per_residue_metrics¶

Bindings for core::simple_metrics::per_residue_metrics namespace

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric¶

Bases: PerResidueRealMetric

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

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

property cache_prefix_¶

property cache_suffix_¶

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::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>

property fail_on_missing_cache_¶

static get_current_probabilities(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_unsigned_long_double¶

calculate the delta

C++: core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::get_current_probabilities(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 &) –> class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

property metric_¶

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::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_fail_on_missing_cache(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric, 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::per_residue_metrics::CurrentProbabilityMetric::set_fail_on_missing_cache(bool) –> void

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

Set the PerResidueProbabilitiesMetric that will be used to calculate the delta

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

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric, 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::per_residue_metrics::CurrentProbabilityMetric::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.per_residue_metrics.CurrentProbabilityMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric¶

Bases: PerResidueRealMetric

A metric to report the total h-bonds residues from a selection to all [OTHER] residues, or from a set of residues to another set of residues. If No selection is given, will report ALL vs ALL.

Tips:

Use the SummaryMetric to get total hbonds of a selection or total number of residues having some number of hbonds. . See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds.

By default does not report self-self hbonds

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::HbondMetric::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_include_self(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric, include_self: bool) → None¶

Set to include hbonds as so:

resi - resi

Default false.

Will only find these if selector1 and selector2 contain the same residue.

C++: core::simple_metrics::per_residue_metrics::HbondMetric::set_include_self(bool) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_residue_selector2(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Optionally set a second residue selector to get bridged hbonds between: bothselections.

C++: core::simple_metrics::per_residue_metrics::HbondMetric::set_residue_selector2(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric¶

Bases: PerResidueProbabilitiesMetric

A class to load a probabilities weights file into a PerResidueProbabilitiesMetric

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

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

Calculate the metric.

This map is Rosetta Resnum->(AA, value)

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

The sequence of the pose

A map containing the predicted logits for each position

A string defining the name of the output file

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

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

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

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

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

This simple metric is unpublished. It returns Moritz Ertelt as its author.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::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_filename(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric, filename: str) → None¶

set the filename of the probabilities weights file to be loaded

C++: core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::set_filename(const std::string &) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

set_probabilities_from_lines(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric, lines: pyrosetta.rosetta.utility.vector1_std_string) → None¶

load amino acid probabilities from a given vectors of lines in format (POSNUM, AA_TYPE, WEIGHT)

C++: core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::set_probabilities_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

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

Set a ResidueSelector for which we will calculate values over.

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric¶

Bases: PerResidueRealMetric

A SimpleMetric that calculates the total number of atom-atom clashes from a residue in a residue selector to all other residues defined in a second residue selector using the LJ radius of each atom.

Can use a soft radius, which reduces it by 33%.

Does NOT calculate INTRA-RESIDUE clashes! Default is to calculate clashes of each residue to ALL OTHER residues (including those in the primary selector)

Set a secondary selector if you want other behavior

We use a SCORED pose to only calculate energies if fa_rep between a pair of residues under consideration is NOT 0: This is in order to speed up the calculation.

INTRA-residue clashes can be done through the PUBLIC is_clashing method to calculate atomic-clashes.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

is_clashing(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, pose: pyrosetta.rosetta.core.pose.Pose, resA: int, atomA: int, resB: int, atomB: int) → bool¶

Are these atoms clashing using soft or hard definition?

C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long) const –> bool

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_secondary_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the Residue Selector to use for TO other residues.

C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_secondary_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_soft_dampening(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, dampening: float) → None¶

Set the dampening of the LJ to use for soft-clash.: Default=.33

C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_soft_dampening(double) –> void

set_use_hydrogens(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, use_hydrogens: bool) → None¶

Should we calculate only heavy-heavy atom clashes: Default True

C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_use_hydrogens(bool) –> void

set_use_soft_clash(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric, soft_clash_check: bool) → None¶

When we calculate atom-atom distances using LJ distances,: Default True

clash if distance < (atomI_LJ + atomJ_LJ)*(1 - soft_clash)

C++: core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_use_soft_clash(bool) –> 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.per_residue_metrics.PerResidueClashMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric¶

Bases: PerResidueRealMetric

A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore.

Zscore Uses weighted sum of density, density-compared-to-neighbors, rama (where applicable) and cart_bonded to compute

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

match_res_mode(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric) → bool¶

Is this match res mode?

C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::match_res_mode() const –> bool

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::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_match_mode(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric, match_mode: bool) → None¶

Use density correlation instead of a zscore to fit to density: Default False. Useful for comparison to other densities of different resolution.

C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_match_mode(bool) –> void

set_mixed_sliding_window(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric, mixed_sliding_window: bool) → None¶

Set the code to use a mixed sliding window depending on the residue. 3 for protein, 1 for everything else.: Only used for Z-score mode.

C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_mixed_sliding_window(bool) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_sliding_window_size(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric, window_size: int) → None¶

Set the sliding window size. Default is 3. If you have anything other than protein, you probably want 1.: Only used for Z-score mode.

