simple_metrics¶

metrics

Bindings for core::simple_metrics namespace

class pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric¶

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetric

A class that is derived to calculate a set of core::Real values. Apply(pose) method calculates this metric and adds it to the pose score for output.

Calculate(pose) method calculates core::Real values and returns them as a map<std::string, Real>: Name:Value

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the pose as a score.

labeled as prefix+calc_name+”_”+metric+suffix. calc_name is the individual component of the composite values calculated here

Score is added through setPoseExtraScore and is output: into the score table/ score file at pose output.

C++: core::simple_metrics::CompositeRealMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, : pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric) → pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric¶: C++: core::simple_metrics::CompositeRealMetric::operator=(const class core::simple_metrics::CompositeRealMetric &) –> class core::simple_metrics::CompositeRealMetric &

calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double¶

Calculate the metric.

C++: core::simple_metrics::CompositeRealMetric::calculate(const class core::pose::Pose &) const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

clone(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::CompositeRealMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric) → str¶

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric) → str¶

Name of the class

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

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, 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::CompositeRealMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

class pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric¶

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetric

A class that is derived to calculate a set of string values. Apply(pose) method calculates this metric and adds it to the pose score for output.

Calculate(pose) method calculates multiple string values and returns them as a map<string, string>: Name:Value

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the pose as a score.

labeled as prefix+calc_name+”_”+metric+suffix. calc_name is the individual component of the composite values calculated here

Score is added through setPoseExtraScore and is output: into the score table/ score file at pose output.

C++: core::simple_metrics::CompositeStringMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, : pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric) → pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric¶: C++: core::simple_metrics::CompositeStringMetric::operator=(const class core::simple_metrics::CompositeStringMetric &) –> class core::simple_metrics::CompositeStringMetric &

calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_std_string¶

Calculate the metric.

C++: core::simple_metrics::CompositeStringMetric::calculate(const class core::pose::Pose &) const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

clone(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::CompositeStringMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric) → str¶

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric) → str¶

Name of the class

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

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, 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::CompositeStringMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

class pyrosetta.rosetta.core.simple_metrics.RealMetric¶

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetric

A class that is derived to calculate a Real (float) value.

Apply(pose) method calculates this metric and adds it to the pose score for output. Calculate(pose) method returns a core::Real

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the pose as a score.

labeled as prefix+metric+suffix.

Score is added through setPoseExtraScore and is output: into the score table/ score file at pose output.

C++: core::simple_metrics::RealMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, : pyrosetta.rosetta.core.simple_metrics.RealMetric) → pyrosetta.rosetta.core.simple_metrics.RealMetric¶: C++: core::simple_metrics::RealMetric::operator=(const class core::simple_metrics::RealMetric &) –> class core::simple_metrics::RealMetric &

calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Calculate the metric.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::RealMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

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.RealMetric) → str¶

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) → str¶

Name of the class

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

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, 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::RealMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

class pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Bases: pybind11_builtins.pybind11_object

The base class for Metrics in the Metric/Filter/Reporter system

The non-templated base class allows us to build one from a factory and interact with it through RosettaScripts

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix.: Must be implemented by derived classes

C++: core::simple_metrics::SimpleMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::SimpleMetric::operator=(const class core::simple_metrics::SimpleMetric &) –> class core::simple_metrics::SimpleMetric &

clone(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::SimpleMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

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

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

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

Get the name of the Metric

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

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

Get the name of SimpleMetric class

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

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, 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::SimpleMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

class pyrosetta.rosetta.core.simple_metrics.StringMetric¶

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetric

A class that is derived to calculate a string value.

Apply(pose) method calculates this metric and adds it to the pose score for output. Calculate(pose) method returns a string

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the pose as a score.

labeled as prefix+metric+suffix.

Score is added through setPoseExtraScore and is output: into the score table/ score file at pose output.

C++: core::simple_metrics::StringMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, : pyrosetta.rosetta.core.simple_metrics.StringMetric) → pyrosetta.rosetta.core.simple_metrics.StringMetric¶: C++: core::simple_metrics::StringMetric::operator=(const class core::simple_metrics::StringMetric &) –> class core::simple_metrics::StringMetric &

calculate(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose) → str¶

Calculate the metric.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.StringMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::StringMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

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.StringMetric) → str¶

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.StringMetric) → str¶

Name of the class

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

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.StringMetric, 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::StringMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

class pyrosetta.rosetta.core.simple_metrics.TestStringMetric¶

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

Create subclasses for each type of metric.

apply(*args, **kwargs)¶

Overloaded function.

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

Calculate the metric and add it to the pose as a score.

labeled as prefix+metric+suffix.

Score is added through setPoseExtraScore and is output: into the score table/ score file at pose output.

C++: core::simple_metrics::StringMetric::apply(class core::pose::Pose &, class std::basic_string<char>, class std::basic_string<char>) const –> void

assign(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetric, : pyrosetta.rosetta.core.simple_metrics.TestStringMetric) → pyrosetta.rosetta.core.simple_metrics.TestStringMetric¶: C++: core::simple_metrics::TestStringMetric::operator=(const class core::simple_metrics::TestStringMetric &) –> class core::simple_metrics::TestStringMetric &

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetric, : pyrosetta.rosetta.core.pose.Pose) → str¶: C++: core::simple_metrics::TestStringMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::TestStringMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

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.TestStringMetric) → str¶: C++: core::simple_metrics::TestStringMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetric) → str¶

Name of the class

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

name_static() → str¶

Name of the class for creator.

C++: core::simple_metrics::TestStringMetric::name_static() –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::simple_metrics::TestStringMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: core::simple_metrics::TestStringMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::type() const –> std::string

pyrosetta.rosetta.core.simple_metrics.complex_type_name_for_simple_metric(metric_name: str) → str¶: C++: core::simple_metrics::complex_type_name_for_simple_metric(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.simple_metrics.get_metric_from_datamap_and_subtags(*args, **kwargs)¶

Overloaded function.

get_metric_from_datamap_and_subtags(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric
get_metric_from_datamap_and_subtags(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap, tag_name: str) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::get_metric_from_datamap_and_subtags(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, class std::basic_string<char>) –> class std::shared_ptr<const class core::simple_metrics::SimpleMetric>

pyrosetta.rosetta.core.simple_metrics.get_metrics_from_datamap_and_subtags(*args, **kwargs)¶

Overloaded function.

get_metrics_from_datamap_and_subtags(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t
get_metrics_from_datamap_and_subtags(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap, tag_name: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t

C++: core::simple_metrics::get_metrics_from_datamap_and_subtags(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, class std::basic_string<char>) –> class utility::vector1<class std::shared_ptr<const class core::simple_metrics::SimpleMetric>, class std::allocator<class std::shared_ptr<const class core::simple_metrics::SimpleMetric> > >

pyrosetta.rosetta.core.simple_metrics.xsd_simple_metric_type_definition_w_attributes(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, simple_metric_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: core::simple_metrics::xsd_simple_metric_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void