metrics

Bindings for core::simple_metrics::metrics namespace

class pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A metric which can combine other metrics

add_constant(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric, name: str, value: float) None

For the varible name in the equation, use the passed constant value

C++: core::simple_metrics::metrics::CalculatorMetric::add_constant(const std::string &, double) –> void

add_reported_value(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric, name: str, report_key: str) None

For the variable name in the equation, look up the report_key scoreterm stored in the Pose

C++: core::simple_metrics::metrics::CalculatorMetric::add_reported_value(const std::string &, const std::string &) –> void

add_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric, name: str, metric: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) None
For the particular variable name in the equation, use the passed metric.

The passed metric must be a RealMetric, else you’ll get an error message.

C++: core::simple_metrics::metrics::CalculatorMetric::add_simple_metric(const std::string &, class std::shared_ptr<const class core::simple_metrics::SimpleMetric>) –> void

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric) pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric

C++: core::simple_metrics::metrics::CalculatorMetric::operator=(const class core::simple_metrics::metrics::CalculatorMetric &) –> class core::simple_metrics::metrics::CalculatorMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

C++: core::simple_metrics::metrics::CalculatorMetric::calculate(const class core::pose::Pose &) const –> double

check_equation(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric) bool
Do a quick check to make sure the equation parsing worked out.

Returns true on success, false on failure

C++: core::simple_metrics::metrics::CalculatorMetric::check_equation() –> bool

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::CalculatorMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric) str

Name of the metric

C++: core::simple_metrics::metrics::CalculatorMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric) str

Name of the class

C++: core::simple_metrics::metrics::CalculatorMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::CalculatorMetric::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.core.simple_metrics.metrics.CalculatorMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::CalculatorMetric::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.metrics.CalculatorMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::CalculatorMetric::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

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.core.simple_metrics.metrics.CalculatorMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator

C++: core::simple_metrics::metrics::CalculatorMetricCreator::operator=(const class core::simple_metrics::metrics::CalculatorMetricCreator &) –> class core::simple_metrics::metrics::CalculatorMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::CalculatorMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator) str

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

C++: core::simple_metrics::metrics::CalculatorMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::CalculatorMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

A simple metric that allows an arbitrary, user- or developer-set string to be cached in a pose.

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.core.simple_metrics.metrics.CustomStringValueMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric) pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric

C++: core::simple_metrics::metrics::CustomStringValueMetric::operator=(const class core::simple_metrics::metrics::CustomStringValueMetric &) –> class core::simple_metrics::metrics::CustomStringValueMetric &

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.core.simple_metrics.metrics.CustomStringValueMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Calculate the metric.

Returns the cached value.

C++: core::simple_metrics::metrics::CustomStringValueMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::CustomStringValueMetric::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.core.simple_metrics.metrics.CustomStringValueMetric) str

Name of the metric

C++: core::simple_metrics::metrics::CustomStringValueMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric) str

Name of the class

C++: core::simple_metrics::metrics::CustomStringValueMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::CustomStringValueMetric::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.core.simple_metrics.metrics.CustomStringValueMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::CustomStringValueMetric::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++: core::simple_metrics::metrics::CustomStringValueMetric::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_value(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric, value_in: str) None

Set the value that we’re going to cache in the pose.

C++: core::simple_metrics::metrics::CustomStringValueMetric::set_value(const std::string &) –> 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.core.simple_metrics.metrics.CustomStringValueMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator

C++: core::simple_metrics::metrics::CustomStringValueMetricCreator::operator=(const class core::simple_metrics::metrics::CustomStringValueMetricCreator &) –> class core::simple_metrics::metrics::CustomStringValueMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::CustomStringValueMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator) str

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

C++: core::simple_metrics::metrics::CustomStringValueMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::CustomStringValueMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector.

This is the normalized metric in degrees

Metric described in:

North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256.

NOTE: Only works for Protein and Carbohydrate residues as dihedral definitions in Rosetta are still aweful.

Metric is computed on the protein and carbohydrate backbone.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric) pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric

C++: core::simple_metrics::metrics::DihedralDistanceMetric::operator=(const class core::simple_metrics::metrics::DihedralDistanceMetric &) –> class core::simple_metrics::metrics::DihedralDistanceMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, pose: pyrosetta.rosetta.core.pose.Pose) float
Calculate DihedralDistance metric.