C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_sliding_window_size(unsigned long) –> void

set_use_selector_as_zscore_mask(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric, selector_as_mask: bool) → None¶

Use the selector as true mask to calculate the Zscore. Otherwise, use it just as a selection for result. Default true.

C++: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_use_selector_as_zscore_mask(bool) –> 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.per_residue_metrics.PerResidueDensityFitMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric¶

Bases: PerResidueRealMetric

A per-residue metric that will calculate/output per residue total energies or a specific score component. WEIGHTED. Correctly decomposes energies to per-residue.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

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

C++: core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::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_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

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

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

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

set_scoretype(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric, scoretype: pyrosetta.rosetta.core.scoring.ScoreType) → None¶

Set the scoretype data that we return. Default is total_score.

C++: core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::set_scoretype(enum core::scoring::ScoreType) –> 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.per_residue_metrics.PerResidueEnergyMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric¶

Bases: PerResidueRealMetric

A metric that outputs the layer of the glycan tree as measured by the residue distance to the root.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric¶

Bases: PerResidueRealMetric

A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

clone(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::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>

create_atom_id_map(*args, **kwargs)¶

Overloaded function.

create_atom_id_map(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID
create_atom_id_map(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose, desymmetrize_res_selector: bool) -> pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

Create an AtomID map according to options set in this class.: If desymmetrize_res_selector is true, we only consider the master subunit.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(const class core::pose::Pose &, bool) const –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

create_atom_id_map(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

Create an AtomID map according to residue_map.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(const class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set a reference pose to calculate rmsd

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

set_corresponding_atoms_robust(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, robust: bool) → None¶

Set this to false to fail instead.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_corresponding_atoms_robust(bool) –> 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_desymmetrize_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, desym: bool) → None¶

Should we de-symmetrize the residue selector(s) where we only consider the master subunit?: Default True.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_desymmetrize_residue_selector(bool) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

set_residue_mapping(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, rmsd_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) → None¶

Set a map to compute the RMSD on input->reference residue numbers.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_mapping(const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> void

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

Set a ResidueSelector for which we will calculate values over.

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

set_residue_selector_reference(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set a reference residue selector. Both selectors should return the same number of residues.: If not set, will use the main residue selector.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_reference(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_super(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Optional - Set a residue selector specifically for superposition.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_super(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector_super_reference(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set a reference residue selector for superposition. Both selectors should return the same number of residues.: If not set, but super selector is set, will use that.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_super_reference(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_rmsd_type(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, rmsd_type: pyrosetta.rosetta.core.scoring.rmsd_atoms) → None¶

Set what we will be calculating the RMSD on.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_rmsd_type(enum core::scoring::rmsd_atoms) –> void

set_run_superimpose(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric, super: bool) → None¶

Run a superimpose on the residues selected in the residue selector (or all): default False.

C++: core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_run_superimpose(bool) –> 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.per_residue_metrics.PerResidueRMSDMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric¶

Bases: PerResidueRealMetric

A per-residue metric that will calculate SASA for each residue given in a selector.

Virtual atoms are skipped completely.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

mode(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric) → pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode¶

Get the SASA mode (all SASA, polar only, hydrophobic only, etc.).

The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::mode() const –> enum core::scoring::sasa::SasaMethodHPMode

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::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_mode(*args, **kwargs)¶

Overloaded function.

set_mode(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric, mode_in: pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode) -> None

Set the SASA mode (all SASA, polar only, hydrophobic only, etc.).

The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::set_mode(const enum core::scoring::sasa::SasaMethodHPMode) –> void

set_mode(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric, mode_in: str) -> None

Set the SASA mode (all SASA, polar only, hydrophobic only, etc.).

The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.

Vikram K. Mulligan (vmulligan.org).

C++: core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::set_mode(const std::string &) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric¶

Bases: PerResidueRealMetric

A metric for calculating the conservation of a position given some predicted probabilities (using the relative Shannon Entropy).

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

property cache_prefix_¶

property cache_suffix_¶

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

clone(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::per_residue_metrics::ProbabilityConservationMetric::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_conservation(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, 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) → pyrosetta.rosetta.std.map_unsigned_long_double¶

calculate the delta

C++: core::simple_metrics::per_residue_metrics::ProbabilityConservationMetric::compute_conservation(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 std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

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.PerResidueRealMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

property metric_¶

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::ProbabilityConservationMetric::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_fail_on_missing_cache(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, 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::per_residue_metrics::ProbabilityConservationMetric::set_fail_on_missing_cache(bool) –> void

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

Set the PerResidueProbabilitiesMetric that will be used to calculate the conservation.

