A metric for calculating the (pseudo-)perplexity of a sequence. More...

#include <PseudoPerplexityMetric.hh>

Inheritance diagram for protocols::esm_perplexity::PseudoPerplexityMetric:

[legend]

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

	PseudoPerplexityMetric (core::simple_metrics::PerResidueProbabilitiesMetricCOP metric)

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

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

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 pseudo-perplexity. 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_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	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...

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 core::Real	compute_perplexity (core::pose::Pose const &pose, std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &values)
	Function to return the (pseudo-)perplexity from a map of probabilities. 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

Private Member Functions
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 (pseudo-)perplexity of a sequence.

Constructor & Destructor Documentation

◆ PseudoPerplexityMetric() [1/3]

protocols::esm_perplexity::PseudoPerplexityMetric::PseudoPerplexityMetric ( )

Constructors ///.

Default constructor

◆ PseudoPerplexityMetric() [2/3]

protocols::esm_perplexity::PseudoPerplexityMetric::PseudoPerplexityMetric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

References metric(), and set_metric().

◆ PseudoPerplexityMetric() [3/3]

protocols::esm_perplexity::PseudoPerplexityMetric::PseudoPerplexityMetric ( PseudoPerplexityMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PseudoPerplexityMetric()

protocols::esm_perplexity::PseudoPerplexityMetric::~PseudoPerplexityMetric ( )

overridedefault

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

Member Function Documentation

◆ calculate()

core::Real protocols::esm_perplexity::PseudoPerplexityMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::RealMetric.

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

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::esm_perplexity::PseudoPerplexityMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::RealMetric.

◆ compute_perplexity()

core::Real protocols::esm_perplexity::PseudoPerplexityMetric::compute_perplexity	(	core::pose::Pose const &	pose,
		std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &	values
	)

static

Function to return the (pseudo-)perplexity from a map of probabilities.

Takes a map of amino acid probabilities, gets the amino acid present in the pose, add the logarithm of its probability to a sum and then returns the exp of the negative ratio of this sum divided by the total length.

Parameters

[in]	pose	The pose used to refer which core::chemical::AA types are actually present
[in]	values	The resulting values of a PerResidueProbabilitiesMetric

Returns: A core::Real value representing the pseud-perplexity

References core::conformation::Residue::aa(), core::chemical::aa_unk, and core::pose::Pose::residue().

Referenced by calculate().

◆ metric()

std::string protocols::esm_perplexity::PseudoPerplexityMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

References name_static().

Referenced by parse_my_tag(), PseudoPerplexityMetric(), and set_metric().

◆ name()

std::string protocols::esm_perplexity::PseudoPerplexityMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

◆ name_static()

std::string protocols::esm_perplexity::PseudoPerplexityMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::esm_perplexity::PseudoPerplexityMetricCreator::keyname(), metric(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::esm_perplexity::PseudoPerplexityMetric::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 fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), metric(), set_fail_on_missing_cache(), set_metric(), and set_use_cached_data().

◆ provide_citation_info()

void protocols::esm_perplexity::PseudoPerplexityMetric::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 protocols::esm_perplexity::PseudoPerplexityMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::esm_perplexity::PseudoPerplexityMetricCreator::provide_xml_schema().

◆ set_fail_on_missing_cache()

void protocols::esm_perplexity::PseudoPerplexityMetric::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 protocols::esm_perplexity::PseudoPerplexityMetric::set_metric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity.

References metric(), and metric_.

Referenced by parse_my_tag(), and PseudoPerplexityMetric().

◆ set_use_cached_data()

void protocols::esm_perplexity::PseudoPerplexityMetric::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_, protocols::TR(), and use_cache_.

Referenced by parse_my_tag().

Member Data Documentation

◆ cache_prefix_

std::string protocols::esm_perplexity::PseudoPerplexityMetric::cache_prefix_

Referenced by calculate(), and set_use_cached_data().

◆ cache_suffix_

std::string protocols::esm_perplexity::PseudoPerplexityMetric::cache_suffix_

Referenced by calculate(), and set_use_cached_data().

◆ fail_on_missing_cache_

bool protocols::esm_perplexity::PseudoPerplexityMetric::fail_on_missing_cache_ = true

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

◆ metric_

core::simple_metrics::PerResidueProbabilitiesMetricCOP protocols::esm_perplexity::PseudoPerplexityMetric::metric_ = nullptr

Referenced by calculate(), and set_metric().

◆ use_cache_

bool protocols::esm_perplexity::PseudoPerplexityMetric::use_cache_ = false

Referenced by calculate(), and set_use_cached_data().

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

src/protocols/esm_perplexity/PseudoPerplexityMetric.hh
src/protocols/esm_perplexity/PseudoPerplexityMetric.cc

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ PseudoPerplexityMetric() [1/3]

◆ PseudoPerplexityMetric() [2/3]

◆ PseudoPerplexityMetric() [3/3]

◆ ~PseudoPerplexityMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ compute_perplexity()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_fail_on_missing_cache()

◆ set_metric()

◆ set_use_cached_data()

Member Data Documentation

◆ cache_prefix_

◆ cache_suffix_

◆ fail_on_missing_cache_

◆ metric_

◆ use_cache_