inverse_folding¶

Bindings for protocols::inverse_folding namespace

class pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric¶

Bases: PerResidueProbabilitiesMetric

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

_pybind11_conduit_v1_()¶

static add_schema(complex_schema: utility::tag::XMLSchemaComplexTypeGenerator) → None¶

Add options to the schema from this base class.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::add_schema(class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>) –> void

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose as a score.

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

assign(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, : pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric) → pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric¶: C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::operator=(const class protocols::inverse_folding::MIFSTProbabilitiesMetric &) –> class protocols::inverse_folding::MIFSTProbabilitiesMetric &

cached_calculate(*args, **kwargs)¶

Overloaded function.

cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool, use_ref_pose_for_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,
for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::cached_calculate(const class core::pose::Pose &, bool, const std::string &, const std::string &, bool, bool) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

calculate(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t¶

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.

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::calculate(const class core::pose::Pose &) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

clone(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

get_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶

Output data name will be prefix+custom_type+type+suffix

C++: core::simple_metrics::SimpleMetric::get_custom_type() const –> std::string

get_final_sm_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

C++: core::simple_metrics::SimpleMetric::get_final_sm_type() const –> std::string

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

C++: core::simple_metrics::PerResidueProbabilitiesMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_selector(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the set residue selector of this class.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::get_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

metric(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric) → str¶

Name of the metric

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric) → str¶

Name of the class

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::name() const –> std::string

static name_static() → str¶

Name of the class for creator.

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::name_static() –> std::string

static output_sequence_profile(sequence: str, logit_map: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, output_filename: str) → None¶

Format the probabilities in psi-blast position-specific-scoring-matrix (PSSM) format and write to file

The sequence of the pose

A map containing the predicted logits for each position

A string defining the name of the output file

C++: core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(const std::string &, const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, const std::string &) –> void

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) → None¶

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

called by parse_my_tag – should not be used directly

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

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

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_selector(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the residue selector.

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

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) → None¶: C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_feature_selector(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

A second optional residue selector for feature selection.

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::set_feature_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_multirun(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, multirun: bool) → None¶

set the multirun option

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::set_multirun(bool) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::set_output_as_pdb_nums(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the residue selector that we’ll be using.

Passing nullptr results in no residue selector being used.

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_use_gpu(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric, use_gpu: bool) → None¶

set the use_gpu option

C++: protocols::inverse_folding::MIFSTProbabilitiesMetric::set_use_gpu(bool) –> void

simple_metric_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::simple_metric_type() const –> std::string

class pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator¶

Bases: SimpleMetricCreator

_pybind11_conduit_v1_()¶

assign(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator, : pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator) → pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator¶: C++: protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::operator=(const class protocols::inverse_folding::MIFSTProbabilitiesMetricCreator &) –> class protocols::inverse_folding::MIFSTProbabilitiesMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Instantiate a particular SimpleMetric

C++: protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator) → str¶

Return a string that will be used to instantiate the particular SimpleMetric

C++: protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::inverse_folding::MIFSTProbabilitiesMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.inverse_folding.tokenize(seq: str, mask_position: int) → pyrosetta.rosetta.std.vector_unsigned_long¶

function to tokenize sequence into MIF-ST Alphabet

C++: protocols::inverse_folding::tokenize(const std::string &, unsigned long) –> class std::vector<unsigned long, class std::allocator<unsigned long> >