This is the normalized metric in degrees

Metric described in:

North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::DihedralDistanceMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric) str

Name of the metric

C++: core::simple_metrics::metrics::DihedralDistanceMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric) str

Name of the class

C++: core::simple_metrics::metrics::DihedralDistanceMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::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.core.simple_metrics.metrics.DihedralDistanceMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::DihedralDistanceMetric::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.metrics.DihedralDistanceMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, pose: pyrosetta.rosetta.core.pose.Pose) None

Set a reference pose to calculate rmsd

C++: core::simple_metrics::metrics::DihedralDistanceMetric::set_comparison_pose(class std::shared_ptr<const class core::pose::Pose>) –> 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_include_protein_omega(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, include_omega: bool) None
Set the boolean to include protein omega.

Default false.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::set_include_protein_omega(bool) –> void

set_residue_mapping(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, res_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None

Set a map to compute the Dihedral distance on input->reference residue numbers.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_mapping(const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector to calculate total energy of a subset of residues.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_reference(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric, residue_selector_ref: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector for the comparison pose.

C++: core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_selector_reference(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

class pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator

C++: core::simple_metrics::metrics::DihedralDistanceMetricCreator::operator=(const class core::simple_metrics::metrics::DihedralDistanceMetricCreator &) –> class core::simple_metrics::metrics::DihedralDistanceMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::DihedralDistanceMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator) str

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

C++: core::simple_metrics::metrics::DihedralDistanceMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::DihedralDistanceMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed

Bases: pyrosetta.rosetta.utility.excn.Exception

Super-simple exception to be thrown when the SS calculator fails to compute

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed, : pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed) pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed

C++: core::simple_metrics::metrics::EXCN_CalcFailed::operator=(const class core::simple_metrics::metrics::EXCN_CalcFailed &) –> class core::simple_metrics::metrics::EXCN_CalcFailed &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed

Bases: pyrosetta.rosetta.utility.excn.Exception

Super-simple exception to be thrown when we can’t initialize the SS calculator

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed, : pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed) pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed

C++: core::simple_metrics::metrics::EXCN_InitFailed::operator=(const class core::simple_metrics::metrics::EXCN_InitFailed &) –> class core::simple_metrics::metrics::EXCN_InitFailed &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions. Pose should be scored!

By default, we skip rama_prepro and pro_close

Scoretypes from REF:

fa_atr fa_rep fa_sol fa_elec lk_ball_wtd pro_close #ignored by default rama_prepro #ignored by default hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric) pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric

C++: core::simple_metrics::metrics::InteractionEnergyMetric::operator=(const class core::simple_metrics::metrics::InteractionEnergyMetric &) –> class core::simple_metrics::metrics::InteractionEnergyMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

C++: core::simple_metrics::metrics::InteractionEnergyMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::InteractionEnergyMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric) str

Name of the metric

C++: core::simple_metrics::metrics::InteractionEnergyMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric) str

Name of the class

C++: core::simple_metrics::metrics::InteractionEnergyMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::InteractionEnergyMetric::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.core.simple_metrics.metrics.InteractionEnergyMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::InteractionEnergyMetric::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.metrics.InteractionEnergyMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::InteractionEnergyMetric::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_ignore_scoretypes(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, ignore_scoretypes: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

Always ignore these scoretypes.

C++: core::simple_metrics::metrics::InteractionEnergyMetric::set_ignore_scoretypes(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) –> void

set_include_only_scoretypes(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, include_only_scoretypes: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

Set this to include only these score types.

C++: core::simple_metrics::metrics::InteractionEnergyMetric::set_include_only_scoretypes(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) –> void

set_include_rama_prepro_and_proclose(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, include: bool) None
Include Rama PrePro and ProClose?

Default False

C++: core::simple_metrics::metrics::InteractionEnergyMetric::set_include_rama_prepro_and_proclose(bool) –> void

set_residue_selectors(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selectors we will use to calculate the interaction energies.

