simple_metrics

Bindings for protocols::pose_sewing::simple_metrics namespace

class pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric

Bases: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric

composite metric returning motif scores that pass per block

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label.

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

/

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::operator=(const class protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric &) –> class protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_double

Calculate the metric.

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::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.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::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.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric) str

Name of the metric

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric) str

Name of the class

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

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

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

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

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

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

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

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

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

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::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_distance_mode(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, in: bool) None

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_distance_mode(bool) –> void

set_drop_best(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, in: bool) None

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_drop_best(bool) –> void

set_normalize_by_residues(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, in: bool) None

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_normalize_by_residues(bool) –> void

set_selector(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_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.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator::operator=(const class protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator &) –> class protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator) str

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

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric

Bases: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric

composite metric returning shape complementarities that pass per block

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label.

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

/

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::operator=(const class protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric &) –> class protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_double

Calculate the metric.

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::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.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::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.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric) str

Name of the metric

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric) str

Name of the class

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

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

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

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

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

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

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

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

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

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::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_filtered_area(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, filtered_area: float) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::set_filtered_area(double) –> void

set_filtered_d_median(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, filtered_d_median: float) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::set_filtered_d_median(double) –> void

set_filtered_sc(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, filtered_sc: float) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::set_filtered_sc(double) –> void

set_scale_by_length(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, in: bool) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::set_scale_by_length(bool) –> void

set_selector(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::set_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.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetricCreator::operator=(const class protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetricCreator &) –> class protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator) str

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

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

min dist

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label.

Score is added to the SimpleMetricData cache

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

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::operator=(const class protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric &) –> class protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

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

clone(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::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.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric) str

Name of the metric

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric) str

Name of the class

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

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

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

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

provide_citation_info(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide authorship information for an unpublished Rosetta module.

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::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_selectors(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric, A_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, B_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, all_atom_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::set_selectors(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, 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.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetricCreator::operator=(const class protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetricCreator &) –> class protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator) str

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

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric

Bases: pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric

composite metric returning motif scores per window

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label.

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

/

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::operator=(const class protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric &) –> class protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_double

Calculate the metric.

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::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.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::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.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric) str

Name of the metric

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric) str

Name of the class

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

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

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

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

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

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

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

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

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

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::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_distance_mode(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, in: bool) None

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::set_distance_mode(bool) –> void

set_selector(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_window_width(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric, in: int) None

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::set_window_width(unsigned long) –> void

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

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

class pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator, : pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator) pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetricCreator::operator=(const class protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetricCreator &) –> class protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator) str

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

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void