ptm_prediction¶

Bindings for protocols::ptm_prediction namespace

class pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric¶

Bases: PerResidueRealMetric

A metric for estimating the probability of a given residue(s) to be modified, as predicted by a pre-trained neural network.

class PTMPredictionMetricModes¶

Bases: pybind11_object

enum class to define the different modifications that can be predicted

Members:

INVALID_MODE

ACETYLATION

ARG_METHYLATION

CITRULLINATION

CROTONYLATION

DEAMIDATION

GAMMA_CARBOXY_GLUTAMIC_ACID

GLUTARYLATION

GLUTATHIONYLATION

HYDROXYLATION

LYS_METHYLATION

MALONYLATION

N_LINKED_GLYCOSYLATION

O_LINKED_GLYCOSYLATION

PHOSPHORYLATION

S_NITROSYLATION

SUCCINYLATION

SUMOYLATION

UBIQUITINATION

N_MODES

ACETYLATION = <PTMPredictionMetricModes.ACETYLATION: 1>¶

ARG_METHYLATION = <PTMPredictionMetricModes.ARG_METHYLATION: 2>¶

CITRULLINATION = <PTMPredictionMetricModes.CITRULLINATION: 3>¶

CROTONYLATION = <PTMPredictionMetricModes.CROTONYLATION: 4>¶

DEAMIDATION = <PTMPredictionMetricModes.DEAMIDATION: 5>¶

GAMMA_CARBOXY_GLUTAMIC_ACID = <PTMPredictionMetricModes.GAMMA_CARBOXY_GLUTAMIC_ACID: 6>¶

GLUTARYLATION = <PTMPredictionMetricModes.GLUTARYLATION: 7>¶

GLUTATHIONYLATION = <PTMPredictionMetricModes.GLUTATHIONYLATION: 8>¶

HYDROXYLATION = <PTMPredictionMetricModes.HYDROXYLATION: 9>¶

INVALID_MODE = <PTMPredictionMetricModes.INVALID_MODE: 0>¶

LYS_METHYLATION = <PTMPredictionMetricModes.LYS_METHYLATION: 10>¶

MALONYLATION = <PTMPredictionMetricModes.MALONYLATION: 11>¶

N_LINKED_GLYCOSYLATION = <PTMPredictionMetricModes.N_LINKED_GLYCOSYLATION: 12>¶

N_MODES = <PTMPredictionMetricModes.UBIQUITINATION: 18>¶

O_LINKED_GLYCOSYLATION = <PTMPredictionMetricModes.O_LINKED_GLYCOSYLATION: 13>¶

PHOSPHORYLATION = <PTMPredictionMetricModes.PHOSPHORYLATION: 14>¶

SUCCINYLATION = <PTMPredictionMetricModes.SUCCINYLATION: 16>¶

SUMOYLATION = <PTMPredictionMetricModes.SUMOYLATION: 17>¶

S_NITROSYLATION = <PTMPredictionMetricModes.S_NITROSYLATION: 15>¶

UBIQUITINATION = <PTMPredictionMetricModes.UBIQUITINATION: 18>¶

property name¶

property value¶

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, 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::PerResidueRealMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> pyrosetta.rosetta.std.map_unsigned_long_double
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> pyrosetta.rosetta.std.map_unsigned_long_double
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, 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_double

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::PerResidueRealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool, bool) const –> class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

calculate(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

C++: protocols::ptm_prediction::PTMPredictionMetric::calculate(const class core::pose::Pose &) const –> class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

clone(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: protocols::ptm_prediction::PTMPredictionMetric::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>

static enum_to_string(ptm_mode: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes) → str¶

Convert an enum modification type into the respective string modification type

C++: protocols::ptm_prediction::PTMPredictionMetric::enum_to_string(enum protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetricModes &) –> std::string

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.PerResidueRealMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

metric(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → str¶

Name of the metric

C++: protocols::ptm_prediction::PTMPredictionMetric::metric() const –> std::string

modification(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → str¶

Get the modification type that should be predicted

C++: protocols::ptm_prediction::PTMPredictionMetric::modification() const –> std::string

name(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → str¶

Name of the class

C++: protocols::ptm_prediction::PTMPredictionMetric::name() const –> std::string

static name_static() → str¶

Name of the class for creator.

C++: protocols::ptm_prediction::PTMPredictionMetric::name_static() –> std::string

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.ptm_prediction.PTMPredictionMetric, 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::ptm_prediction::PTMPredictionMetric::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.PerResidueRealMetric, tag: 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::PerResidueRealMetric::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::ptm_prediction::PTMPredictionMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

ptm_mode(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes¶

Get the modification type that should be predicted as enum class type

C++: protocols::ptm_prediction::PTMPredictionMetric::ptm_mode() const –> enum protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetricModes

residue_selector(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric) → 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::ptm_prediction::PTMPredictionMetric::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_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, 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::PerResidueRealMetric::set_output_as_pdb_nums(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric, 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::ptm_prediction::PTMPredictionMetric::set_residue_selector(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

static string_to_enum(modification_type: str) → pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes¶

Convert an string modification type into an enum modification type

C++: protocols::ptm_prediction::PTMPredictionMetric::string_to_enum(std::string &) –> enum protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetricModes

class pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator¶

Bases: SimpleMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator) → str¶

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

C++: protocols::ptm_prediction::PTMPredictionMetricCreator::keyname() const –> std::string

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

class pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol¶

Bases: PTMPredictionTensorflowProtocolBase

Analyze a given residue or residues in a pose, returning an modifcation probability (ranging from 0 to 1).

Moritz Ertelt (moritz.ertelt.com)

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

clone(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol) → pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: protocols::ptm_prediction::PTMPredictionTensorflowProtocol::clone() const –> class std::shared_ptr<class basic::tensorflow_manager::RosettaTensorflowProtocolBase>

static get_selected_residues(selected: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Given a selection, return a vector of selected indices.

C++: protocols::ptm_prediction::PTMPredictionTensorflowProtocolBase::get_selected_residues(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

name(self: pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol) → str¶

Get the name of this protocol.

C++: protocols::ptm_prediction::PTMPredictionTensorflowProtocol::name() const –> std::string

property path_to_model¶

class pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase¶

Bases: RosettaTensorflowProtocolBase

A pure virtual class, derived from RosettaTensorflowProtocolBase, which will serve as a base for protocols for predicting post-translational modifications in proteins.

Moritz Ertelt (moritz.ertelt.com)

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

clone(self: pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase) → pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase¶

Clone operation.

C++: basic::tensorflow_manager::RosettaTensorflowProtocolBase::clone() const –> class std::shared_ptr<class basic::tensorflow_manager::RosettaTensorflowProtocolBase>

static get_selected_residues(selected: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Given a selection, return a vector of selected indices.

C++: protocols::ptm_prediction::PTMPredictionTensorflowProtocolBase::get_selected_residues(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

name(self: pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase) → str¶

Get the name of this RosettaTensorflowProtocol.

Must be implemented by derived class.

C++: basic::tensorflow_manager::RosettaTensorflowProtocolBase::name() const –> std::string