C++: core::simple_metrics::metrics::InteractionEnergyMetric::set_residue_selectors(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_scorefunction(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set a scorefunction. Only used if the pose is not scored. Not recommended, this is our failsafe!

C++: core::simple_metrics::metrics::InteractionEnergyMetric::set_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.core.simple_metrics.metrics.InteractionEnergyMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator

C++: core::simple_metrics::metrics::InteractionEnergyMetricCreator::operator=(const class core::simple_metrics::metrics::InteractionEnergyMetricCreator &) –> class core::simple_metrics::metrics::InteractionEnergyMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::InteractionEnergyMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator) str

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

C++: core::simple_metrics::metrics::InteractionEnergyMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::InteractionEnergyMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A metric to calculate the RMSD between two poses. Can set a subset of residues to calculate via ResidueSelector.

Default is all_heavy

We match all corresponding atoms and do not fail if a residue does not match up.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric) pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric

C++: core::simple_metrics::metrics::RMSDMetric::operator=(const class core::simple_metrics::metrics::RMSDMetric &) –> class core::simple_metrics::metrics::RMSDMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose) float
Calculate the metric. This is the RMSD between the input and the set comparison pose.

Deafult is to calculate all_heavy atoms - but this can be set.

Make sure that reference pose and set pose are the same length or set a map to compare specific residues.

We match all corresponding atoms for each residue to match.

C++: core::simple_metrics::metrics::RMSDMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::RMSDMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric) str

Name of the metric

C++: core::simple_metrics::metrics::RMSDMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric) str

Name of the class

C++: core::simple_metrics::metrics::RMSDMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::RMSDMetric::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.core.simple_metrics.metrics.RMSDMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::RMSDMetric::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.metrics.RMSDMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose) None

Set a reference pose to calculate rmsd

C++: core::simple_metrics::metrics::RMSDMetric::set_comparison_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_corresponding_atoms_robust(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, robust: bool) None

Set this to false to fail instead.

C++: core::simple_metrics::metrics::RMSDMetric::set_corresponding_atoms_robust(bool) –> 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_cyclic_residue_mappings(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, rmsd_maps: pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t) None

Set maps of cyclic pose to compute the RMSDs on input->reference residue numbers.

C++: core::simple_metrics::metrics::RMSDMetric::set_cyclic_residue_mappings(const class std::vector<class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >, class std::allocator<class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > > > &) –> void

set_residue_mapping(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, rmsd_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None

Set a map to compute the RMSD on input->reference residue numbers.

C++: core::simple_metrics::metrics::RMSDMetric::set_residue_mapping(const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector to calculate total energy of a subset of residues.

C++: core::simple_metrics::metrics::RMSDMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_reference(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None
Set a reference residue selector. Both selectors should return the same number of residues.

If not set, will use the main residue selector.

C++: core::simple_metrics::metrics::RMSDMetric::set_residue_selector_reference(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_super(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Optional - Set a residue selector specifically for superposition.

C++: core::simple_metrics::metrics::RMSDMetric::set_residue_selector_super(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_super_reference(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None
Set a reference residue selector for superposition. Both selectors should return the same number of residues.

If not set, but super selector is set, will use that.

C++: core::simple_metrics::metrics::RMSDMetric::set_residue_selector_super_reference(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_rmsd_type(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, rmsd_type: pyrosetta.rosetta.core.scoring.rmsd_atoms) None

Set what we will be calculating the RMSD on.

C++: core::simple_metrics::metrics::RMSDMetric::set_rmsd_type(enum core::scoring::rmsd_atoms) –> void

set_run_superimpose(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric, super: bool) None
Run a superimpose on the residues selected in the residue selector (or all)

default False.

C++: core::simple_metrics::metrics::RMSDMetric::set_run_superimpose(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.core.simple_metrics.metrics.RMSDMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator

C++: core::simple_metrics::metrics::RMSDMetricCreator::operator=(const class core::simple_metrics::metrics::RMSDMetricCreator &) –> class core::simple_metrics::metrics::RMSDMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::RMSDMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator) str

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

C++: core::simple_metrics::metrics::RMSDMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::RMSDMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data.

Can compute totals, means, or the number of residues matching a certain criteria,

/ for example less than or equal to a certain value.

