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Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::protein_mpnn::ProteinMPNNMover Class Reference

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:
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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)
 

Private Member Functions

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

◆ 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

◆ parse_my_tag()

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

◆ 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

◆ 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 
)
private

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().

◆ 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 
)
private

Member Data Documentation

◆ coord_selector_rs_

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

◆ design_selector_rs_

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

◆ deterministic_flag_

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

◆ 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

◆ tied_pos_rs_

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

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