simple_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.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the SimpleMetricData cache in the pose.

labeled as out_label.

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

/

C++: core::simple_metrics::CompositeRealMetric::apply(const std::string &, class core::pose::Pose &, bool) 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 &

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_std_string_double

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

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

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

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

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

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

Calculate the metric.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

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>

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.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_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.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

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

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.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.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose within the SimpleMetricData cache.

labeled as out_label.

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

C++: core::simple_metrics::CompositeStringMetric::apply(const std::string &, class core::pose::Pose &, bool) 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 &

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_std_string_std_string

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

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

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

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

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.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

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>

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.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_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.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

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

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.MetricKey

Bases: pybind11_builtins.pybind11_object

The key needed to set data in our SimpleMetricData. This allows only SimpleMetrics to set data

class pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetric

A class that is derived to calculate a set of core::Real values for each Residue. 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<Size, Real>

Resnum:Value

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, : pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double

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

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

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

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

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums

using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_double
Calculate the metric.

This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::PerResidueRealMetric::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.PerResidueRealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

metric(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) str

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) str

Name of the class

C++: core::simple_metrics::PerResidueRealMetric::name() const –> 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.PerResidueRealMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::simple_metrics::PerResidueRealMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

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

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) None
Set to output in PDB numbering instead of Rosetta during the Apply function,

which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueRealMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueRealMetric::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.PerResidueStringMetric

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

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, 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. calc_name is the individual component of the composite values calculated here

Score is added to the SimpleMetricData cache in the pose.

A ReferencePose is created with out_label as a name for further access. Data is added to the final score file.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, : pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric) pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_string

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

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

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

  5. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool, use_ref_pose_for_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_string

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums

using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_std_string
Calculate the metric.

This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::PerResidueStringMetric::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.PerResidueStringMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric) str

Name of the metric

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

name(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric) str

Name of the class

C++: core::simple_metrics::PerResidueStringMetric::name() const –> 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.PerResidueStringMetric, 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::PerResidueStringMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueStringMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

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

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, output_as_pdb_nums: bool) None
Set to output in PDB numbering instead of Rosetta during the Apply function,

which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueStringMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueStringMetric::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.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.

  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.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 &

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.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

Calculate and return the value. This function can not store the value. Use the apply function to store the value in the pose.

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>

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.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_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.RealMetric, tag: 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

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

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.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.

You should derive from RealMetric, StringMetric, etc. when making a new SimpleMetric. NOT this class!

apply(*args, **kwargs)

Overloaded function.

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

  2. apply(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the Score, which is output into a scorefile - labeled as label

Must be implemented by derived classes

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

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

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

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

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

Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix.

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

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.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_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.SimpleMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: core::simple_metrics::SimpleMetric::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

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.SimpleMetricCreator

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator, : pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator) str

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.SimpleMetricData

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

A container class for all Simple Metrics stored in the pose.

assign(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, : pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.core.simple_metrics.SimpleMetricData

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

clear(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) None

Clear all data held by this class

C++: core::simple_metrics::SimpleMetricData::clear() –> void

clone(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::simple_metrics::SimpleMetricData::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_all_sm_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct

Geet ALL RAW SimpleMetric information for IO/PyRosetta

C++: core::simple_metrics::SimpleMetricData::get_all_sm_data() const –> const struct core::simple_metrics::SimpleMetricStruct &

get_composite_real_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t

Get all CompositeRealMetric data

C++: core::simple_metrics::SimpleMetricData::get_composite_real_metric_data() const –> const class std::map<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > > &

get_composite_string_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

Get all CompositeStringMetric data

C++: core::simple_metrics::SimpleMetricData::get_composite_string_metric_data() const –> const class std::map<std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > > > > &

get_per_residue_real_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t
Get all PerResidueRealMetric data

Raw data - no ref-pose conversions.

C++: core::simple_metrics::SimpleMetricData::get_per_residue_real_metric_data() const –> const class std::map<std::string, class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > > > > &

get_per_residue_real_metric_output(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t

Get all PerResidueRealMetric output

C++: core::simple_metrics::SimpleMetricData::get_per_residue_real_metric_output() const –> const class std::map<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > > &

get_per_residue_string_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t
Get all PerResidueStringMetric data

Raw data - no ref-pose conversions.