Useful for summarizing metrics or using more complex functions for filters.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric) pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric

C++: core::simple_metrics::metrics::ResidueSummaryMetric::operator=(const class core::simple_metrics::metrics::ResidueSummaryMetric &) –> class core::simple_metrics::metrics::ResidueSummaryMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

C++: core::simple_metrics::metrics::ResidueSummaryMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::ResidueSummaryMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric) str

Name of the metric

C++: core::simple_metrics::metrics::ResidueSummaryMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric) str

Name of the class

C++: core::simple_metrics::metrics::ResidueSummaryMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::ResidueSummaryMetric::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.core.simple_metrics.metrics.ResidueSummaryMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::ResidueSummaryMetric::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.metrics.ResidueSummaryMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_action(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, sum_type: pyrosetta.rosetta.core.simple_metrics.metrics.summary_type) None
Set the summary behavior of this class.

Default mean

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_action(enum core::simple_metrics::metrics::summary_type) –> void

set_action_value(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, cutoff: float) None
Set any cutoff for summing n_residues

Default 0

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_action_value(double) –> 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_epsilon(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, epsilon: float) None
Set the sigfigs we will use in our comparisons.

Default is .0001;

The absolute value of the difference between two numbers, below which they will be considered to be equal.

Used when comparing numbers if action = n_res_eq or n_res_ne.

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_epsilon(double) –> void

set_fail_on_missing_cache(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, fail: bool) None
If use_cache is set to false, do we fail if no data is found in the pose?

Default True

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_fail_on_missing_cache(bool) –> void

set_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) None

Set the SimpleMetric that we will be using to filter.

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_metric(class std::shared_ptr<const class core::simple_metrics::PerResidueRealMetric>) –> void

set_use_cached_data(*args, **kwargs)

Overloaded function.

  1. set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, use_cache: bool) -> None

  2. set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, use_cache: bool, prefix: str) -> None

  3. set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric, use_cache: bool, prefix: str, suffix: str) -> None

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric.

Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

C++: core::simple_metrics::metrics::ResidueSummaryMetric::set_use_cached_data(bool, std::string, std::string) –> 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.core.simple_metrics.metrics.ResidueSummaryMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator

C++: core::simple_metrics::metrics::ResidueSummaryMetricCreator::operator=(const class core::simple_metrics::metrics::ResidueSummaryMetricCreator &) –> class core::simple_metrics::metrics::ResidueSummaryMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::ResidueSummaryMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator) str

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

C++: core::simple_metrics::metrics::ResidueSummaryMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::ResidueSummaryMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A Metric to cacluate overall sasa of a pose.

Use the Apply method to calculate and add the metric to the pose score to be written

Virtual atoms are skipped completely.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric

C++: core::simple_metrics::metrics::SasaMetric::operator=(const class core::simple_metrics::metrics::SasaMetric &) –> class core::simple_metrics::metrics::SasaMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate The total sasa of the pose or the SASA of the residues given in a residue selector.

C++: core::simple_metrics::metrics::SasaMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SasaMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SasaMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric) str

Name of the class

C++: core::simple_metrics::metrics::SasaMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SasaMetric::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.core.simple_metrics.metrics.SasaMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SasaMetric::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.metrics.SasaMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SasaMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sasa_metric_mode(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric) pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode

Get the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::metrics::SasaMetric::sasa_metric_mode() const –> enum core::scoring::sasa::SasaMethodHPMode

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_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector to calculate total sasa of residues in the selector.

C++: core::simple_metrics::metrics::SasaMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sasa_metric_mode(*args, **kwargs)

Overloaded function.

  1. set_sasa_metric_mode(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric, mode_in: pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode) -> None

Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::metrics::SasaMetric::set_sasa_metric_mode(const enum core::scoring::sasa::SasaMethodHPMode) –> void

  1. set_sasa_metric_mode(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric, mode_in: str) -> None

Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::metrics::SasaMetric::set_sasa_metric_mode(const std::string &) –> 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.core.simple_metrics.metrics.SasaMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator

C++: core::simple_metrics::metrics::SasaMetricCreator::operator=(const class core::simple_metrics::metrics::SasaMetricCreator &) –> class core::simple_metrics::metrics::SasaMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SasaMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator) str

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

C++: core::simple_metrics::metrics::SasaMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SasaMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP

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.core.simple_metrics.metrics.SecondaryStructureMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric

C++: core::simple_metrics::metrics::SecondaryStructureMetric::operator=(const class core::simple_metrics::metrics::SecondaryStructureMetric &) –> class core::simple_metrics::metrics::SecondaryStructureMetric &

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.core.simple_metrics.metrics.SecondaryStructureMetric, pose: pyrosetta.rosetta.core.pose.Pose) str
Calculate the metric. Return the SS string using DSSP.

