A metric for estimating the amino acid probabilities using the ESM language model family. More...

#include <PerResidueEsmProbabilitiesMetric.hh>

Inheritance diagram for protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric:

[legend]

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

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

	~PerResidueEsmProbabilitiesMetric () 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	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::string	model () const
	Get the ESM model that will be used for prediction. More...

std::string	write_pssm () const
	Get the output filename of the pssm. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the residue selector that we'll be using. More...

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

void	set_residue_selector2 (core::select::residue_selector::ResidueSelectorCOP selector)
	A second optional residue selector for attention masking. 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
std::string	get_selection_sequence (std::string const &pose_sequence, std::map< core::Size, utility::vector1< core::Real >> const &position_map) const
	Get the sequence of the selection. More...

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	This metric is unpublished.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

Static Private Member Functions
static void	fill_return_map (const std::map< core::Size, utility::vector1< core::Real >> &softmax_map, std::map< core::Size, std::map< core::chemical::AA, core::Real >> &return_map)
	Fill the return_map with the probabilities from the softmax_map for all amino acids. More...

Private Attributes
std::string	model_
	The ESM model to use for prediction. More...

std::string	write_pssm_
	The output filename of the pssm. More...

bool	multirun_ {}
	Whether to multirun the network. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr
	An optional residue selector. More...

EsmPerplexityTensorflowProtocolCOP	tensorflow_protocol_ = nullptr
	The tensorflow protocol used. More...

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

Detailed Description

A metric for estimating the amino acid probabilities using the ESM language model family.

Constructor & Destructor Documentation

◆ PerResidueEsmProbabilitiesMetric() [1/2]

protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::PerResidueEsmProbabilitiesMetric ( )

Constructors ///.

Default constructor

◆ PerResidueEsmProbabilitiesMetric() [2/2]

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

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PerResidueEsmProbabilitiesMetric()

protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::~PerResidueEsmProbabilitiesMetric ( )

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 > > protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References fill_return_map(), get_selection_sequence(), multirun_, core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(), residue_selector_, selector_two_, core::pose::Pose::sequence(), protocols::esm_perplexity::EsmPerplexityTensorflowProtocol::softmax(), tensorflow_protocol_, core::pose::Pose::total_residue(), and write_pssm_.

◆ clone()

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

overridevirtual

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

◆ fill_return_map()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::fill_return_map	(	const std::map< core::Size, utility::vector1< core::Real >> &	softmax_map,
		std::map< core::Size, std::map< core::chemical::AA, core::Real >> &	return_map
	)

staticprivate

Fill the return_map with the probabilities from the softmax_map for all amino acids.

Parameters

[in]	softmax_map	The map containing all probabilities or logits returned from ESM (including special tokens)
[in]	return_map	The map that will be returned by the calculate function, will be filled with probabilities/logits by this function
[in]	softmax_map	The map containing all probabilities or logits returned from ESM (including special tokens)
[in]	return_map	The map that will be returned by the calculate function, will be filled with probabilities by this function

References core::chemical::aa_from_oneletter_code(), protocols::esm_perplexity::EsmPerplexityTensorflowProtocol::alphabet_, core::scoring::pair, and protocols::simple_moves::bb_sampler::probability.

Referenced by calculate().

◆ get_selection_sequence()

std::string protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::get_selection_sequence	(	std::string const &	pose_sequence,
		std::map< core::Size, utility::vector1< core::Real >> const &	position_map
	)		const

private

Get the sequence of the selection.

References core::scoring::pair.

Referenced by calculate().

◆ metric()

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ model()

std::string protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::model ( ) const

inline

Get the ESM model that will be used for prediction.

References model_.

◆ name()

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

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name_static()

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

static

Name of the class for creator.

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

◆ parse_my_tag()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::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 model_, multirun_, core::select::residue_selector::parse_residue_selector(), set_residue_selector(), set_residue_selector2(), tensorflow_protocol_, and write_pssm_.

◆ provide_citation_info()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::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.

References protocols::esm_perplexity::EsmPerplexityTensorflowProtocol::get_ESM_neural_net_citation().

◆ provide_xml_schema()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::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::esm_perplexity::PerResidueEsmProbabilitiesMetricCreator::provide_xml_schema().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::residue_selector ( ) const

Get the residue selector.

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

References residue_selector_.

◆ set_residue_selector()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

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_residue_selector2()

void protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::set_residue_selector2 ( core::select::residue_selector::ResidueSelectorCOP selector )

A second optional residue selector for attention masking.

set the optional residue selector for the attention masking

References selector_two_.

Referenced by parse_my_tag().

◆ write_pssm()

std::string protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::write_pssm ( ) const

inline

Get the output filename of the pssm.

References write_pssm_.

Member Data Documentation

◆ model_

std::string protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::model_

private

The ESM model to use for prediction.

Referenced by model(), and parse_my_tag().

◆ multirun_

bool protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::multirun_ {}

private

Whether to multirun the network.

Referenced by calculate(), and parse_my_tag().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::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::esm_perplexity::PerResidueEsmProbabilitiesMetric::selector_two_ = nullptr

private

Residue selector for attention masking.

Referenced by calculate(), and set_residue_selector2().

◆ tensorflow_protocol_

EsmPerplexityTensorflowProtocolCOP protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::tensorflow_protocol_ = nullptr

private

The tensorflow protocol used.

Referenced by calculate(), and parse_my_tag().

◆ write_pssm_

std::string protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::write_pssm_

private

The output filename of the pssm.

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

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

src/protocols/esm_perplexity/PerResidueEsmProbabilitiesMetric.hh
src/protocols/esm_perplexity/PerResidueEsmProbabilitiesMetric.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PerResidueEsmProbabilitiesMetric() [1/2]

◆ PerResidueEsmProbabilitiesMetric() [2/2]

◆ ~PerResidueEsmProbabilitiesMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ fill_return_map()

◆ get_selection_sequence()

◆ metric()

◆ model()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ residue_selector()

◆ set_residue_selector()

◆ set_residue_selector2()

◆ write_pssm()

Member Data Documentation

◆ model_

◆ multirun_

◆ residue_selector_

◆ selector_two_

◆ tensorflow_protocol_

◆ write_pssm_