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

#include <ShapeSimilarityMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::ShapeSimilarityMetric:

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)
RealMetric &	operator= (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)
SimpleMetric &	operator= (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

typedef core::scoring::sc::RESULTS core::simple_metrics::metrics::ShapeSimilarityMetric::ShapeSimilarityCalculatorResults

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

calc shape similarity, returns results of the ShapeSimilarityCalculator

Compute the overall shape similarity of two surfaces.

Implements core::simple_metrics::RealMetric.

References core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), core::scoring::sc::MolecularSurfaceCalculator::density, dist_weight_, core::scoring::sc::MolecularSurfaceCalculator::Init(), core::scoring::sc::ShapeSimilarityCalculator::median, median_, quick_, reference_pose_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), selector1_, selector2_, core::scoring::sc::MolecularSurfaceCalculator::settings, tr(), and core::scoring::sc::MolecularSurfaceCalculator::weight.

SimpleMetricOP core::simple_metrics::metrics::ShapeSimilarityMetric::clone ( ) const

inlineoverridevirtual

Implements core::simple_metrics::RealMetric.

References ShapeSimilarityMetric().

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

Name of the class for creator.

Referenced by core::simple_metrics::metrics::ShapeSimilarityMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::metrics::ShapeSimilarityMetric::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data_map  )

overridevirtual

parse xml

Implements core::simple_metrics::RealMetric.

References dist_weight_, core::select::residue_selector::get_residue_selector(), median_, core::simple_metrics::SimpleMetric::parse_base_tag(), quick_, reference_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), selector1_, selector2_, tr(), verbose_, and write_int_area_.

void core::simple_metrics::metrics::ShapeSimilarityMetric::print_ss_result ( std::ostream &  tr, ShapeSimilarityCalculatorResults const &  r, core::Real const  nsubs_scalefactor  ) const

private

prints results to given tracer in a human-readable format

Parameters

[out]	tr	std::ostream object to write to
[in]	r	ShapeSimilarityCalculatorResults object containing results

References core::scoring::sc::_RESULTS::area, core::scoring::sc::_RESULTS::d_mean, core::scoring::sc::_RESULTS::d_median, core::scoring::sc::_RESULTS::distance, core::scoring::sc::_RESULTS::nAllDots, core::scoring::sc::_RESULTS::nAtoms, core::scoring::sc::_RESULTS::nBlockedAtoms, core::scoring::sc::_RESULTS::nBuriedAtoms, core::scoring::sc::_RESULTS::nTrimmedDots, core::scoring::sc::_RESULTS::s_mean, core::scoring::sc::_RESULTS::s_median, core::scoring::sc::_RESULTS::sc, core::scoring::sc::_RESULTS::surface, and core::scoring::sc::_RESULTS::trimmedArea.

void core::simple_metrics::metrics::ShapeSimilarityMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::metrics::ShapeSimilarityMetricCreator::provide_xml_schema().

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]	pose	Pose to be analyzed
[out]	ssc	Initialized, 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

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

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::ShapeSimilarityMetric::selector2_

private

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

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().

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

• src/core/simple_metrics/metrics/ShapeSimilarityMetric.hh
• src/core/simple_metrics/metrics/ShapeSimilarityMetric.cc