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core::simple_metrics::metrics::ResidueSummaryMetric Class Reference

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:
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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...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation information for the simple metric that it uses.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 This simple metric is unpublished (returns true).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 This simple metric is unpublished.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 Jared Adolf-Bryfogle. 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)
 
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 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
core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::ResidueSummaryMetric::clone ( ) const
overridevirtual
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_authorship_info_for_unpublished().

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

This simple metric is unpublished. It returns Jared Adolf-Bryfogle.

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 metric_, and name().

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

This simple metric is unpublished, but can provide citation information for the simple metric 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 metric_.

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

bool core::simple_metrics::metrics::ResidueSummaryMetric::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

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
bool core::simple_metrics::metrics::ResidueSummaryMetric::fail_on_missing_cache_ = true
private
PerResidueRealMetricCOP core::simple_metrics::metrics::ResidueSummaryMetric::metric_ = nullptr
private
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: