This mover uses the given pose and threads the predicted sequence from the ProteinMPNN model onto it. More...

#include <ProteinMPNNMover.hh>

Inheritance diagram for protocols::protein_mpnn::ProteinMPNNMover:

Public Member Functions
	ProteinMPNNMover ()=default
	Default constructor. More...

	~ProteinMPNNMover () override
	Destructor. More...

void	apply (core::pose::Pose &pose) override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override

moves::MoverOP	clone () const override

moves::MoverOP	fresh_instance () const override

std::string	get_name () const override

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provides the citation for this module. More...

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

void	set_temperature (core::Real temperature)
	Set the sampling temperature of the model. More...

void	set_omit_AAs (utility::vector1< char > omit_AAs)
	Set globally disallowed AA types. Each character is a single-letter AA code. More...

void	set_design_selector_rs (core::select::residue_selector::ResidueSelectorCOP design_selector_rs)
	Set designable residues. 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_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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	validate_residue_selectors (utility::vector1< utility::vector1< core::Size > > const &selection_positions, core::Size const expected_size)

static utility::vector1< utility::vector1< core::Size > >	residue_selectors_to_indices (core::pose::Pose const &pose, utility::vector1< core::select::residue_selector::ResidueSelectorCOP > const &residue_selectors)
	Turn a bunch of residue selectors into a bunch of lists of resnums selected by those residue selectors. More...

Private Attributes
bool	deterministic_flag_ = false

core::Real	temperature_ = 0.1

utility::vector1< char >	omit_AAs_

core::select::residue_selector::ResidueSelectorCOP	design_selector_rs_

core::select::residue_selector::ResidueSelectorCOP	coord_selector_rs_

utility::vector1< utility::vector1< core::select::residue_selector::ResidueSelectorCOP > >	tied_pos_rs_

core::pack::task::TaskFactoryOP	task_factory_

Detailed Description

This mover uses the given pose and threads the predicted sequence from the ProteinMPNN model onto it.

Constructor & Destructor Documentation

◆ ProteinMPNNMover()

protocols::protein_mpnn::ProteinMPNNMover::ProteinMPNNMover ( )

default

Default constructor.

◆ ~ProteinMPNNMover()

protocols::protein_mpnn::ProteinMPNNMover::~ProteinMPNNMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::protein_mpnn::ProteinMPNNMover::apply ( core::pose::Pose & pose )

override

References core::pack::task::ResidueLevelTask::allowed_residue_types(), clone(), coord_selector_rs_, design_selector_rs_, deterministic_flag_, core::pose::symmetry::is_symmetric(), core::conformation::Residue::name1(), omit_AAs_, core::pose::Pose::residue(), residue_selectors_to_indices(), core::select::residue_selector::selection_positions(), core::pose::symmetry::symmetry_info(), task_factory_, temperature_, tied_pos_rs_, core::pose::Pose::total_residue(), protocols::protein_mpnn::TR(), and validate_residue_selectors().

◆ clone()

protocols::moves::MoverOP protocols::protein_mpnn::ProteinMPNNMover::clone ( ) const

override

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::protein_mpnn::ProteinMPNNMover::fresh_instance ( ) const

override

◆ get_name()

std::string protocols::protein_mpnn::ProteinMPNNMover::get_name ( ) const

override

References mover_name().

◆ mover_name()

std::string protocols::protein_mpnn::ProteinMPNNMover::mover_name ( )

static

Referenced by get_name(), protocols::protein_mpnn::ProteinMPNNMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::protein_mpnn::ProteinMPNNMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

override

References coord_selector_rs_, design_selector_rs_, deterministic_flag_, core::select::residue_selector::get_residue_selector(), omit_AAs_, core::pack::task::parse_task_operations(), task_factory_, temperature_, and tied_pos_rs_.

◆ provide_citation_info()

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

override

Provides the citation for this module.

References protocols::simple_moves::SimpleThreadingMover::provide_citation_info().

◆ provide_xml_schema()

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

static

References core::pack::task::attributes_for_parse_task_operations(), protocols::moves::complex_type_name_for_mover(), and mover_name().

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

◆ residue_selectors_to_indices()

utility::vector1< utility::vector1< core::Size > > protocols::protein_mpnn::ProteinMPNNMover::residue_selectors_to_indices	(	core::pose::Pose const &	pose,
		utility::vector1< core::select::residue_selector::ResidueSelectorCOP > const &	residue_selectors
	)

static

Turn a bunch of residue selectors into a bunch of lists of resnums selected by those residue selectors.

References core::select::residue_selector::selection_positions().

Referenced by apply(), and protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::calculate().

◆ set_coord_selector_rs()

void protocols::protein_mpnn::ProteinMPNNMover::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_design_selector_rs()

void protocols::protein_mpnn::ProteinMPNNMover::set_design_selector_rs ( core::select::residue_selector::ResidueSelectorCOP design_selector_rs )

Set designable residues.

References design_selector_rs_.

◆ set_deterministic_flag()

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

Set to true to run in deterministic mode. Will override temperature.

References deterministic_flag_.

◆ set_omit_AAs()

void protocols::protein_mpnn::ProteinMPNNMover::set_omit_AAs ( utility::vector1< char > omit_AAs )

Set globally disallowed AA types. Each character is a single-letter AA code.

Note: "X" for unknown residue type should be included.

References omit_AAs_.

◆ set_temperature()

void protocols::protein_mpnn::ProteinMPNNMover::set_temperature ( core::Real temperature )

Set the sampling temperature of the model.

References temperature_.

◆ set_tied_pos_rs()

void protocols::protein_mpnn::ProteinMPNNMover::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_.

◆ validate_residue_selectors()

void protocols::protein_mpnn::ProteinMPNNMover::validate_residue_selectors	(	utility::vector1< utility::vector1< core::Size > > const &	selection_positions,
		core::Size const	expected_size
	)

static

References core::select::residue_selector::selection_positions().

Referenced by apply(), and protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::calculate().

Member Data Documentation

◆ coord_selector_rs_

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

private

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

◆ design_selector_rs_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_mpnn::ProteinMPNNMover::design_selector_rs_

private

Referenced by apply(), parse_my_tag(), and set_design_selector_rs().

◆ deterministic_flag_

bool protocols::protein_mpnn::ProteinMPNNMover::deterministic_flag_ = false

private

Referenced by apply(), parse_my_tag(), and set_deterministic_flag().

◆ omit_AAs_

utility::vector1< char > protocols::protein_mpnn::ProteinMPNNMover::omit_AAs_

private

Referenced by apply(), parse_my_tag(), and set_omit_AAs().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::protein_mpnn::ProteinMPNNMover::task_factory_

private

Referenced by apply(), and parse_my_tag().

◆ temperature_

core::Real protocols::protein_mpnn::ProteinMPNNMover::temperature_ = 0.1

private

Referenced by apply(), parse_my_tag(), and set_temperature().

◆ tied_pos_rs_

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

private

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

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

src/protocols/protein_mpnn/ProteinMPNNMover.hh
src/protocols/protein_mpnn/ProteinMPNNMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProteinMPNNMover()

◆ ~ProteinMPNNMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ residue_selectors_to_indices()

◆ set_coord_selector_rs()

◆ set_design_selector_rs()

◆ set_deterministic_flag()

◆ set_omit_AAs()

◆ set_temperature()

◆ set_tied_pos_rs()

◆ validate_residue_selectors()

Member Data Documentation

◆ coord_selector_rs_

◆ design_selector_rs_

◆ deterministic_flag_

◆ omit_AAs_

◆ task_factory_

◆ temperature_

◆ tied_pos_rs_