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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  MetricKey
 The key needed to set data in our SimpleMetricData. This allows only SimpleMetrics to set data. 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  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  TestCompositeRealMetric
 
class  TestCompositeRealMetricCreator
 
class  TestCompositeStringMetric
 
class  TestCompositeStringMetricCreator
 
class  TestPerResidueRealMetric
 
class  TestPerResidueRealMetricCreator
 
class  TestPerResidueStringMetric
 
class  TestPerResidueStringMetricCreator
 
class  TestRealMetric
 
class  TestRealMetricCreator
 
class  TestStringMetric
 Create subclasses for each type of metric. More...
 
class  TestStringMetricCreator
 

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
< 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
< 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_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< SimpleMetricCOPget_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

typedef utility::pointer::shared_ptr< CompositeRealMetric const > core::simple_metrics::CompositeRealMetricCOP
typedef utility::pointer::shared_ptr< CompositeRealMetricCreator const > core::simple_metrics::CompositeRealMetricCreatorCOP
typedef utility::pointer::shared_ptr< CompositeRealMetricCreator > core::simple_metrics::CompositeRealMetricCreatorOP
typedef utility::pointer::shared_ptr< CompositeRealMetric > core::simple_metrics::CompositeRealMetricOP
typedef utility::pointer::shared_ptr< CompositeStringMetric const > core::simple_metrics::CompositeStringMetricCOP
typedef utility::pointer::shared_ptr< CompositeStringMetricCreator const > core::simple_metrics::CompositeStringMetricCreatorCOP
typedef utility::pointer::shared_ptr< CompositeStringMetricCreator > core::simple_metrics::CompositeStringMetricCreatorOP
typedef utility::pointer::shared_ptr< PerResidueRealMetric const > core::simple_metrics::PerResidueRealMetricCOP
typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator const > core::simple_metrics::PerResidueRealMetricCreatorCOP
typedef utility::pointer::shared_ptr< PerResidueRealMetricCreator > core::simple_metrics::PerResidueRealMetricCreatorOP
typedef utility::pointer::shared_ptr< PerResidueRealMetric > core::simple_metrics::PerResidueRealMetricOP
typedef utility::pointer::shared_ptr< PerResidueStringMetric const > core::simple_metrics::PerResidueStringMetricCOP
typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator const > core::simple_metrics::PerResidueStringMetricCreatorCOP
typedef utility::pointer::shared_ptr< PerResidueStringMetricCreator > core::simple_metrics::PerResidueStringMetricCreatorOP
typedef utility::pointer::shared_ptr< RealMetric const > core::simple_metrics::RealMetricCOP
typedef utility::pointer::shared_ptr< RealMetricCreator const > core::simple_metrics::RealMetricCreatorCOP
typedef utility::pointer::shared_ptr< RealMetricCreator > core::simple_metrics::RealMetricCreatorOP
typedef utility::pointer::shared_ptr< RealMetric > core::simple_metrics::RealMetricOP
typedef utility::pointer::shared_ptr< SimpleMetric const > core::simple_metrics::SimpleMetricCOP
typedef utility::pointer::shared_ptr< SimpleMetricCreator const > core::simple_metrics::SimpleMetricCreatorCOP
typedef utility::pointer::shared_ptr< SimpleMetricCreator > core::simple_metrics::SimpleMetricCreatorOP
typedef utility::pointer::weak_ptr< SimpleMetricData > core::simple_metrics::SimpleMetricDataAP
typedef utility::pointer::weak_ptr< SimpleMetricData const > core::simple_metrics::SimpleMetricDataCAP
typedef utility::pointer::shared_ptr< SimpleMetricData const > core::simple_metrics::SimpleMetricDataCOP
typedef utility::pointer::shared_ptr< SimpleMetricData > core::simple_metrics::SimpleMetricDataOP
typedef utility::pointer::shared_ptr< SimpleMetric > core::simple_metrics::SimpleMetricOP
typedef utility::pointer::shared_ptr< StringMetric const > core::simple_metrics::StringMetricCOP
typedef utility::pointer::shared_ptr< StringMetricCreator const > core::simple_metrics::StringMetricCreatorCOP
typedef utility::pointer::shared_ptr< StringMetricCreator > core::simple_metrics::StringMetricCreatorOP
typedef utility::pointer::shared_ptr< StringMetric > core::simple_metrics::StringMetricOP
typedef utility::pointer::shared_ptr< TestCompositeRealMetric const > core::simple_metrics::TestCompositeRealMetricCOP
typedef utility::pointer::shared_ptr< TestPerResidueRealMetric const > core::simple_metrics::TestPerResidueRealMetricCOP
typedef utility::pointer::shared_ptr< TestRealMetric const > core::simple_metrics::TestRealMetricCOP
typedef utility::pointer::shared_ptr< TestRealMetric > core::simple_metrics::TestRealMetricOP
typedef utility::pointer::shared_ptr< TestStringMetric const > core::simple_metrics::TestStringMetricCOP
typedef utility::pointer::shared_ptr< TestStringMetric > core::simple_metrics::TestStringMetricOP

Function Documentation

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::PerResidueStringMetric::add_schema(), and core::simple_metrics::PerResidueRealMetric::add_schema().

void core::simple_metrics::clear_sm_data ( core::pose::Pose pose)
std::string core::simple_metrics::complex_type_name_for_simple_metric ( std::string const &  simple_metric_name)
SimpleMetricCOP core::simple_metrics::get_metric_from_datamap_and_subtags ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap,
std::string  tag_name 
)
utility::vector1< SimpleMetricCOP > core::simple_metrics::get_metrics_from_datamap_and_subtags ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap,
std::string  tag_name 
)
SimpleMetricDataOP core::simple_metrics::get_sm_data ( core::pose::Pose pose)
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.

bool core::simple_metrics::has_sm_data ( core::pose::Pose const &  pose)
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().

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

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::simple_metrics::TestStringMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResidueCountMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::provide_xml_schema(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema(), protocols::filters::FilterValueMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_xml_schema(), core::simple_metrics::metrics::SecondaryStructureMetric::provide_xml_schema(), core::simple_metrics::metrics::TimingProfileMetric::provide_xml_schema(), core::simple_metrics::metrics::SasaMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema(), protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ProtocolSettingsMetric::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), core::simple_metrics::TestRealMetric::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceMetric::provide_xml_schema(), core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema(), core::simple_metrics::TestCompositeStringMetric::provide_xml_schema(), core::simple_metrics::TestCompositeRealMetric::provide_xml_schema(), core::simple_metrics::TestPerResidueRealMetric::provide_xml_schema(), and core::simple_metrics::TestPerResidueStringMetric::provide_xml_schema().

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 
)