burial_metrics

Bindings for protocols::analysis::burial_metrics namespace

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

Bases: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

  6. 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.

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

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

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

  4. 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: pyrosetta.rosetta.core.simple_metrics.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