Reduced, 3 letter alphabet as the default.

C++: core::simple_metrics::metrics::SecondaryStructureMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SecondaryStructureMetric::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.core.simple_metrics.metrics.SecondaryStructureMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SecondaryStructureMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric) str

Name of the class

C++: core::simple_metrics::metrics::SecondaryStructureMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SecondaryStructureMetric::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.core.simple_metrics.metrics.SecondaryStructureMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SecondaryStructureMetric::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.metrics.SecondaryStructureMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SecondaryStructureMetric::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_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::simple_metrics::metrics::SecondaryStructureMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_use_dssp_reduced(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric, reduced: bool) None
Set to use the reduced DSSP alphabet or not.

Default true.

C++: core::simple_metrics::metrics::SecondaryStructureMetric::set_use_dssp_reduced(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.core.simple_metrics.metrics.SecondaryStructureMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator

C++: core::simple_metrics::metrics::SecondaryStructureMetricCreator::operator=(const class core::simple_metrics::metrics::SecondaryStructureMetricCreator &) –> class core::simple_metrics::metrics::SecondaryStructureMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SecondaryStructureMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator) str

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

C++: core::simple_metrics::metrics::SecondaryStructureMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SecondaryStructureMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A SimpleMetric that counts the number of residues in a residue selection.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::operator=(const class core::simple_metrics::metrics::SelectedResidueCountMetric &) –> class core::simple_metrics::metrics::SelectedResidueCountMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric) str

Name of the class

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::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.core.simple_metrics.metrics.SelectedResidueCountMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::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.metrics.SelectedResidueCountMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

remove_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric) None

Remove the residue selector.

In the absence of a residue selector, this metric returns the number of residues in a pose.

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::remove_residue_selector() –> 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_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector.

Copies the input pointer; doesn’t clone the object.

C++: core::simple_metrics::metrics::SelectedResidueCountMetric::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

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator

C++: core::simple_metrics::metrics::SelectedResidueCountMetricCreator::operator=(const class core::simple_metrics::metrics::SelectedResidueCountMetricCreator &) –> class core::simple_metrics::metrics::SelectedResidueCountMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SelectedResidueCountMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator) str

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

C++: core::simple_metrics::metrics::SelectedResidueCountMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SelectedResidueCountMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

Output residue-selected residues to a score file as rosetta resnums or pdbnums.

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.core.simple_metrics.metrics.SelectedResiduesMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric

C++: core::simple_metrics::metrics::SelectedResiduesMetric::operator=(const class core::simple_metrics::metrics::SelectedResiduesMetric &) –> class core::simple_metrics::metrics::SelectedResiduesMetric &

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.core.simple_metrics.metrics.SelectedResiduesMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Output a comma-separated list of residues either in PDB (default) or Rosetta numbers.

C++: core::simple_metrics::metrics::SelectedResiduesMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SelectedResiduesMetric::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.core.simple_metrics.metrics.SelectedResiduesMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SelectedResiduesMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric) str

Name of the class

C++: core::simple_metrics::metrics::SelectedResiduesMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SelectedResiduesMetric::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.core.simple_metrics.metrics.SelectedResiduesMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SelectedResiduesMetric::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.metrics.SelectedResiduesMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SelectedResiduesMetric::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_output_in_rosetta_num(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric, output_in_rosetta_num: bool) None

Set the mode in which we will output the selected residues.

C++: core::simple_metrics::metrics::SelectedResiduesMetric::set_output_in_rosetta_num(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the required residue selector.

