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core::simple_metrics::metrics::SequenceSimilarityMetric Class Reference

compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62. More...

#include <SequenceSimilarityMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SequenceSimilarityMetric:
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Public Member Functions

 SequenceSimilarityMetric ()
 
 SequenceSimilarityMetric (select::residue_selector::ResidueSelectorCOP selector)
 
 SequenceSimilarityMetric (SequenceSimilarityMetric const &src)
 
 ~SequenceSimilarityMetric () override
 
core::Real calculate (pose::Pose const &pose) const override
 Calculate the metric. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 the selector will decide which positions will be scored More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector, bool apply_selector_to_native)
 
void set_native_pose (core::pose::PoseCOP setting)
 
void set_apply_selector_to_native (bool setting)
 
void set_native_pose (core::pose::PoseCOP setting, bool apply_selector_to_native)
 
void set_normalize (bool setting)
 
std::string name () const override
 Name of the class. More...
 
std::string metric () const override
 Name of the metric. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 called by parse_my_tag – should not be used directly More...
 
SimpleMetricOP clone () const override
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation information for the residue selector that it uses. More...
 
bool simple_metric_is_unpublished () const override
 This simple metric is unpublished (returns true). More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This simple metric is unpublished. It returns Jack Maguire. More...
 
- Public Member Functions inherited from core::simple_metrics::RealMetric
 RealMetric ()
 
 ~RealMetric () override
 
 RealMetric (RealMetric const &other)
 
void apply (pose::Pose &pose, std::string prefix="", std::string suffix="", bool override_existing_data=false) const override
 Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix. More...
 
core::Real cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true) const
 Grab the data from the pose if it exists or calculate the metric. More...
 
utility::vector1< std::string > get_metric_names () const override
 Get the metric name(s) that this Metric will calculate. More...
 
- Public Member Functions inherited from core::simple_metrics::SimpleMetric
 SimpleMetric (std::string const &simple_metric_type)
 
 ~SimpleMetric () override
 
 SimpleMetric (SimpleMetric const &other)
 
void set_custom_type (std::string const &custom_type)
 
std::string get_custom_type () const
 Additional setting to prefix/suffix. More...
 
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 bool simple_metric_provides_citation_info () const
 Does this simple metric provide information about how to cite it? More...
 

Static Public Member Functions

static core::Real score (std::string const &seq1, std::string const &seq2, bool normalize)
 
static std::string name_static ()
 Name of the class for creator. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::pose::PoseCOP native_pose_
 
bool apply_selector_to_native_
 
bool normalize_
 

Detailed Description

compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( )
core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( select::residue_selector::ResidueSelectorCOP  selector)
core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( SequenceSimilarityMetric const &  src)
core::simple_metrics::metrics::SequenceSimilarityMetric::~SequenceSimilarityMetric ( )
override

Member Function Documentation

core::Real core::simple_metrics::metrics::SequenceSimilarityMetric::calculate ( pose::Pose const &  pose) const
overridevirtual

Calculate the metric.

Calculate and return the value. This function can not store the value. Use the apply function to store the value in the pose.

Implements core::simple_metrics::RealMetric.

References apply_selector_to_native_, native_pose_, normalize_, core::pose::Pose::pdb_info(), score(), selector_, core::pose::Pose::sequence(), and core::pose::Pose::size().

SimpleMetricOP core::simple_metrics::metrics::SequenceSimilarityMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::SequenceSimilarityMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

std::string core::simple_metrics::metrics::SequenceSimilarityMetric::name ( ) const
overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

Referenced by provide_authorship_info_for_unpublished().

std::string core::simple_metrics::metrics::SequenceSimilarityMetric::name_static ( )
static
void core::simple_metrics::metrics::SequenceSimilarityMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::simple_metrics::metrics::SequenceSimilarityMetric::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This simple metric is unpublished. It returns Jack Maguire.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::simple_metrics::metrics::SequenceSimilarityMetric::provide_citation_info ( ) const
overridevirtual

This simple metric is unpublished, but can provide citation information for the residue selector that it uses.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References selector_.

void core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Real core::simple_metrics::metrics::SequenceSimilarityMetric::score ( std::string const &  seq1,
std::string const &  seq2,
bool  normalize 
)
static
void core::simple_metrics::metrics::SequenceSimilarityMetric::set_apply_selector_to_native ( bool  setting)
inline
void core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose ( core::pose::PoseCOP  setting)
inline

References native_pose_.

Referenced by set_native_pose().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose ( core::pose::PoseCOP  setting,
bool  apply_selector_to_native 
)
inline
void core::simple_metrics::metrics::SequenceSimilarityMetric::set_normalize ( bool  setting)
inline

References normalize_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)
inline

the selector will decide which positions will be scored

References selector_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector,
bool  apply_selector_to_native 
)
inline
bool core::simple_metrics::metrics::SequenceSimilarityMetric::simple_metric_is_unpublished ( ) const
overridevirtual

This simple metric is unpublished (returns true).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

Member Data Documentation

bool core::simple_metrics::metrics::SequenceSimilarityMetric::apply_selector_to_native_
private
core::pose::PoseCOP core::simple_metrics::metrics::SequenceSimilarityMetric::native_pose_
mutableprivate
bool core::simple_metrics::metrics::SequenceSimilarityMetric::normalize_
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::SequenceSimilarityMetric::selector_
private

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