composite_metrics¶

Bindings for core::simple_metrics::composite_metrics namespace

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric¶

Bases: CompositeRealMetric

A metric for calculating the probability delta between the current amino acid and the most likely from a PerResidueProbabilitiesMetric.

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

property cache_prefix_¶

property cache_suffix_¶

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.composite_metrics.BestMutationsFromProbabilitiesMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double¶

Calculate the metric.

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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.composite_metrics.BestMutationsFromProbabilitiesMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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>

compute_deltas(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, values: 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) → pyrosetta.rosetta.std.map_std_string_double¶

calculate the delta

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas(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 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> > >

property delta_cutoff_¶

property fail_on_missing_cache_¶

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 > >

property max_number_mutations_¶

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

Name of the metric

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

property metric_¶

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::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.composite_metrics.BestMutationsFromProbabilitiesMetric, 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::composite_metrics::BestMutationsFromProbabilitiesMetric::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::composite_metrics::BestMutationsFromProbabilitiesMetric::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_cutoffs(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, max_number_mutations: int, delta_cutoff: float) → None¶

Set cutoffs for the amount of mutations and delta probability which will be reported

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_cutoffs(unsigned long, double) –> void

set_fail_on_missing_cache(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, fail: bool) → None¶

If use_cache is set to false, do we fail if no data is found in the pose?: Default True

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_fail_on_missing_cache(bool) –> void

set_metric(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → None¶

Set the PerResidueProbabilitiesMetric that will be used to calculate the delta

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_metric(class std::shared_ptr<const class core::simple_metrics::PerResidueProbabilitiesMetric>) –> void

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric, use_cache: bool, prefix: str, suffix: str) -> None

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

Optionally pass any set prefix/suffix.

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

C++: core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::set_use_cached_data(bool, const std::string &, 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 use_cache_¶

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric¶

Bases: CompositeRealMetric

A metric to report/calculate all of the energies of a scorefunction that are not 0 or the delta of each energy between another input pose

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

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.composite_metrics.CompositeEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double¶

Calculate the metric.

C++: core::simple_metrics::composite_metrics::CompositeEnergyMetric::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.composite_metrics.CompositeEnergyMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::composite_metrics::CompositeEnergyMetric::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.composite_metrics.CompositeEnergyMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

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

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

C++: core::simple_metrics::composite_metrics::CompositeEnergyMetric::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.composite_metrics.CompositeEnergyMetric, 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::composite_metrics::CompositeEnergyMetric::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::composite_metrics::CompositeEnergyMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set a pose into to calculate/report delta of total energy.: (apply_pose - comparison_pose)

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

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) → None¶: C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

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

Set a residue selector to each energy term for the subset of residues.

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

set_scorefunction(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

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

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

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

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed¶

Bases: Exception

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

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

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

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

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

Will set the raw message.

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

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

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

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

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

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed¶

Bases: Exception

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

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

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

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

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

Will set the raw message.

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

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

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

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

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

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric¶

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

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.composite_metrics.ElectrostaticComplementarityMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::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.composite_metrics.ElectrostaticComplementarityMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::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.composite_metrics.ElectrostaticComplementarityMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

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

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

ignore_radius(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, ignore_radius: float) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::ignore_radius(double) –> void

interface_trim_radius(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, interface_trim_radius: float) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::interface_trim_radius(double) –> void

jump_id(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, jump: int) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::jump_id(unsigned long) –> void

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

report_all_ec(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, report: bool) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::report_all_ec(bool) –> void

residue_selector1(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::residue_selector1(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

residue_selector2(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::residue_selector2(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> 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.composite_metrics.ElectrostaticComplementarityMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric¶

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

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.composite_metrics.ElectrostaticSimilarityMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double¶: C++: core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::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.composite_metrics.ElectrostaticSimilarityMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::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.composite_metrics.ElectrostaticSimilarityMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

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

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

report_all_es(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric, report: bool) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::report_all_es(bool) –> void

residue_selector1(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::residue_selector1(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

residue_selector2(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::residue_selector2(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> 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.composite_metrics.ElectrostaticSimilarityMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric¶

Bases: CompositeStringMetric

This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables.

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

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.composite_metrics.ProtocolSettingsMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_std_string¶

Calculate the metric.

C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::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.composite_metrics.ProtocolSettingsMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::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.composite_metrics.ProtocolSettingsMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

parse_options(*args, **kwargs)¶

Overloaded function.

parse_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None
parse_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, options: pyrosetta.rosetta.utility.options.OptionCollection, base_name_option_only: bool) -> None
parse_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, options: pyrosetta.rosetta.utility.options.OptionCollection, base_name_option_only: bool, get_script_vars: bool) -> None
parse_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, options: pyrosetta.rosetta.utility.options.OptionCollection, base_name_option_only: bool, get_script_vars: bool, get_user_options: bool) -> None
parse_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, options: pyrosetta.rosetta.utility.options.OptionCollection, base_name_option_only: bool, get_script_vars: bool, get_user_options: bool, skip_corrections: bool) -> None

Parse an options collection into a set of string-string pairs.

C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::parse_options(const class utility::options::OptionCollection &, bool, bool, bool, bool) –> 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::composite_metrics::ProtocolSettingsMetric::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_job_tag(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, job_tag: str) → None¶

Set a specific job tag that will be output as job_tag for this particular run.: Used for benchmarking.

C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::set_job_tag(const std::string &) –> void

set_only_report_these_options(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, select_opts: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Only return these options. If not getting full namespaces, these are ONLY the base names.

C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::set_only_report_these_options(const class utility::vector1<std::string, class std::allocator<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

split_script_vars(self: pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric, script_vars_option_string: str, options_values: pyrosetta.rosetta.std.map_std_string_std_string) → None¶

Split the script_vars string into individual options and place them into options_values map.

C++: core::simple_metrics::composite_metrics::ProtocolSettingsMetric::split_script_vars(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 –> void

class pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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