A metric for estimating amino acid probabilities using the ProteinMPNN model. More...

#include <ProteinMPNNProbabilitiesMetric.hh>

Inheritance diagram for protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric:

[legend]

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

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

	~ProteinMPNNProbabilitiesMetric () 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	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...

void	set_coord_selector_rs (core::select::residue_selector::ResidueSelectorCOP coord_selector_rs)
	Set residues whose coordinates should be passed to ProteinMPNN. More...

void	set_sequence_mask_selector_rs (core::select::residue_selector::ResidueSelectorCOP sequence_mask_selector_rs)
	Set residues whose sequence should be masked. More...

void	set_tied_pos_rs (utility::vector1< utility::vector1< core::select::residue_selector::ResidueSelectorCOP > > tied_pos_rs)
	Set tied positions. This is a collection of lists, each list containing residue selectors that should be tied. More...

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

void	set_deterministic_flag (bool deterministic_flag)
	Set to true to run in deterministic mode. More...

bool	deterministic_flag () const
	Get the deterministic_flag mode. 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 currently unpublished, returns ME as author and the ProteinMPNN paper. More...

Static Private Member Functions
static std::string	get_selection_sequence (std::string const &pose_sequence, std::map< core::Size, utility::vector1< core::Real >> const &position_map)
	Get the sequence of the selection. More...

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

utility::vector1< utility::vector1< core::select::residue_selector::ResidueSelectorCOP > >	tied_pos_rs_
	A vector of vectors of residue selectors to specify tied positions for ProteinMPNN. More...

core::select::residue_selector::ResidueSelectorCOP	coord_selector_rs_
	A residue selector to specify backbone coordinates to be used as input for ProteinMPNN (default all) More...

core::select::residue_selector::ResidueSelectorCOP	sequence_mask_selector_rs_
	A residue selector to mask specific parts of the input sequence for ProteinMPNN. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr
	An optional residue selector to limit the returned probabilities to a selection. More...

bool	deterministic_flag_ = false
	An optional boolean flag to run in deterministic mode. More...

Detailed Description

A metric for estimating amino acid probabilities using the ProteinMPNN model.

Constructor & Destructor Documentation

◆ ProteinMPNNProbabilitiesMetric() [1/2]

protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::ProteinMPNNProbabilitiesMetric ( )

Constructors ///.

Default constructor

◆ ProteinMPNNProbabilitiesMetric() [2/2]

protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::ProteinMPNNProbabilitiesMetric ( ProteinMPNNProbabilitiesMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~ProteinMPNNProbabilitiesMetric()

protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::~ProteinMPNNProbabilitiesMetric ( )

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::protein_mpnn::ProteinMPNNProbabilitiesMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References clone(), coord_selector_rs_, deterministic_flag_, get_selection_sequence(), core::pose::symmetry::is_symmetric(), core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(), residue_selector_, protocols::protein_mpnn::ProteinMPNNMover::residue_selectors_to_indices(), core::select::residue_selector::selection_positions(), core::pose::Pose::sequence(), sequence_mask_selector_rs_, core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), tied_pos_rs_, core::pose::Pose::total_residue(), protocols::protein_mpnn::ProteinMPNNMover::validate_residue_selectors(), and write_pssm_.

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

Referenced by calculate().

◆ deterministic_flag()

bool protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::deterministic_flag ( ) const

Get the deterministic_flag mode.

References deterministic_flag_.

Referenced by set_deterministic_flag().

◆ get_selection_sequence()

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

staticprivate

Get the sequence of the selection.

Get the sequence of the selection from a map of positions->logits value.

References core::scoring::pair.

Referenced by calculate().

◆ metric()

std::string protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name()

std::string protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueProbabilitiesMetric.

References name_static().

◆ name_static()

std::string protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator::keyname(), metric(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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 coord_selector_rs_, deterministic_flag_, core::select::residue_selector::get_residue_selector(), residue_selector_, sequence_mask_selector_rs_, set_residue_selector(), tied_pos_rs_, and write_pssm_.

◆ provide_citation_info()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overrideprivatevirtual

This metric is currently unpublished, returns ME as author and the ProteinMPNN paper.

Reimplemented from core::simple_metrics::SimpleMetric.

◆ provide_xml_schema()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator::provide_xml_schema().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::residue_selector ( ) const

Get the residue selector.

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

References residue_selector_.

◆ set_coord_selector_rs()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_coord_selector_rs ( core::select::residue_selector::ResidueSelectorCOP coord_selector_rs )

Set residues whose coordinates should be passed to ProteinMPNN.

References coord_selector_rs_.

◆ set_deterministic_flag()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_deterministic_flag ( bool deterministic_flag )

Set to true to run in deterministic mode.

References deterministic_flag(), and deterministic_flag_.

◆ set_residue_selector()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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_sequence_mask_selector_rs()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_sequence_mask_selector_rs ( core::select::residue_selector::ResidueSelectorCOP sequence_mask_selector_rs )

Set residues whose sequence should be masked.

References sequence_mask_selector_rs_.

◆ set_tied_pos_rs()

void protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_tied_pos_rs ( utility::vector1< utility::vector1< core::select::residue_selector::ResidueSelectorCOP > > tied_pos_rs )

Set tied positions. This is a collection of lists, each list containing residue selectors that should be tied.

The first residues of each selector will be tied together, then the second, etc. Each residue selector must have the same number of residues.

References tied_pos_rs_.

◆ write_pssm()

std::string protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::write_pssm ( ) const

inline

Get the output filename of the pssm.

References write_pssm_.

Member Data Documentation

◆ coord_selector_rs_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::coord_selector_rs_

private

A residue selector to specify backbone coordinates to be used as input for ProteinMPNN (default all)

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

◆ deterministic_flag_

bool protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::deterministic_flag_ = false

private

An optional boolean flag to run in deterministic mode.

Referenced by calculate(), deterministic_flag(), parse_my_tag(), and set_deterministic_flag().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::residue_selector_ = nullptr

private

An optional residue selector to limit the returned probabilities to a selection.

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

◆ sequence_mask_selector_rs_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::sequence_mask_selector_rs_

private

A residue selector to mask specific parts of the input sequence for ProteinMPNN.

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

◆ tied_pos_rs_

utility::vector1< utility::vector1< core::select::residue_selector::ResidueSelectorCOP > > protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::tied_pos_rs_

private

A vector of vectors of residue selectors to specify tied positions for ProteinMPNN.

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

◆ write_pssm_

std::string protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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/protein_mpnn/ProteinMPNNProbabilitiesMetric.hh
src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProteinMPNNProbabilitiesMetric() [1/2]

◆ ProteinMPNNProbabilitiesMetric() [2/2]

◆ ~ProteinMPNNProbabilitiesMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ deterministic_flag()

◆ get_selection_sequence()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ residue_selector()

◆ set_coord_selector_rs()

◆ set_deterministic_flag()

◆ set_residue_selector()

◆ set_sequence_mask_selector_rs()

◆ set_tied_pos_rs()

◆ write_pssm()

Member Data Documentation

◆ coord_selector_rs_

◆ deterministic_flag_

◆ residue_selector_

◆ sequence_mask_selector_rs_

◆ tied_pos_rs_

◆ write_pssm_