burial_metrics¶

Bindings for protocols::analysis::burial_metrics namespace

class pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric¶

Bases: StringMetric

A string metric that generates a string of PyMol commands to colour a structure’s polar groups based on burial.

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, 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.: Data is output into the final score file, but can be accessed if needed through the cache.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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.

C++: core::simple_metrics::StringMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> std::string

calculate(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric, original_pose: pyrosetta.rosetta.core.pose.Pose) → str¶

Calculate the metric.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::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.StringMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the metric name that this Metric will calculate

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

metric(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric) → str¶

Name (descriptive) of the metric.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric) → str¶

Name of the class

Calls name_static().

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::name() const –> std::string

static name_static() → str¶

Name of the class for creator.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::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.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Given an XML tag, configure an instance of this class.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::parse_my_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::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Set the scorefunction.

Used for definition of burial. Input pointer is copied without cloning.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_verbose(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric, setting: bool) → None¶

Set whether this metric should also output to tracer when evaluated.

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_verbose(const 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.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator¶

Bases: SimpleMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Instantiate a particular SimpleMetric

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator) → str¶

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

C++: protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator::keyname() const –> std::string

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