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core::simple_metrics::metrics::ShapeSimilarityMetric Class Reference

#include <ShapeSimilarityMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::ShapeSimilarityMetric:
Inheritance graph
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Public Types

typedef core::scoring::sc::RESULTS ShapeSimilarityCalculatorResults
 

Public Member Functions

 ShapeSimilarityMetric ()
 default constructor More...
 
 ~ShapeSimilarityMetric () override=default
 
SimpleMetricOP clone () const override
 
std::string name () const override
 Name of the class. More...
 
std::string metric () const override
 Name of the metric. More...
 
void quick (core::Size const &quick)
 
void verbose (core::Size const &verbose)
 
void write_int_area (bool const &write_int_area)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
 parse xml More...
 
core::Real calculate (pose::Pose const &pose) const override
 calc shape similarity, returns results of the ShapeSimilarityCalculator More...
 
- Public Member Functions inherited from core::simple_metrics::RealMetric
 RealMetric ()
 
 ~RealMetric () override
 
 RealMetric (RealMetric const &other)
 
RealMetricoperator= (RealMetric const &)
 
void apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
 Calculate the metric and add it to the pose as a score. labeled as out_label. 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)
 
SimpleMetricoperator= (SimpleMetric const &)
 
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...
 
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 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 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 Member Functions

void setup_from_selectors (pose::Pose const &pose, scoring::sc::ShapeSimilarityCalculator &ssc) const
 Uses residue selectors to set up the ShapeSimilarityCalculator. More...
 
void print_ss_result (std::ostream &tr, ShapeSimilarityCalculatorResults const &r, core::Real const nsubs_scalefactor) const
 prints results to given tracer in a human-readable format More...
 

Private Attributes

core::Size quick_
 
core::Size verbose_
 
core::pose::PoseCOP reference_pose_
 
core::select::residue_selector::ResidueSelectorCOP selector1_
 
core::select::residue_selector::ResidueSelectorCOP selector2_
 
bool write_int_area_
 
Real dist_weight_
 
bool median_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::simple_metrics::metrics::ShapeSimilarityMetric::ShapeSimilarityMetric ( )

default constructor

Referenced by clone().

core::simple_metrics::metrics::ShapeSimilarityMetric::~ShapeSimilarityMetric ( )
overridedefault

Member Function Documentation

core::Real core::simple_metrics::metrics::ShapeSimilarityMetric::calculate ( pose::Pose const &  pose) const
overridevirtual
SimpleMetricOP core::simple_metrics::metrics::ShapeSimilarityMetric::clone ( ) const
inlineoverridevirtual
std::string core::simple_metrics::metrics::ShapeSimilarityMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

std::string core::simple_metrics::metrics::ShapeSimilarityMetric::name_static ( )
static
void core::simple_metrics::metrics::ShapeSimilarityMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data_map 
)
overridevirtual
void core::simple_metrics::metrics::ShapeSimilarityMetric::print_ss_result ( std::ostream &  tr,
ShapeSimilarityCalculatorResults const &  r,
core::Real const  nsubs_scalefactor 
) const
private
void core::simple_metrics::metrics::ShapeSimilarityMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::ShapeSimilarityMetric::quick ( core::Size const &  quick)
inline

References quick(), and quick_.

Referenced by quick().

void core::simple_metrics::metrics::ShapeSimilarityMetric::setup_from_selectors ( pose::Pose const &  pose,
scoring::sc::ShapeSimilarityCalculator ssc 
) const
private

Uses residue selectors to set up the ShapeSimilarityCalculator.

Parameters
[in]posePose to be analyzed
[out]sscInitialized, empty ShapeSimilarityCalculator, to which pose residues are added

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::Pose::residue(), selector1_, selector2_, and tr().

void core::simple_metrics::metrics::ShapeSimilarityMetric::verbose ( core::Size const &  verbose)
inline

References verbose(), and verbose_.

Referenced by verbose().

void core::simple_metrics::metrics::ShapeSimilarityMetric::write_int_area ( bool const &  write_int_area)
inline

References write_int_area(), and write_int_area_.

Referenced by write_int_area().

Member Data Documentation

Real core::simple_metrics::metrics::ShapeSimilarityMetric::dist_weight_
private

Referenced by calculate(), and parse_my_tag().

bool core::simple_metrics::metrics::ShapeSimilarityMetric::median_
private

Referenced by calculate(), and parse_my_tag().

core::Size core::simple_metrics::metrics::ShapeSimilarityMetric::quick_
private

Referenced by calculate(), parse_my_tag(), and quick().

core::pose::PoseCOP core::simple_metrics::metrics::ShapeSimilarityMetric::reference_pose_
private

Referenced by calculate(), and parse_my_tag().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::ShapeSimilarityMetric::selector1_
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::ShapeSimilarityMetric::selector2_
private
core::Size core::simple_metrics::metrics::ShapeSimilarityMetric::verbose_
private

Referenced by parse_my_tag(), and verbose().

bool core::simple_metrics::metrics::ShapeSimilarityMetric::write_int_area_
private

Referenced by parse_my_tag(), and write_int_area().


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