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core::simple_metrics::SimpleMetric Class Referenceabstract

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

#include <SimpleMetric.hh>

Inheritance diagram for core::simple_metrics::SimpleMetric:
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Public Member Functions

 SimpleMetric (std::string const &simple_metric_type)
 
 ~SimpleMetric () override
 
 SimpleMetric (SimpleMetric const &other)
 
SimpleMetricoperator= (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_ = ""
 

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::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::metrics::SequenceMetric, core::simple_metrics::PerResidueRealMetric, 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, 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, protocols::quantum_annealing::InteractionGraphSummaryMetric, 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, and core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric.

utility::tag::XMLSchemaComplexTypeGeneratorOP core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric ( utility::tag::XMLSchemaDefinition &  )
static
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
virtual utility::vector1< std::string > core::simple_metrics::SimpleMetric::get_metric_names ( ) const
pure virtual
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::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::metrics::InteractionEnergyMetric, 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::composite_metrics::ElectrostaticComplementarityMetric, 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::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::PerResidueRealMetric, 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::TestStringMetric, and core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric.

SimpleMetric & core::simple_metrics::SimpleMetric::operator= ( SimpleMetric const &  ot)
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_, and set_custom_type().

Referenced by 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::metrics::SequenceMetric::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::RMSDMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::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::per_residue_metrics::PerResidueClashMetric, core::simple_metrics::metrics::RMSDMetric, core::simple_metrics::metrics::InteractionEnergyMetric, core::simple_metrics::PerResidueRealMetric, core::simple_metrics::metrics::SequenceMetric, 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, 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, protocols::quantum_annealing::InteractionGraphSummaryMetric, 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, and core::simple_metrics::TestStringMetric.

void core::simple_metrics::SimpleMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList &  ) const
virtual
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
std::string core::simple_metrics::SimpleMetric::simple_metric_type_
private

Type of SimpleMetric. AKA RealMetric, StringMetric, etc.

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


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