C++: core::simple_metrics::metrics::SelectedResiduesMetric::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

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator

C++: core::simple_metrics::metrics::SelectedResiduesMetricCreator::operator=(const class core::simple_metrics::metrics::SelectedResiduesMetricCreator &) –> class core::simple_metrics::metrics::SelectedResiduesMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SelectedResiduesMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator) str

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

C++: core::simple_metrics::metrics::SelectedResiduesMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SelectedResiduesMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

A utility metric to output a string of selected residues from a residue selector as a pymol selection.

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.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::operator=(const class core::simple_metrics::metrics::SelectedResiduesPyMOLMetric &) –> class core::simple_metrics::metrics::SelectedResiduesPyMOLMetric &

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.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Output the selected residues froms a ResidueSelector as a PyMol selection string.

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::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.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric) str

Name of the class

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::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.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::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.metrics.SelectedResiduesPyMOLMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::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_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the required Residue Selector

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_use_rosetta_numbering(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric, setting: bool) None

Set whether we use Rosetta numbering in the output.

By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::set_use_rosetta_numbering(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

use_rosetta_numbering(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric) bool

Get whether we use Rosetta numbering in the output.

By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::use_rosetta_numbering() const –> bool

class pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator::operator=(const class core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator &) –> class core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator) str

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

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector.

static allowed_output_modes() str

Returns all allowed output modes.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::allowed_output_modes() –> std::string

static allowed_output_modes_as_vector() pyrosetta.rosetta.utility.vector1_std_string

Returns all allowed output modes as a vector of strings.

Note that this is a bit inefficient. It generates the vector each time, and returns it by copy. Not intended for repeated calls.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::allowed_output_modes_as_vector() –> class utility::vector1<std::string, class std::allocator<std::string > >

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.core.simple_metrics.metrics.SequenceMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric

C++: core::simple_metrics::metrics::SequenceMetric::operator=(const class core::simple_metrics::metrics::SequenceMetric &) –> class core::simple_metrics::metrics::SequenceMetric &

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.core.simple_metrics.metrics.SequenceMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Calculate the metric.

C++: core::simple_metrics::metrics::SequenceMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SequenceMetric::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.core.simple_metrics.metrics.SequenceMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SequenceMetric::metric() const –> std::string

static mode_enum_from_name(mode_string: str) pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode

Given an output mode string, get its enum.

Returns SequenceMetricMode::INVALID_MODE if invalid.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::mode_enum_from_name(const std::string &) –> enum core::simple_metrics::metrics::SequenceMetricMode

static mode_name_from_enum(mode_enum: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode) str

Given an output mode enum, get its string representation.

Returns “INVALID” if invalid.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::mode_name_from_enum(const enum core::simple_metrics::metrics::SequenceMetricMode) –> const std::string &

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric) str

Name of the class

C++: core::simple_metrics::metrics::SequenceMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SequenceMetric::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.core.simple_metrics.metrics.SequenceMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SequenceMetric::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.metrics.SequenceMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SequenceMetric::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_output_mode(*args, **kwargs)

Overloaded function.

  1. set_output_mode(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric, mode_in: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode) -> None

Set the output mode – one-letter code (e.g. Y), three-letter code (e.g. DTY), residue base name (e.g. DTYR), or

full residue name (e.g. DTYR:CtermProteinFull).

Throws an error if invalid enum provided.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::set_output_mode(const enum core::simple_metrics::metrics::SequenceMetricMode) –> void

  1. set_output_mode(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric, mode_in: str) -> None

Set the output mode using the string corresponding to the output mode.

Throws an error if string is invalid.

Vikram K. Mulligan (vmulligan.org)

C++: core::simple_metrics::metrics::SequenceMetric::set_output_mode(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::simple_metrics::metrics::SequenceMetric::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

class pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator

C++: core::simple_metrics::metrics::SequenceMetricCreator::operator=(const class core::simple_metrics::metrics::SequenceMetricCreator &) –> class core::simple_metrics::metrics::SequenceMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SequenceMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator) str

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

C++: core::simple_metrics::metrics::SequenceMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SequenceMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode

Bases: pybind11_builtins.pybind11_object

The mode for this metric. If you add to this list, be sure to update the map associating this enum

with corresponding strings in the .cc file.

