simple_metrics

Bindings for protocols::analysis::simple_metrics namespace

class pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric

Bases: pyrosetta.rosetta.core.simple_metrics.StringMetric

A simple metric that writes out all the constraints in a pose or sub-region of a pose, in a format matching the (non-enzdes) constraints file format.

Vikram K. Mulligan (vmulligan.org)

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label

Score is added to the SimpleMetricData cache in the pose.

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

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

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric, : pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric) pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric

C++: protocols::analysis::simple_metrics::ConstraintsMetric::operator=(const class protocols::analysis::simple_metrics::ConstraintsMetric &) –> class protocols::analysis::simple_metrics::ConstraintsMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric, pose: pyrosetta.rosetta.core.pose.Pose) str

Calculate the metric.

C++: protocols::analysis::simple_metrics::ConstraintsMetric::calculate(const class core::pose::Pose &) const –> std::string

clone(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::analysis::simple_metrics::ConstraintsMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

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

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

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

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

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

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

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

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.StringMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name that this Metric will calculate

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

metric(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric) str

Name of the metric

C++: protocols::analysis::simple_metrics::ConstraintsMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric) str

Name of the class

C++: protocols::analysis::simple_metrics::ConstraintsMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::analysis::simple_metrics::ConstraintsMetric::name_static() –> std::string

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

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

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

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

called by parse_my_tag – should not be used directly

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

provide_citation_info(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

This simple metric is unpublished. It returns Vikram K. Mulligan as its author.

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

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

C++: protocols::analysis::simple_metrics::ConstraintsMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_selector(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector.

C++: protocols::analysis::simple_metrics::ConstraintsMetric::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector. Use nullptr to clear the residue selector.

Does not clone the input residue selector, but stores the const owning pointer directly.

C++: protocols::analysis::simple_metrics::ConstraintsMetric::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.protocols.analysis.simple_metrics.ConstraintsMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator, : pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator) pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator

C++: protocols::analysis::simple_metrics::ConstraintsMetricCreator::operator=(const class protocols::analysis::simple_metrics::ConstraintsMetricCreator &) –> class protocols::analysis::simple_metrics::ConstraintsMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator) str

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

C++: protocols::analysis::simple_metrics::ConstraintsMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator, : utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file. with the given prefix and suffix. (prefix+metric_name+suffix)

add_simple_metric(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, metric: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) None

Add a simple metric to run.

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::add_simple_metric(class std::shared_ptr<const class core::simple_metrics::SimpleMetric>) –> void

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None

Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file.

with the given prefix and suffix. (prefix+metric_name+suffix)

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply(class core::pose::Pose &, const std::string &, const std::string &) –> void

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

Run the set of SimpleMetrics. Add the data to the Pose, which will be output in the score file.

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, : pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover) pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::operator=(const class protocols::analysis::simple_metrics::RunSimpleMetricsMover &) –> class protocols::analysis::simple_metrics::RunSimpleMetricsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover) str

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

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

parse XML tag (to use this Mover in Rosetta Scripts)

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

provide_citation_info(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_override(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, override_existing_data: bool) None
Should we override existing data?

Default False.

If existing data is found and this option is false, we will throw an exception.

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_override(bool) –> void

set_prefix(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, prefix: str) None

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_prefix(const std::string &) –> void

set_simple_metrics(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, metrics: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_simple_metrics_SimpleMetric_t) None

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_simple_metrics(class utility::vector1<class std::shared_ptr<const class core::simple_metrics::SimpleMetric>, class std::allocator<class std::shared_ptr<const class core::simple_metrics::SimpleMetric> > >) –> void

set_suffix(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover, suffix: str) None

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_suffix(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator, : pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator) pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator::operator=(const class protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator &) –> class protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator) str

C++: protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

Calculate sequence recovery statistics on a protein, relative to a reference.

There’s several options for how the sequence recovery is calculated, depending on what parameters are set. Each metric is only calculated over the set of residues specified by the residue selector.

  • Standard - Used when PSSM isn’t set but reference pose is

    This is a strict match/no-match fraction.

  • Pass/Fail PSSM - Used when PSSM is set and use_ave_pssm is not (does not use reference pose)

    This is the PSSM recovery metric from DeLuca, Dorr & Meiler 2011 Biochem 50(40):8521 Residue identities with positive (or zero) values in the PSSM count as a match, those with negative vales as no-match.

  • Ave PSSM - Used when PSSM is set, use_ave_pssm is true, and no reference PDB is given

    This value is the average of the values in the PSSM matrix for the residue identities.

  • Delta PSSM - Used when PSSM is set, use_ave_pssm is true, and a reference PDB is provided.

    This value is the average of the change in value of the PSSM matrix (mut - ref)

For PSSM metrics, it’s assumed that the Pose numbering of both the main and reference structure matches the numbering of the PSSM.

apply(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

labeled as out_label.

Score is added to the SimpleMetricData cache

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

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

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, : pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric) pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::operator=(const class protocols::analysis::simple_metrics::SequenceRecoveryMetric &) –> class protocols::analysis::simple_metrics::SequenceRecoveryMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

calculate(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

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

clone(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

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

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

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

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

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

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

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

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

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

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

load_pssm(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, pssm_filename: str) None

Load the PSSM for reference from the given file.

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::load_pssm(const std::string &) –> void

metric(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric) str

Name of the metric

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric) str

Name of the class

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::name_static() –> std::string

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

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

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

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

called by parse_my_tag – should not be used directly

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

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

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

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

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

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

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_comparison_pose(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, pose: pyrosetta.rosetta.core.pose.Pose) None

Set a reference pose

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_comparison_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector to calculate the recovery from a subset of residues

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

set_residue_selector_ref(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None
Set a residue selector (for the reference) to calculate the recovery from a subset of residues

This needs to select the same number of residues as the set_residue_selector If not set (or nullptr), will use the same list as the selector passed to set_residue_selector()

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_residue_selector_ref(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_use_ave_pssm(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric, setting: bool) None

Set if we want to use a average PSSM value metric, or the pass/fail setting.

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_use_ave_pssm(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.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator, : pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator) pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator::operator=(const class protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator &) –> class protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

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

keyname(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator) str

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

C++: protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator, : utility::tag::XMLSchemaDefinition) None

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