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

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric, 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::per_residue_metrics::ProbabilityConservationMetric::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.per_residue_metrics.ProbabilityConservationMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric¶

Bases: PerResidueRealMetric

A metric for calculating each sidechains neighbors based on cones. This metric uses the same core code as the LayerSelector. It can be combined with the SimpleMetricSelector to select any set of residues based on burial.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

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

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_angle_exponent(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, angle_exponent: float) → None¶

Set the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::set_angle_exponent(double) –> void

set_angle_shift_factor(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, angle_shift_factor: float) → None¶

Set the shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::set_angle_shift_factor(double) –> 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_dist_exponent(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, dist_exponent: float) → None¶

Set the exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::set_dist_exponent(double) –> void

set_dist_midpoint(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, dist_midpoint: float) → None¶

Midpoint of the distance falloff sigmoid.

Defaults to 9.0. Only used by the sidchain_neighbors code.

C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::set_dist_midpoint(double) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

set_res_denominator(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric, res_denom: float) → None¶

Factor by which number of residue neighbors is divided.

Defaults to 1.0.

C++: core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::set_res_denominator(double) –> void

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

Set a ResidueSelector for which we will calculate values over.

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric¶

Bases: PerResidueRealMetric

A metric to measure hydrogen bonds between a set of residues that are water-mediated.

DEPTH:

We only traverse a depth of 1 by default. Make sure to set the -ignore_waters flag to false in order to have Rosetta include the HOH residues.

SELECTION:

If one residue selector is given, will calculate bridged waters between residues of the selection and all [OTHER] residues, otherwise it will calculate bridges between one selection and another.

If NO SELECTION is give, will report ALL bridged hbonds in a pose [by default without self-water-self hbonds].

HBOND:

Since these are bridged hbonds, and h-bond networks can be rather complex, the numbers: reported here are the unique h-bond paths from sele1 to sele2. If you give only a single residue selector, these are bridged hbonds from sele1 to OTHER residues in sele1. By default we do not include mediated hbonds back on itself, but this is an option.

TIPS:

It is generally recommended to repack the waters using the OptH TaskOperation before input into this metric, especially if only Oxygens were present. Using the option -include_vrt false will keep all waters present in the resulting structure. Use the option -corrections::water::wat_rot_sampling 10 to decrease the angle of sampling from a default of 30 to 10. This will result in many more rotamers, but will improve networks.

Hydration shells can be calculated by passing selection1 as all waters in the pose, selection2 as the protein or chain, and then reporting only a single depth (with max_depth at 0 and 1 for the first and second shell waters.”

It is also recommended to use the Beta scorefunction as this can improve hydrogen bond detection.

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

Add options to the schema from this base class.

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

apply(*args, **kwargs)¶

Overloaded function.

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose: A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

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

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

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

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

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

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

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums
using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_double¶

Calculate the metric.

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

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

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

clone(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::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>

find_hb_paths(*args, **kwargs)¶

Overloaded function.

find_hb_paths(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, local_waters: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int) -> None
find_hb_paths(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, local_waters: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int) -> None
find_hb_paths(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, local_waters: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str) -> None
find_hb_paths(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, local_waters: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str, current_depth: int) -> None
find_hb_paths(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, local_waters: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str, current_depth: int, prev_hb: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> None

Recursive function to find all unique HBond paths involving water and ending: with a residue that is not in our water list.

Populates paths as the reference. Path is a splittalbe string of the connections.

ex: 191-221-333 where residue 221 is a water in our list.

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::find_hb_paths(const class core::scoring::hbonds::HBondSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > > &, const unsigned long, const unsigned long, const std::string &, const unsigned long, class std::shared_ptr<const class core::scoring::hbonds::HBond>) const –> void

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

Output data name will be prefix+custom_type+type+suffix

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

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

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

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

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

Get the submetric names that this Metric will calculate

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

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

Get the set residue selector of this class.

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

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

Name of the metric

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

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

Name of the class

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

static name_static() → str¶

Name of the class for creator.

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::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_depth(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, depth: int) → None¶

Set the depth we will go to find hbonds.: Default is 1. IE resi - water -resj

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_depth(const unsigned long) –> void

set_include_only_set_depth(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, include_only_depth: bool) → None¶

Set to include only the depth that is set instead of Up to the max depth.

IE - if depth is set to 2, we only include hbond paths mediated by two waters.: Default false

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_only_set_depth(bool) –> void

set_include_self(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, include_self: bool) → None¶

Set to include hbonds as so:

resi - water - resi

Default false.

Will only find these if selector1 and selector2 contain the same residue.

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_self(bool) –> void

set_include_virt_waters(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, include_virt_waters: bool) → None¶

After packing, some waters become HOH_v if they don’t match certain ref energy.: The option -include_vrt false will have them all be HOH during packing. Set this option to true to incude them in our calculation if they are still virts.

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_virt_waters(bool) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) → None¶

Set to output in PDB numbering instead of Rosetta during the Apply function,: which adds the data to pose as extra scores.

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

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

Set a ResidueSelector for which we will calculate values over.

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

set_residue_selector2(self: pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Optionally set a second residue selector to get bridged hbonds between: both selections.

C++: core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_residue_selector2(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

class pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator¶

Bases: SimpleMetricCreator

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

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

Instantiate a particular SimpleMetric

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

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

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

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

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