Vikram K. Mulligan (vmulligan.org)

Members:

ONELETTER_CODE

THREELETTER_CODE

BASE_NAME

FULL_NAME

INVALID_MODE

END_OF_LIST

BASE_NAME = <SequenceMetricMode.BASE_NAME: 3>
END_OF_LIST = <SequenceMetricMode.INVALID_MODE: 5>
FULL_NAME = <SequenceMetricMode.FULL_NAME: 4>
INVALID_MODE = <SequenceMetricMode.INVALID_MODE: 5>
ONELETTER_CODE = <SequenceMetricMode.ONELETTER_CODE: 1>
THREELETTER_CODE = <SequenceMetricMode.THREELETTER_CODE: 2>
property name
class pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric) pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::operator=(const class core::simple_metrics::metrics::SequenceSimilarityMetric &) –> class core::simple_metrics::metrics::SequenceSimilarityMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric) str

Name of the metric

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric) str

Name of the class

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::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.core.simple_metrics.metrics.SequenceSimilarityMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::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.metrics.SequenceSimilarityMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static score(seq1: str, seq2: str, normalize: bool) float

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::score(const std::string &, const std::string &, bool) –> double

set_apply_selector_to_native(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, setting: bool) None

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_apply_selector_to_native(bool) –> 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_native_pose(*args, **kwargs)

Overloaded function.

  1. set_native_pose(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, setting: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

  1. set_native_pose(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, setting: pyrosetta.rosetta.core.pose.Pose, apply_selector_to_native: bool) -> None

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose(class std::shared_ptr<const class core::pose::Pose>, bool) –> void

set_normalize(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, setting: bool) None

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_normalize(bool) –> void

set_residue_selector(*args, **kwargs)

Overloaded function.

  1. set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

the selector will decide which positions will be scored

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

  1. set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, apply_selector_to_native: bool) -> None

C++: core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, 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.core.simple_metrics.metrics.SequenceSimilarityMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator

C++: core::simple_metrics::metrics::SequenceSimilarityMetricCreator::operator=(const class core::simple_metrics::metrics::SequenceSimilarityMetricCreator &) –> class core::simple_metrics::metrics::SequenceSimilarityMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::SequenceSimilarityMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator) str

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

C++: core::simple_metrics::metrics::SequenceSimilarityMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::SequenceSimilarityMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric) pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::operator=(const class core::simple_metrics::metrics::ShapeSimilarityMetric &) –> class core::simple_metrics::metrics::ShapeSimilarityMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

calc shape similarity, returns results of the ShapeSimilarityCalculator

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric) str

Name of the metric

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric) str

Name of the class

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::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.core.simple_metrics.metrics.ShapeSimilarityMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::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++: core::simple_metrics::metrics::ShapeSimilarityMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

quick(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric, quick: int) None

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::quick(const unsigned long &) –> 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

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

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

verbose(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric, verbose: int) None

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::verbose(const unsigned long &) –> void

write_int_area(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric, write_int_area: bool) None

C++: core::simple_metrics::metrics::ShapeSimilarityMetric::write_int_area(const bool &) –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator

C++: core::simple_metrics::metrics::ShapeSimilarityMetricCreator::operator=(const class core::simple_metrics::metrics::ShapeSimilarityMetricCreator &) –> class core::simple_metrics::metrics::ShapeSimilarityMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::ShapeSimilarityMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator) str

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

C++: core::simple_metrics::metrics::ShapeSimilarityMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::ShapeSimilarityMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric) pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric

C++: core::simple_metrics::metrics::TimingProfileMetric::operator=(const class core::simple_metrics::metrics::TimingProfileMetric &) –> class core::simple_metrics::metrics::TimingProfileMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calc_time(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric) float

Core calculation that does not require pose.

C++: core::simple_metrics::metrics::TimingProfileMetric::calc_time() const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric, pose: pyrosetta.rosetta.core.pose.Pose) float
Returns time from construction to the call of this function in minutes, with decimal.

Options are available to calculate in hours instead.