C++: core::simple_metrics::SimpleMetricData::get_per_residue_string_metric_data() const –> const class std::map<std::string, class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > > > > &

get_per_residue_string_metric_output(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

Get all PerResidueStringMetric output

C++: core::simple_metrics::SimpleMetricData::get_per_residue_string_metric_output() const –> const class std::map<std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > > > > &

get_real_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_double

Get all RealMetric data

C++: core::simple_metrics::SimpleMetricData::get_real_metric_data() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

get_string_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.std.map_std_string_std_string

Get all StringMetric data

C++: core::simple_metrics::SimpleMetricData::get_string_metric_data() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

get_value(*args, **kwargs)

Overloaded function.

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: float) -> bool

Get RealMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, double &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: str) -> bool

Get StringMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, std::string &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_std_string_double) -> bool

Get CompositeRealMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_std_string_std_string) -> bool

Get CompositeStringMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_double) -> bool

Get PerResidueRealMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_std_string) -> bool

Get PerResidueStringMetric data. Return success status.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_double, pose: pyrosetta.rosetta.core.pose.Pose, use_ref_pose: bool) -> bool

Get PerResidueRealMetric data, optionally convert using refpose.

Any resnum not in current is removed.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > &, const class core::pose::Pose &, bool) const –> bool

  1. get_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_std_string, pose: pyrosetta.rosetta.core.pose.Pose, use_ref_pose: bool) -> bool

Get PerResidueStringMetric data, optionally convert using refpose.

Any resnum not in current is removed.

Returns true if data was present.

C++: core::simple_metrics::SimpleMetricData::get_value(const std::string &, class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &, const class core::pose::Pose &, bool) const –> bool

set_all_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, data: pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct) None

Set all SimpleMetric data for IO

C++: core::simple_metrics::SimpleMetricData::set_all_data(class core::simple_metrics::MetricKey, const struct core::simple_metrics::SimpleMetricStruct &) –> void

set_value(*args, **kwargs)

Overloaded function.

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, name: str, value: float) -> None

Set RealMetric data

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, const std::string &, double) –> void

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, name: str, value: str) -> None

Set StringMetric data

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, const std::string &, const std::string &) –> void

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, name: str, value: pyrosetta.rosetta.std.map_std_string_double) -> None

Set CompositeRealMetric data

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, const std::string &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, name: str, value: pyrosetta.rosetta.std.map_std_string_std_string) -> None

Set CompositeStringMetric data

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, const std::string &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_double) -> None

  2. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_double, outut_as_pdb_nums: bool) -> None

Set PerResidueRealMetric data

Creates a ReferencePose with the given name for the pose to maintain data integrity

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, class core::pose::Pose &, const std::string &, const class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > &, bool) –> void

  1. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_std_string) -> None

  2. set_value(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData, mk: pyrosetta.rosetta.core.simple_metrics.MetricKey, pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: pyrosetta.rosetta.std.map_unsigned_long_std_string, output_as_pdb_nums: bool) -> None

Set PerResidueStringMetric data

Creates a ReferencePose with the given name for the pose to maintain data integrity Creates an ouput map of the given data

C++: core::simple_metrics::SimpleMetricData::set_value(class core::simple_metrics::MetricKey, class core::pose::Pose &, const std::string &, const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &, bool) –> void

shared_from_this(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) pyrosetta.rosetta.core.simple_metrics.SimpleMetricData

C++: core::simple_metrics::SimpleMetricData::shared_from_this() –> class std::shared_ptr<class core::simple_metrics::SimpleMetricData>

show(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) None

C++: core::simple_metrics::SimpleMetricData::show() const –> void

class pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_core_simple_metrics_SimpleMetricFactory_t

define_simple_metric_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, xsd: utility::tag::XMLSchemaDefinition) None

C++: core::simple_metrics::SimpleMetricFactory::define_simple_metric_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, creator: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator) None

C++: core::simple_metrics::SimpleMetricFactory::factory_register(class std::shared_ptr<class core::simple_metrics::SimpleMetricCreator>) –> void

get_citation_humanreadable(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, metric_name: str) str

Get a human-readable listing of the citations for a given simple metric, by metric name.

