protein_mpnn

Bindings for protocols::protein_mpnn namespace

class pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover

Bases: Mover

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

apply(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::protein_mpnn::ProteinMPNNMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, : pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover) → pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover

C++: protocols::protein_mpnn::ProteinMPNNMover::operator=(const class protocols::protein_mpnn::ProteinMPNNMover &) –> class protocols::protein_mpnn::ProteinMPNNMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::protein_mpnn::ProteinMPNNMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::protein_mpnn::ProteinMPNNMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover) → str

C++: protocols::protein_mpnn::ProteinMPNNMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str

C++: protocols::protein_mpnn::ProteinMPNNMover::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provides the citation for this module.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::protein_mpnn::ProteinMPNNMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

static residue_selectors_to_indices(pose: pyrosetta.rosetta.core.pose.Pose, residue_selectors: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

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

C++: protocols::protein_mpnn::ProteinMPNNMover::residue_selectors_to_indices(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > > &) –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

set_coord_selector_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, coord_selector_rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set residues whose coordinates should be passed to ProteinMPNN

C++: protocols::protein_mpnn::ProteinMPNNMover::set_coord_selector_rs(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_design_selector_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, design_selector_rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set designable residues

C++: protocols::protein_mpnn::ProteinMPNNMover::set_design_selector_rs(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_deterministic_flag(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, deterministic_flag: bool) → None

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

C++: protocols::protein_mpnn::ProteinMPNNMover::set_deterministic_flag(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_omit_AAs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, omit_AAs: pyrosetta.rosetta.utility.vector1_char) → None

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

“X” for unknown residue type should be included.

C++: protocols::protein_mpnn::ProteinMPNNMover::set_omit_AAs(class utility::vector1<char, class std::allocator<char> >) –> void

set_temperature(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, temperature: float) → None

Set the sampling temperature of the model.

C++: protocols::protein_mpnn::ProteinMPNNMover::set_temperature(double) –> void

set_tied_pos_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover, tied_pos_rs: pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t) → None

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.

C++: protocols::protein_mpnn::ProteinMPNNMover::set_tied_pos_rs(class utility::vector1<class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > > > >) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

static validate_residue_selectors(selection_positions: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, expected_size: int) → None

C++: protocols::protein_mpnn::ProteinMPNNMover::validate_residue_selectors(const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const unsigned long) –> void

class pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator, : pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator) → pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator

C++: protocols::protein_mpnn::ProteinMPNNMoverCreator::operator=(const class protocols::protein_mpnn::ProteinMPNNMoverCreator &) –> class protocols::protein_mpnn::ProteinMPNNMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.MoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Return a new mover.

C++: protocols::moves::MoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.MoverCreator) → str

Return the tag name associated with this factory.

C++: protocols::moves::MoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric

Bases: PerResidueProbabilitiesMetric

A metric for estimating amino acid probabilities using the ProteinMPNN model

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.

1. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None

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

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

5. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

6. 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.protein_mpnn.ProteinMPNNProbabilitiesMetric, : pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric) → pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::operator=(const class protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric &) –> class protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

1. 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

2. 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

3. 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

4. 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

5. 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.protein_mpnn.ProteinMPNNProbabilitiesMetric, 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.

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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.protein_mpnn.ProteinMPNNProbabilitiesMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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.protein_mpnn.ProteinMPNNProbabilitiesMetric) → str

Name of the metric

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric) → str

Name of the class

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::name() const –> std::string

static name_static() → str

Name of the class for creator.

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::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.protein_mpnn.ProteinMPNNProbabilitiesMetric, 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::protein_mpnn::ProteinMPNNProbabilitiesMetric::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.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

C++: core::simple_metrics::SimpleMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_selector(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric) → 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::protein_mpnn::ProteinMPNNProbabilitiesMetric::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_coord_selector_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric, coord_selector_rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set residues whose coordinates should be passed to ProteinMPNN

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_coord_selector_rs(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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_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.protein_mpnn.ProteinMPNNProbabilitiesMetric, 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::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sequence_mask_selector_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric, sequence_mask_selector_rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set residues whose sequence should be masked

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_sequence_mask_selector_rs(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_tied_pos_rs(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric, tied_pos_rs: pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t) → None

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.

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::set_tied_pos_rs(class utility::vector1<class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > > > >) –> void

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

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

write_pssm(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric) → str

Get the output filename of the pssm

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetric::write_pssm() const –> std::string

class pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator

Bases: SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator, : pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator) → pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator::operator=(const class protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator &) –> class protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator) → str

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

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator, : utility::tag::XMLSchemaDefinition) → None

C++: protocols::protein_mpnn::ProteinMPNNProbabilitiesMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void