A PerResidueProbabilitiesMetric that stores amino acid probabilities predicted by the MIF-ST model. More...

#include <MIFSTProbabilitiesMetric.hh>

Inheritance diagram for protocols::inverse_folding::MIFSTProbabilitiesMetric:

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

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

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Metric Methods ///. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the residue selector. More...

void	set_feature_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	A second optional residue selector for feature selection. More...

void	set_multirun (bool multirun)
	set the multirun option More...

void	set_use_gpu (bool use_gpu)
	set the use_gpu option More...

std::map< core::Size, std::map< core::chemical::AA, core::Real > >	calculate (core::pose::Pose const &pose) const override
	Calculate the metric. This map is Rosetta Resnum->(AA, value) and includes only those residues selected. 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
	This simple metric is unpublished. It returns Moritz Ertelt as its author. 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::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 Attributes
core::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr
	An optional residue selector. More...

core::select::residue_selector::ResidueSelectorCOP	selector_two_ = nullptr
	Residue selector for attention masking. More...

bool	multirun_ = true
	whether to run inference on all residues at once, or one-by-one More...

bool	use_gpu_ = false
	whether to run inference on the GPU (if one is available) More...

Detailed Description

A PerResidueProbabilitiesMetric that stores amino acid probabilities predicted by the MIF-ST model.

Constructor & Destructor Documentation

◆ MIFSTProbabilitiesMetric()

protocols::inverse_folding::MIFSTProbabilitiesMetric::MIFSTProbabilitiesMetric ( )

Constructors ///.

Default constructor

◆ ~MIFSTProbabilitiesMetric()

protocols::inverse_folding::MIFSTProbabilitiesMetric::~MIFSTProbabilitiesMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::inverse_folding::MIFSTProbabilitiesMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Calculate the metric. This map is Rosetta Resnum->(AA, value) and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References multirun_, residue_selector_, selector_two_, core::pose::Pose::total_residue(), and use_gpu_.

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::inverse_folding::MIFSTProbabilitiesMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

◆ metric()

std::string protocols::inverse_folding::MIFSTProbabilitiesMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

◆ name()

std::string protocols::inverse_folding::MIFSTProbabilitiesMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name_static()

std::string protocols::inverse_folding::MIFSTProbabilitiesMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::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 core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), set_feature_selector(), set_multirun(), set_residue_selector(), and set_use_gpu().

◆ provide_citation_info()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

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

Reimplemented from core::simple_metrics::SimpleMetric.

◆ provide_xml_schema()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::provide_xml_schema().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::inverse_folding::MIFSTProbabilitiesMetric::residue_selector ( ) const

Get the residue selector.

If this returns nullptr, it means that no residue selector is being used.

References residue_selector_.

◆ set_feature_selector()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::set_feature_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

A second optional residue selector for feature selection.

set the optional residue selector for feature selection

References selector_two_.

Referenced by parse_my_tag().

◆ set_multirun()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::set_multirun ( bool multirun )

set the multirun option

References multirun_.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Metric Methods ///.

Set the residue selector that we'll be using.

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.

Set the residue selector that we'll be using.

Passing nullptr results in no residue selector being used.

References residue_selector_.

Referenced by parse_my_tag().

◆ set_use_gpu()

void protocols::inverse_folding::MIFSTProbabilitiesMetric::set_use_gpu ( bool use_gpu )

set the use_gpu option

set the gpu option

References use_gpu_.

Referenced by parse_my_tag().

Member Data Documentation

◆ multirun_

bool protocols::inverse_folding::MIFSTProbabilitiesMetric::multirun_ = true

private

whether to run inference on all residues at once, or one-by-one

Referenced by calculate(), and set_multirun().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::inverse_folding::MIFSTProbabilitiesMetric::residue_selector_ = nullptr

private

An optional residue selector.

Referenced by calculate(), residue_selector(), and set_residue_selector().

◆ selector_two_

core::select::residue_selector::ResidueSelectorCOP protocols::inverse_folding::MIFSTProbabilitiesMetric::selector_two_ = nullptr

private

Residue selector for attention masking.

Referenced by calculate(), and set_feature_selector().

◆ use_gpu_

bool protocols::inverse_folding::MIFSTProbabilitiesMetric::use_gpu_ = false

private

whether to run inference on the GPU (if one is available)

Referenced by calculate(), and set_use_gpu().

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

src/protocols/inverse_folding/MIFSTProbabilitiesMetric.hh
src/protocols/inverse_folding/MIFSTProbabilitiesMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MIFSTProbabilitiesMetric()

◆ ~MIFSTProbabilitiesMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ residue_selector()

◆ set_feature_selector()

◆ set_multirun()

◆ set_residue_selector()

◆ set_use_gpu()

Member Data Documentation

◆ multirun_

◆ residue_selector_

◆ selector_two_

◆ use_gpu_