simple_metrics¶

Bindings for core::simple_metrics namespace

class pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric¶

Bases: SimpleMetric

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

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

apply(*args, **kwargs)¶

Overloaded function.

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

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
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
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
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: SimpleMetric

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

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

apply(*args, **kwargs)¶

Overloaded function.

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

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
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
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
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_object

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

class pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric¶

Bases: SimpleMetric

A class that is derived to calculate probabilities for different residue types 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, map< AA, Real>>: Resnum:(Restype:Value)

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t

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::PerResidueProbabilitiesMetric::cached_calculate(const class core::pose::Pose &, bool, const std::string &, const std::string &, bool, bool) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

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

Calculate the metric.

This map is Rosetta Resnum->(ResType->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::PerResidueProbabilitiesMetric::calculate(const class core::pose::Pose &) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

clone(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::PerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

get_selector(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static output_sequence_profile(sequence: str, logit_map: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, output_filename: str) → None¶

Format the probabilities in psi-blast position-specific-scoring-matrix (PSSM) format and write to file

The sequence of the pose

A map containing the predicted logits for each position

A string defining the name of the output file

C++: core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(const std::string &, const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, const std::string &) –> void

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.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::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.PerResidueRealMetric¶

Bases: 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.

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

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
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
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
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
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) → pyrosetta.rosetta.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: pyrosetta.rosetta.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: 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.

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

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
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
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
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
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: SimpleMetric

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

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

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

apply(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
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_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: 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_std_allocator_std_pair_const_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_std_allocator_std_pair_const_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_probabilities_metric_data(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) → pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t¶

Get all PerResidueProbabilitiesMetric data: Raw data - no ref-pose conversions.

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

get_per_residue_probabilities_metric_output(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricData) → pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t¶

Get all PerResidueProbabilitiesMetric output

C++: core::simple_metrics::SimpleMetricData::get_per_residue_probabilities_metric_output() const –> const class std::map<std::string, 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> > > > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, 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_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_std_allocator_std_pair_const_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_std_allocator_std_pair_const_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_std_allocator_std_pair_const_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_std_allocator_std_pair_const_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.

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

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

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

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

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

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

Get PerResidueProbabilitiesMetric 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, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &) const –> bool

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

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

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

Get PerResidueProbabilitiesMetric 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, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, const class core::pose::Pose &, bool) const –> bool

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.

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

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

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

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

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
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

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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t) -> None
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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, outut_as_pdb_nums: bool) -> None

Set PerResidueProbabilitiesMetric 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, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, bool) –> void

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
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: SingletonBase_core_simple_metrics_SimpleMetricFactory_t

creator_map(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t¶

Access the map of name->creator. Used only for testing.

C++: core::simple_metrics::SimpleMetricFactory::creator_map() const –> const class std::map<std::string, class std::shared_ptr<class core::simple_metrics::SimpleMetricCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::simple_metrics::SimpleMetricCreator> > > > &

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_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_probabilities_data_¶

property per_residue_probabilities_output_¶

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: SimpleMetric

A class that is derived to calculate a string value.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose.: Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.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.

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

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

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

This function is meant to support caching metrics, so values do not need to be calculated twice,
for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

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

calculate(self: pyrosetta.rosetta.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: CompositeRealMetric

apply(*args, **kwargs)¶

Overloaded function.

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

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
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
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
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: 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: CompositeStringMetric

apply(*args, **kwargs)¶

Overloaded function.

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

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
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
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
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: 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.TestPerResidueProbabilitiesMetric¶

Bases: PerResidueProbabilitiesMetric

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, 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_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t

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::PerResidueProbabilitiesMetric::cached_calculate(const class core::pose::Pose &, bool, const std::string &, const std::string &, bool, bool) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

calculate(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t¶: C++: core::simple_metrics::TestPerResidueProbabilitiesMetric::calculate(const class core::pose::Pose &) const –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

clone(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::TestPerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

get_selector(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the set residue selector of this class.

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

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

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

static name_static() → str¶: C++: core::simple_metrics::TestPerResidueProbabilitiesMetric::name_static() –> std::string

static output_sequence_profile(sequence: str, logit_map: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, output_filename: str) → None¶

Format the probabilities in psi-blast position-specific-scoring-matrix (PSSM) format and write to file

The sequence of the pose

A map containing the predicted logits for each position

A string defining the name of the output file

C++: core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(const std::string &, const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, const std::string &) –> void

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.TestPerResidueProbabilitiesMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::simple_metrics::TestPerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::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::TestPerResidueProbabilitiesMetric::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.PerResidueProbabilitiesMetric, 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::PerResidueProbabilitiesMetric::set_output_as_pdb_nums(bool) –> void

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

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueProbabilitiesMetric::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.TestPerResidueProbabilitiesMetricCreator¶

Bases: SimpleMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator) → str¶

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

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

provide_xml_schema(self: pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::TestPerResidueProbabilitiesMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric¶

Bases: 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.

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

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
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
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
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
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) → pyrosetta.rosetta.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: pyrosetta.rosetta.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: 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: 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.

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

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
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
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
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
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: 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: RealMetric

apply(*args, **kwargs)¶

Overloaded function.

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

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

Create subclasses for each type of metric.

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose.: Data is output into the final score file, but can be accessed if needed through the cache.

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

assign(self: pyrosetta.rosetta.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.

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

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

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

This function is meant to support caching metrics, so values do not need to be calculated twice,
for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

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

calculate(self: pyrosetta.rosetta.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: 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.

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

C++: core::simple_metrics::get_metric_from_datamap_and_subtags(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, 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.

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

C++: core::simple_metrics::get_metrics_from_datamap_and_subtags(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, 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.

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>

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.

run_metrics(pose: pyrosetta.rosetta.core.pose.Pose, metrics: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t) -> None
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
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_probabilities_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 PerResidueProbabilitiesMetric base classes.: Add any additional schema options from sub-derived classes

C++: core::simple_metrics::xsd_per_residue_probabilities_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_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