A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data. More...

#include <ResidueSummaryMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::ResidueSummaryMetric:

Public Member Functions
	ResidueSummaryMetric ()
	Constructors ///. More...

	ResidueSummaryMetric (PerResidueRealMetricCOP metric)

	ResidueSummaryMetric (ResidueSummaryMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~ResidueSummaryMetric () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

core::Real	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_metric (core::simple_metrics::PerResidueRealMetricCOP metric)
	Set the SimpleMetric that we will be using to filter. More...

void	set_action (summary_type sum_type)
	Set the summary behavior of this class. Default mean. More...

void	set_action_value (core::Real cutoff)
	Set any cutoff for summing n_residues Default 0. More...

void	set_use_cached_data (bool use_cache, std::string prefix="", std::string suffix="")
	Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix. More...

void	set_fail_on_missing_cache (bool fail)
	If use_cache is set to false, do we fail if no data is found in the pose? Default True. More...

void	set_epsilon (core::Real epsilon)
	Set the sigfigs we will use in our comparisons. Default is .0001;. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name of the metric. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

core::simple_metrics::SimpleMetricOP	clone () const override

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...

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 Attributes
PerResidueRealMetricCOP	metric_ = nullptr

core::Real	cutoff_ = 0

core::Real	epsilon_ = .0001

summary_type	action_ = mean

bool	use_cache_ = false

std::string	cache_prefix_ = ""

std::string	cache_suffix_ = ""

bool	fail_on_missing_cache_ = true

Detailed Description

A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data.

Can compute totals, means, or the number of residues matching a certain criteria, for example less than or equal to a certain value. Useful for summarizing metrics or using more complex functions for filters.

Constructor & Destructor Documentation

core::simple_metrics::metrics::ResidueSummaryMetric::ResidueSummaryMetric ( )

Constructors ///.

Default constructor

Referenced by clone().

core::simple_metrics::metrics::ResidueSummaryMetric::ResidueSummaryMetric ( PerResidueRealMetricCOP metric )

References set_metric().

core::simple_metrics::metrics::ResidueSummaryMetric::ResidueSummaryMetric ( ResidueSummaryMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::metrics::ResidueSummaryMetric::~ResidueSummaryMetric ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

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

overridevirtual

Metric Methods ///.

Defined in RealMetric:

Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix.

Score is added through setExtraScorePose and is output into the score tables/file at pose output. Calculate the metric.

Implements core::simple_metrics::RealMetric.

References action_, core::simple_metrics::metrics::bogus, cache_prefix_, cache_suffix_, cutoff_, epsilon_, fail_on_missing_cache_, core::simple_metrics::metrics::mean, metric_, core::simple_metrics::metrics::n_res_eq, core::simple_metrics::metrics::n_res_gt, core::simple_metrics::metrics::n_res_gt_or_eq, core::simple_metrics::metrics::n_res_lt, core::simple_metrics::metrics::n_res_lt_or_eq, core::simple_metrics::metrics::n_res_ne, core::simple_metrics::metrics::sum, TR(), and use_cache_.

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

overridevirtual

Implements core::simple_metrics::RealMetric.

References ResidueSummaryMetric().

std::string core::simple_metrics::metrics::ResidueSummaryMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

Referenced by parse_my_tag(), and set_metric().

std::string core::simple_metrics::metrics::ResidueSummaryMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

Referenced by provide_citation_info().

std::string core::simple_metrics::metrics::ResidueSummaryMetric::name_static ( )

static

Name of the class for creator.

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

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

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::RealMetric.

References epsilon_, fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), metric(), core::simple_metrics::SimpleMetric::parse_base_tag(), set_action(), set_action_value(), set_epsilon(), set_fail_on_missing_cache(), set_metric(), set_use_cached_data(), and core::simple_metrics::metrics::summary_string_to_type().

void core::simple_metrics::metrics::ResidueSummaryMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References metric_, and name().

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

static

References core::simple_metrics::metrics::get_summary_type_strings(), name_static(), core::id::to_string(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

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

void core::simple_metrics::metrics::ResidueSummaryMetric::set_action ( summary_type sum_type )

Set the summary behavior of this class. Default mean.

References action_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::ResidueSummaryMetric::set_action_value ( core::Real cutoff )

Set any cutoff for summing n_residues Default 0.

References cutoff_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::ResidueSummaryMetric::set_epsilon ( core::Real epsilon )

Set the sigfigs we will use in our comparisons. Default is .0001;.

The absolute value of the difference between two numbers, below which they will be considered to be equal. Used when comparing numbers if action = n_res_eq or n_res_ne.

References epsilon_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::ResidueSummaryMetric::set_fail_on_missing_cache ( bool fail )

If use_cache is set to false, do we fail if no data is found in the pose? Default True.

References fail_on_missing_cache_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::ResidueSummaryMetric::set_metric ( core::simple_metrics::PerResidueRealMetricCOP metric )

Set the SimpleMetric that we will be using to filter.

References metric(), and metric_.

Referenced by parse_my_tag(), and ResidueSummaryMetric().

void core::simple_metrics::metrics::ResidueSummaryMetric::set_use_cached_data	(	bool	use_cache,
		std::string	prefix = `""`,
		std::string	suffix = `""`
	)

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

References cache_prefix_, cache_suffix_, TR(), and use_cache_.

Referenced by parse_my_tag().

Member Data Documentation

summary_type core::simple_metrics::metrics::ResidueSummaryMetric::action_ = mean

private

Referenced by calculate(), and set_action().

std::string core::simple_metrics::metrics::ResidueSummaryMetric::cache_prefix_ = ""

private

Referenced by calculate(), and set_use_cached_data().

std::string core::simple_metrics::metrics::ResidueSummaryMetric::cache_suffix_ = ""

private

Referenced by calculate(), and set_use_cached_data().

core::Real core::simple_metrics::metrics::ResidueSummaryMetric::cutoff_ = 0

private

Referenced by calculate(), and set_action_value().

core::Real core::simple_metrics::metrics::ResidueSummaryMetric::epsilon_ = .0001

private

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

bool core::simple_metrics::metrics::ResidueSummaryMetric::fail_on_missing_cache_ = true

private

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

PerResidueRealMetricCOP core::simple_metrics::metrics::ResidueSummaryMetric::metric_ = nullptr

private

Referenced by calculate(), provide_citation_info(), and set_metric().

bool core::simple_metrics::metrics::ResidueSummaryMetric::use_cache_ = false

private

Referenced by calculate(), and set_use_cached_data().

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

src/core/simple_metrics/metrics/ResidueSummaryMetric.hh
src/core/simple_metrics/metrics/ResidueSummaryMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation