per_residue_metrics

Bindings for core::simple_metrics::per_residue_metrics namespace

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

Bases: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.PerResidueClashMetric

Bases: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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.

  1. 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

  2. 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> > >

  1. 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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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.

  1. 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

  1. 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: pyrosetta.rosetta.core.simple_metrics.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.SidechainNeighborCountMetric

Bases: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

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

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

assign(self: pyrosetta.rosetta.core.simple_metrics.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.

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

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

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

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.core.simple_metrics.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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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: pyrosetta.rosetta.core.simple_metrics.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