Returns an empty string if there are no citations.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::SimpleMetricFactory::get_citation_humanreadable(const std::string &) const –> std::string

static get_instance() core::simple_metrics::SimpleMetricFactory

C++: utility::SingletonBase<core::simple_metrics::SimpleMetricFactory>::get_instance() –> class core::simple_metrics::SimpleMetricFactory *

has_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, simple_metric_name: str) bool

C++: core::simple_metrics::SimpleMetricFactory::has_type(const std::string &) const –> bool

new_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, constraint_generator_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::SimpleMetricFactory::new_simple_metric(const std::string &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory, selector_name: str, xsd: utility::tag::XMLSchemaDefinition) None

Get the XML schema for a given residue selector.

Throws an error if the residue selector is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: core::simple_metrics::SimpleMetricFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

static simple_metric_xml_schema_group_name() str

C++: core::simple_metrics::SimpleMetricFactory::simple_metric_xml_schema_group_name() –> std::string

class pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct

Bases: pybind11_builtins.pybind11_object

Structure for all SimpleMetric Data. Used for mmTF IO and multistage protocols.

assign(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct, : pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct) pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct

C++: core::simple_metrics::SimpleMetricStruct::operator=(const struct core::simple_metrics::SimpleMetricStruct &) –> struct core::simple_metrics::SimpleMetricStruct &

property composite_real_data_
property composite_string_data_
has_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct) bool

Does this struct contain any data?

C++: core::simple_metrics::SimpleMetricStruct::has_data() const –> bool

property per_residue_real_data_
property per_residue_real_output_
property per_residue_string_data_
property per_residue_string_output_
property real_data_
property string_data_
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.

  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.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 &

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.StringMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Calculate the metric.

Calculate and return the value. This function can not store the value. Use the apply function to store the value in the pose.

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>

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.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_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.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

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

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.TestCompositeRealMetric

Bases: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the SimpleMetricData cache in the pose.

labeled as out_label.

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

/

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

assign(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric, : pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric) pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_std_string_double

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

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

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

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_double

C++: core::simple_metrics::TestCompositeRealMetric::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.TestCompositeRealMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::TestCompositeRealMetric::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.TestCompositeRealMetric) pyrosetta.rosetta.utility.vector1_std_string

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

metric(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric) str

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

name(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric) str

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

static name_static() str

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

C++: core::simple_metrics::TestCompositeRealMetric::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::TestCompositeRealMetric::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.TestCompositeRealMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator) str

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric

Bases: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose within the SimpleMetricData cache.

labeled as out_label.

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric, : pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric) pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_std_string_std_string

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::simple_metrics::TestCompositeStringMetric::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.TestCompositeStringMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::TestCompositeStringMetric::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.TestCompositeStringMetric) pyrosetta.rosetta.utility.vector1_std_string

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

metric(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric) str

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

name(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric) str

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

static name_static() str

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

C++: core::simple_metrics::TestCompositeStringMetric::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::TestCompositeStringMetric::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.TestCompositeStringMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator) str

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric

Bases: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric, : pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric) pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double

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

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

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

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

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums

using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_double

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

clone(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::TestPerResidueRealMetric::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.PerResidueRealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

metric(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric) str

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

name(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric) str

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

static name_static() str

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

C++: core::simple_metrics::TestPerResidueRealMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

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

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

C++: core::simple_metrics::TestPerResidueRealMetric::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_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) None
Set to output in PDB numbering instead of Rosetta during the Apply function,

which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueRealMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueRealMetric::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.TestPerResidueRealMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator) str

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric

Bases: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, 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. calc_name is the individual component of the composite values calculated here

Score is added to the SimpleMetricData cache in the pose.

A ReferencePose is created with out_label as a name for further access. Data is added to the final score file.

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

assign(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric, : pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric) pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric

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

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_string

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

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

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

  5. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool, use_ref_pose_for_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_string

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums

using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_std_string

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

clone(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::TestPerResidueStringMetric::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.PerResidueStringMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

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

metric(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric) str

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

name(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric) str

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

static name_static() str

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

C++: core::simple_metrics::TestPerResidueStringMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueStringMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.

