScoreMetric, core::simple_metrics::CompositeStringMetric, core::simple_metrics::RealMetric, core::simple_metrics::metrics::CalculatorMetric, core::simple_metrics::StringMetric, core::simple_metrics::metrics::SequenceSimilarityMetric, core::simple_metrics::per_residue_metrics::PerResidueSasaMetric, core::simple_metrics::metrics::SasaMetric, core::simple_metrics::metrics::SelectedResiduesMetric, core::simple_metrics::metrics::TimingProfileMetric, protocols::cyclic_peptide::PeptideInternalHbondsMetric, core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric, core::simple_metrics::metrics::SecondaryStructureMetric, core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric, protocols::drug_design::RDKitMetric, core::simple_metrics::metrics::SelectedResiduesPyMOLMetric, protocols::filters::FilterValueMetric, protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric, core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric, core::simple_metrics::metrics::SelectedResidueCountMetric, core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric, core::simple_metrics::TestStringMetric, and core::simple_metrics::metrics::ShapeSimilarityMetric.

void core::simple_metrics::SimpleMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList &  ) const

virtual

Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

Reimplemented in protocols::cyclic_peptide::PeptideInternalHbondsMetric, core::simple_metrics::metrics::ResidueSummaryMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::metrics::SequenceMetric, core::simple_metrics::metrics::DihedralDistanceMetric, core::simple_metrics::metrics::TotalEnergyMetric, core::simple_metrics::metrics::SelectedResiduesPyMOLMetric, core::simple_metrics::metrics::SequenceSimilarityMetric, core::simple_metrics::metrics::SasaMetric, core::simple_metrics::metrics::TimingProfileMetric, core::simple_metrics::metrics::SecondaryStructureMetric, core::simple_metrics::metrics::SelectedResidueCountMetric, core::simple_metrics::metrics::CalculatorMetric, core::simple_metrics::metrics::SelectedResiduesMetric, and core::simple_metrics::metrics::RMSDMetric.

void core::simple_metrics::SimpleMetric::set_custom_type

(

std::string const &

custom_type

)

References custom_type_.

Referenced by parse_base_tag().

std::string core::simple_metrics::SimpleMetric::simple_metric_type ( ) const

inline

References simple_metric_type_.

Member Data Documentation

std::string core::simple_metrics::SimpleMetric::custom_type_ = ""

private

Referenced by get_custom_type(), operator=(), parse_base_tag(), and set_custom_type().

std::string core::simple_metrics::SimpleMetric::simple_metric_type_

private

Type of SimpleMetric. AKA RealMetric, StringMetric, etc.

Referenced by operator=(), and simple_metric_type().

std::string core::simple_metrics::SimpleMetric::tag_name_ = ""

private

Referenced by get_final_sm_type(), and parse_base_tag().

---

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

• src/core/simple_metrics/SimpleMetric.hh
• src/core/simple_metrics/SimpleMetric.cc