C++: core::simple_metrics::metrics::TimingProfileMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::TimingProfileMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric) str

Name of the metric

C++: core::simple_metrics::metrics::TimingProfileMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric) str

Name of the class

C++: core::simple_metrics::metrics::TimingProfileMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::TimingProfileMetric::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.core.simple_metrics.metrics.TimingProfileMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::TimingProfileMetric::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.metrics.TimingProfileMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::TimingProfileMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_calc_in_hours(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric, calc_in_hours: bool) None
Set option to calculate the timings in hours.

Default false (minutes)

C++: core::simple_metrics::metrics::TimingProfileMetric::set_calc_in_hours(bool) –> 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

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.core.simple_metrics.metrics.TimingProfileMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator

C++: core::simple_metrics::metrics::TimingProfileMetricCreator::operator=(const class core::simple_metrics::metrics::TimingProfileMetricCreator &) –> class core::simple_metrics::metrics::TimingProfileMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::TimingProfileMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator) str

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

C++: core::simple_metrics::metrics::TimingProfileMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::TimingProfileMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A metric to report the total energy of the system or the delta total energy between another input pose.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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

Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, : pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric) pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric

C++: core::simple_metrics::metrics::TotalEnergyMetric::operator=(const class core::simple_metrics::metrics::TotalEnergyMetric &) –> class core::simple_metrics::metrics::TotalEnergyMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) float
Calculate the metric.

Returns the total score from the scorefunction or the total score of each residue in the residue selector.

If a comparison pose is given,

will calculate the delta between them (pose - comparison_pose).

C++: core::simple_metrics::metrics::TotalEnergyMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::metrics::TotalEnergyMetric::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.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric) str

Name of the metric

C++: core::simple_metrics::metrics::TotalEnergyMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric) str

Name of the class

C++: core::simple_metrics::metrics::TotalEnergyMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::metrics::TotalEnergyMetric::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.core.simple_metrics.metrics.TotalEnergyMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::metrics::TotalEnergyMetric::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.metrics.TotalEnergyMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) None
Set a pose into to calculate/report delta of total energy.

(apply_pose - comparison_pose)

C++: core::simple_metrics::metrics::TotalEnergyMetric::set_comparison_pose(class std::shared_ptr<const class core::pose::Pose>) –> 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_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector to calculate total energy of a subset of residues.

C++: core::simple_metrics::metrics::TotalEnergyMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_scorefunction(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set a scorefunction. Will use default Rosetta scorefunction if not set.

C++: core::simple_metrics::metrics::TotalEnergyMetric::set_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_scoretype(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric, scoretype: pyrosetta.rosetta.core.scoring.ScoreType) None
Set a specific scoretype to report

Default is total_score

C++: core::simple_metrics::metrics::TotalEnergyMetric::set_scoretype(enum core::scoring::ScoreType) –> 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.core.simple_metrics.metrics.TotalEnergyMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator, : pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator) pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator

C++: core::simple_metrics::metrics::TotalEnergyMetricCreator::operator=(const class core::simple_metrics::metrics::TotalEnergyMetricCreator &) –> class core::simple_metrics::metrics::TotalEnergyMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::simple_metrics::metrics::TotalEnergyMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator) str

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

C++: core::simple_metrics::metrics::TotalEnergyMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::metrics::TotalEnergyMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.core.simple_metrics.metrics.get_summary_type_strings() pyrosetta.rosetta.utility.vector1_std_string

C++: core::simple_metrics::metrics::get_summary_type_strings() –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.core.simple_metrics.metrics.summary_type

Bases: pybind11_builtins.pybind11_object

Enum that tells us HOW to summarize the PerResidueMetric data

Members:

sum

mean

n_res_eq

n_res_ne

n_res_gt

n_res_lt

n_res_gt_or_eq

n_res_lt_or_eq

bogus

summary_type_total

bogus = <summary_type.bogus: 9>
mean = <summary_type.mean: 2>
n_res_eq = <summary_type.n_res_eq: 3>
n_res_gt = <summary_type.n_res_gt: 5>
n_res_gt_or_eq = <summary_type.n_res_gt_or_eq: 7>
n_res_lt = <summary_type.n_res_lt: 6>
n_res_lt_or_eq = <summary_type.n_res_lt_or_eq: 8>
n_res_ne = <summary_type.n_res_ne: 4>
property name
sum = <summary_type.sum: 1>
summary_type_total = <summary_type.bogus: 9>