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

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

C++: core::simple_metrics::TestPerResidueStringMetric::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_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric, output_as_pdb_nums: bool) None
Set to output in PDB numbering instead of Rosetta during the Apply function,

which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueStringMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueStringMetric::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.TestPerResidueStringMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator) str

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.TestRealMetric

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.TestRealMetric, : pyrosetta.rosetta.core.simple_metrics.TestRealMetric) pyrosetta.rosetta.core.simple_metrics.TestRealMetric

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

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.TestRealMetric, : pyrosetta.rosetta.core.pose.Pose) float

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

clone(self: pyrosetta.rosetta.core.simple_metrics.TestRealMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::simple_metrics::TestRealMetric::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.TestRealMetric) str

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

name(self: pyrosetta.rosetta.core.simple_metrics.TestRealMetric) str

Name of the class

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

static name_static() str

Name of the class for creator.

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

C++: core::simple_metrics::TestRealMetric::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::TestRealMetric::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

property value_
class pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator) str

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

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

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

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

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.

  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.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 &

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.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>

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.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

static name_static() str

Name of the class for creator.

C++: core::simple_metrics::TestStringMetric::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.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_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::TestStringMetric::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.TestStringMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator, : pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator) str

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

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

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

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

pyrosetta.rosetta.core.simple_metrics.add_per_residue_simple_metric_schema(complex_schema: utility::tag::XMLSchemaComplexTypeGenerator) None

Add the schema for per-residue simple metrics. This is to reduce code dup.

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

pyrosetta.rosetta.core.simple_metrics.clear_sm_data(pose: pyrosetta.rosetta.core.pose.Pose) None

Clear the SM data stored in the pose

C++: core::simple_metrics::clear_sm_data(class core::pose::Pose &) –> void

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 std::string &) –> std::string

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

Overloaded function.

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

  2. 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 &, std::string) –> 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.

  1. 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

  2. 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 &, std::string) –> 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.get_sm_data(*args, **kwargs)

Overloaded function.

  1. get_sm_data(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetricData

Get a modifiable SM data. Use with caution.

Create it in the pose if it does not exist yet. Not for general use.

C++: core::simple_metrics::get_sm_data(class core::pose::Pose &) –> class std::shared_ptr<class core::simple_metrics::SimpleMetricData>

  1. get_sm_data(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetricData

Get a SM Data cache if present.

Otherwise, returns a nullptr.

C++: core::simple_metrics::get_sm_data(const class core::pose::Pose &) –> class std::shared_ptr<const class core::simple_metrics::SimpleMetricData>

pyrosetta.rosetta.core.simple_metrics.has_sm_data(pose: pyrosetta.rosetta.core.pose.Pose) bool

Does the pose have a SMCache?

C++: core::simple_metrics::has_sm_data(const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.simple_metrics.run_metrics(*args, **kwargs)

Overloaded function.

  1. run_metrics(pose: pyrosetta.rosetta.core.pose.Pose, metrics: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t) -> None

  2. run_metrics(pose: pyrosetta.rosetta.core.pose.Pose, metrics: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t, prefix: str) -> None

  3. run_metrics(pose: pyrosetta.rosetta.core.pose.Pose, metrics: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t, prefix: str, suffix: str) -> None

Apply a set of SimpleMetrics

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

pyrosetta.rosetta.core.simple_metrics.throw_sm_override_error(out_tag: str, metric_name: str) None
Get an informative error message if the SM data already exists and is not overriden.

Throws

C++: core::simple_metrics::throw_sm_override_error(const std::string &, const std::string &) –> void

pyrosetta.rosetta.core.simple_metrics.xsd_per_residue_real_metric_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, simple_metric_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None
Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueRealMetric base classes.

Add any additional schema options from sub-derived classes

C++: core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.simple_metrics.xsd_per_residue_string_metric_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, simple_metric_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None
Generate the ComplexTypeGenerator from the SimpleMetric and PerResidueStringMetric base classes.

Add any additional schema options from sub-derived classes

C++: core::simple_metrics::xsd_per_residue_string_metric_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.simple_metrics.xsd_simple_metric_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, simple_metric_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None
Generate the ComplexTypeGenerator from the SimpleMetric base class.

Add any additional schema options from sub-derived classes

C++: core::simple_metrics::xsd_simple_metric_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.simple_metrics.xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements(xsd: utility::tag::XMLSchemaDefinition, simple_metric_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, subelements: utility::tag::XMLSchemaSimpleSubelementList) None

C++: core::simple_metrics::xsd_simple_metric_type_definition_w_attributes_and_repeatable_subelements(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class utility::tag::XMLSchemaSimpleSubelementList &) –> void