A metric for calculating the probability delta between the current amino acid and the most likely from a PerResidueProbabilitiesMetric. More...

#include <BestMutationsFromProbabilitiesMetric.hh>

Inheritance diagram for core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric:

[legend]

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

	BestMutationsFromProbabilitiesMetric (core::simple_metrics::PerResidueProbabilitiesMetricCOP metric)

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

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

std::map< std::string, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

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

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

void	set_metric (core::simple_metrics::PerResidueProbabilitiesMetricCOP metric)
	Set the PerResidueProbabilitiesMetric that will be used to calculate the delta. More...

void	set_use_cached_data (bool use_cache, std::string const &prefix="", std::string const &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_cutoffs (core::Size max_number_mutations, core::Real delta_cutoff)
	Set cutoffs for the amount of mutations and delta probability which will be reported. 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...

std::map< std::string, core::Real >	compute_deltas (std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &values, core::pose::Pose const &pose) const
	calculate the delta 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::CompositeRealMetric
	CompositeRealMetric ()

	~CompositeRealMetric () override

	CompositeRealMetric (CompositeRealMetric const &other)

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 SimpleMetricData cache in the pose. labeled as out_label. More...

std::map< std::string, 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...

virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const=0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as `label` Must be implemented by derived classes. More...

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...

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 &)

Public Attributes
core::simple_metrics::PerResidueProbabilitiesMetricCOP	metric_ = nullptr

bool	use_cache_ = false

std::string	cache_prefix_

std::string	cache_suffix_

bool	fail_on_missing_cache_ = true

core::Size	max_number_mutations_ = 10

core::Real	delta_cutoff_ = 0.0

Private Member Functions
utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	This metric is unpublished. It returns Moritz Ertelt as its author. More...

Detailed Description

A metric for calculating the probability delta between the current amino acid and the most likely from a PerResidueProbabilitiesMetric.

Constructor & Destructor Documentation

◆ BestMutationsFromProbabilitiesMetric() [1/3]

core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::BestMutationsFromProbabilitiesMetric ( )

Constructors ///.

Default constructor

◆ BestMutationsFromProbabilitiesMetric() [2/3]

core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::BestMutationsFromProbabilitiesMetric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

References metric(), and set_metric().

◆ BestMutationsFromProbabilitiesMetric() [3/3]

core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::BestMutationsFromProbabilitiesMetric ( BestMutationsFromProbabilitiesMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~BestMutationsFromProbabilitiesMetric()

core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::~BestMutationsFromProbabilitiesMetric ( )

overridedefault

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

Member Function Documentation

◆ calculate()

std::map< std::string, core::Real > core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::CompositeRealMetric.

References cache_prefix_, cache_suffix_, compute_deltas(), fail_on_missing_cache_, metric_, and use_cache_.

◆ clone()

core::simple_metrics::SimpleMetricOP core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::CompositeRealMetric.

◆ compute_deltas()

std::map< std::string, core::Real > core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas	(	std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &	values,
		core::pose::Pose const &	pose
	)		const

calculate the delta

References core::pose::motif::a(), core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_unk, protocols::match::upstream::b, delta_cutoff_, max_number_mutations_, core::chemical::oneletter_code_from_aa(), core::pose::Pose::residue(), core::id::to_string(), and TR().

Referenced by calculate().

◆ get_metric_names()

utility::vector1< std::string > core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::get_metric_names ( ) const

overrideprivatevirtual

Get the submetric names that this Metric will calculate.

Implements core::simple_metrics::CompositeRealMetric.

References metric().

◆ metric()

std::string core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::CompositeRealMetric.

References name_static().

Referenced by BestMutationsFromProbabilitiesMetric(), get_metric_names(), parse_my_tag(), and set_metric().

◆ name()

std::string core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::CompositeRealMetric.

References name_static().

◆ name_static()

std::string core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetricCreator::keyname(), metric(), name(), and provide_xml_schema().

◆ parse_my_tag()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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::CompositeRealMetric.

References fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), metric(), core::simple_metrics::SimpleMetric::parse_base_tag(), set_cutoffs(), set_fail_on_missing_cache(), set_metric(), and set_use_cached_data().

◆ provide_citation_info()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overrideprivatevirtual

This metric is unpublished. It returns Moritz Ertelt as its author.

Reimplemented from core::simple_metrics::SimpleMetric.

◆ provide_xml_schema()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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::composite_metrics::BestMutationsFromProbabilitiesMetricCreator::provide_xml_schema().

◆ set_cutoffs()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_cutoffs	(	core::Size	max_number_mutations,
		core::Real	delta_cutoff
	)

Set cutoffs for the amount of mutations and delta probability which will be reported.

References delta_cutoff_, and max_number_mutations_.

Referenced by parse_my_tag().

◆ set_fail_on_missing_cache()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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().

◆ set_metric()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_metric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

Set the PerResidueProbabilitiesMetric that will be used to calculate the delta.

References metric(), and metric_.

Referenced by BestMutationsFromProbabilitiesMetric(), and parse_my_tag().

◆ set_use_cached_data()

void core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_use_cached_data	(	bool	use_cache,
		std::string const &	prefix = `""`,
		std::string const &	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

◆ cache_prefix_

std::string core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::cache_prefix_

Referenced by calculate(), and set_use_cached_data().

◆ cache_suffix_

std::string core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::cache_suffix_

Referenced by calculate(), and set_use_cached_data().

◆ delta_cutoff_

core::Real core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::delta_cutoff_ = 0.0

Referenced by compute_deltas(), and set_cutoffs().

◆ fail_on_missing_cache_

bool core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::fail_on_missing_cache_ = true

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

◆ max_number_mutations_

core::Size core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::max_number_mutations_ = 10

Referenced by compute_deltas(), and set_cutoffs().

◆ metric_

core::simple_metrics::PerResidueProbabilitiesMetricCOP core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::metric_ = nullptr

Referenced by calculate(), and set_metric().

◆ use_cache_

bool core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::use_cache_ = false

Referenced by calculate(), and set_use_cached_data().

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

src/core/simple_metrics/composite_metrics/BestMutationsFromProbabilitiesMetric.hh
src/core/simple_metrics/composite_metrics/BestMutationsFromProbabilitiesMetric.cc

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ BestMutationsFromProbabilitiesMetric() [1/3]

◆ BestMutationsFromProbabilitiesMetric() [2/3]

◆ BestMutationsFromProbabilitiesMetric() [3/3]

◆ ~BestMutationsFromProbabilitiesMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ compute_deltas()

◆ get_metric_names()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_cutoffs()

◆ set_fail_on_missing_cache()

◆ set_metric()

◆ set_use_cached_data()

Member Data Documentation

◆ cache_prefix_

◆ cache_suffix_

◆ delta_cutoff_

◆ fail_on_missing_cache_

◆ max_number_mutations_

◆ metric_

◆ use_cache_