A metric for averaging multiple PerResidueProbabilitiesMetrics. More...

#include <AverageProbabilitiesMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::AverageProbabilitiesMetric:

[legend]

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

	AverageProbabilitiesMetric (utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics, utility::vector1< core::Real > weights)

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

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

std::map< core::Size, std::map< core::chemical::AA, 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 (utility::vector1< core::simple_metrics::SimpleMetricCOP > metrics, utility::vector1< core::Real > weights)
	Set the PerResidueProbabilitiesMetric that will be used to calculate. 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

std::map< core::Size, std::map< core::chemical::AA, core::Real > >	compute_average (utility::vector1< std::map< core::Size, std::map< core::chemical::AA, core::Real >>> const &all_values) const
	computest the average between multiple PerResidueProbabilitiesMetrics outputs More...

Public Member Functions inherited from core::simple_metrics::PerResidueProbabilitiesMetric
	PerResidueProbabilitiesMetric ()

	~PerResidueProbabilitiesMetric () override

	PerResidueProbabilitiesMetric (PerResidueProbabilitiesMetric const &other)

PerResidueProbabilitiesMetric &	operator= (PerResidueProbabilitiesMetric 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...

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for which we will calculate values over. More...

void	set_output_as_pdb_nums (bool output_as_pdb_nums)
	Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...

std::map< core::Size, std::map< core::chemical::AA, core::Real > >	cached_calculate (pose::Pose const &pose, bool use_cache, std::string const &prefix="", std::string const &suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_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 submetric names that this Metric will calculate. More...

select::residue_selector::ResidueSelectorCOP	get_selector () const
	Get the set residue selector of this class. More...

virtual void	parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the base class tag. Keep required interface for parse_my_tag. 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::PerResidueProbabilitiesMetric
static void	output_sequence_profile (std::string const &sequence, std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &logit_map, std::string const &output_filename)
	Format the probabilities in psi-blast position-specific-scoring-matrix (PSSM) format and write to file. More...

static void	add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
	Add options to the schema from this base class. More...

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

Private Attributes
utility::vector1< core::simple_metrics::SimpleMetricCOP >	metrics_

utility::vector1< core::Real >	weights_

bool	use_cache_ = false

std::string	cache_prefix_

std::string	cache_suffix_

bool	fail_on_missing_cache_ = true

Detailed Description

A metric for averaging multiple PerResidueProbabilitiesMetrics.

Constructor & Destructor Documentation

◆ AverageProbabilitiesMetric() [1/3]

core::simple_metrics::metrics::AverageProbabilitiesMetric::AverageProbabilitiesMetric ( )

Constructors ///.

Default constructor

◆ AverageProbabilitiesMetric() [2/3]

core::simple_metrics::metrics::AverageProbabilitiesMetric::AverageProbabilitiesMetric	(	utility::vector1< core::simple_metrics::SimpleMetricCOP >	metrics,
		utility::vector1< core::Real >	weights
	)

References set_metric().

◆ AverageProbabilitiesMetric() [3/3]

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

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~AverageProbabilitiesMetric()

core::simple_metrics::metrics::AverageProbabilitiesMetric::~AverageProbabilitiesMetric ( )

overridedefault

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

Member Function Documentation

◆ calculate()

std::map< core::Size, std::map< core::chemical::AA, core::Real > > core::simple_metrics::metrics::AverageProbabilitiesMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References cache_prefix_, cache_suffix_, compute_average(), fail_on_missing_cache_, metrics_, and use_cache_.

◆ clone()

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

overridevirtual

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

◆ compute_average()

std::map< core::Size, std::map< core::chemical::AA, core::Real > > core::simple_metrics::metrics::AverageProbabilitiesMetric::compute_average ( utility::vector1< std::map< core::Size, std::map< core::chemical::AA, core::Real >>> const & all_values ) const

computest the average between multiple PerResidueProbabilitiesMetrics outputs

References protocols::cluster::calibur::aa, core::sequence::end, TR(), and weights_.

Referenced by calculate().

◆ metric()

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name()

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

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name_static()

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

static

Name of the class for creator.

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

◆ parse_my_tag()

void core::simple_metrics::metrics::AverageProbabilitiesMetric::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::PerResidueProbabilitiesMetric.

References fail_on_missing_cache_, core::simple_metrics::get_metrics_from_datamap_and_subtags(), core::simple_metrics::SimpleMetric::parse_base_tag(), set_fail_on_missing_cache(), set_metric(), and set_use_cached_data().

◆ provide_citation_info()

void core::simple_metrics::metrics::AverageProbabilitiesMetric::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::metrics::AverageProbabilitiesMetric::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::AverageProbabilitiesMetricCreator::provide_xml_schema().

◆ set_fail_on_missing_cache()

void core::simple_metrics::metrics::AverageProbabilitiesMetric::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::metrics::AverageProbabilitiesMetric::set_metric	(	utility::vector1< core::simple_metrics::SimpleMetricCOP >	metrics,
		utility::vector1< core::Real >	weights
	)

Set the PerResidueProbabilitiesMetric that will be used to calculate.

References metrics_, and weights_.

Referenced by AverageProbabilitiesMetric(), and parse_my_tag().

◆ set_use_cached_data()

void core::simple_metrics::metrics::AverageProbabilitiesMetric::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::metrics::AverageProbabilitiesMetric::cache_prefix_

private

Referenced by calculate(), and set_use_cached_data().

◆ cache_suffix_

std::string core::simple_metrics::metrics::AverageProbabilitiesMetric::cache_suffix_

private

Referenced by calculate(), and set_use_cached_data().

◆ fail_on_missing_cache_

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

private

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

◆ metrics_

utility::vector1<core::simple_metrics::SimpleMetricCOP> core::simple_metrics::metrics::AverageProbabilitiesMetric::metrics_

private

Referenced by calculate(), and set_metric().

◆ use_cache_

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

private

Referenced by calculate(), and set_use_cached_data().

◆ weights_

utility::vector1< core::Real > core::simple_metrics::metrics::AverageProbabilitiesMetric::weights_

private

Referenced by compute_average(), and set_metric().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AverageProbabilitiesMetric() [1/3]

◆ AverageProbabilitiesMetric() [2/3]

◆ AverageProbabilitiesMetric() [3/3]

◆ ~AverageProbabilitiesMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ compute_average()

◆ 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_

◆ metrics_

◆ use_cache_

◆ weights_