cluster¶

metrics

Bindings for protocols::multistage_rosetta_scripts::cluster namespace

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric) → pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetric::operator=(const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric &) –> class protocols::multistage_rosetta_scripts::cluster::ClusterMetric &

distance(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric, other: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric) → float¶

Measures the distance between this metric and another of the same type.: You can assume that other has the same type as this

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetric::distance(const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric &) const –> double

parse_my_tag(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric, pose: pyrosetta.rosetta.core.pose.Pose, tag: pyrosetta.rosetta.utility.tag.Tag, datacache: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetric::parse_my_tag(const class core::pose::Pose &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator) → pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator::operator=(const class protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator &) –> class protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator &

create_metric(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator) → pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric¶

Return a new metric.

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator::create_metric() const –> class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>

keyname(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator) → str¶

Return the tag name associated with this factory.

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Cluster Metric that this Creator is responsible for

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory¶

Bases: SingletonBase_protocols_multistage_rosetta_scripts_cluster_ClusterMetricFactory_t

static cluster_metric_xml_schema_group_name() → str¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::cluster_metric_xml_schema_group_name() –> std::string

creator_map(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t¶

Read access to the map of creator names to creators – for unit testing purposes only

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::creator_map() const –> const class std::map<std::string, class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator> > > > &

define_cluster_metric_xml_schema(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::define_cluster_metric_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory, creator: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator) → None¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::factory_register(class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator>) –> void

static get_instance() → protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory¶: C++: utility::SingletonBase<protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory>::get_instance() –> class protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory *

has_type(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory, : str) → bool¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::has_type(const std::string &) const –> bool

new_cluster_metric(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory, selector_name: str, pose: pyrosetta.rosetta.core.pose.Pose, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::new_cluster_metric(const std::string &, const class core::pose::Pose &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>

provide_xml_schema(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory, selector_name: str, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

set_throw_on_double_registration(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory) → None¶

Should the Factory throw an exception or call utility::exit when it encounters the: second of two ClusterMetricCreators with the same keyname? It’s default behavior is to call utility::exit, but this method allows you to set it so that it will throw an exception instead (which is unit testable).

C++: protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory::set_throw_on_double_registration() –> void

pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.complex_type_name_for_cluster_metric(cm_type: str) → str¶: C++: protocols::multistage_rosetta_scripts::cluster::complex_type_name_for_cluster_metric(const std::string &) –> std::string

pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.k_medoids_on_the_fly(*args, **kwargs)¶

Overloaded function.

k_medoids_on_the_fly(points: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t, num_medoids: int, medoid_positions: pyrosetta.rosetta.utility.vector1_bool) -> None

Finds “num_medoids” number of clusters from within the “points” vector. If a point becomes the center of a cluster, it’s index in “medoid_positions” is set to true. False otherwise. medoid_positions.size() will equal points.size()

C++: protocols::multistage_rosetta_scripts::cluster::k_medoids_on_the_fly(const class utility::vector1<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>, class std::allocator<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric> > > &, const unsigned short, class utility::vector1<bool, class std::allocator<bool> > &) –> void

k_medoids_on_the_fly(points: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t, num_medoids: int) -> pyrosetta.rosetta.utility.vector1_bool

This overload provides you with the vector of results.: It is mildly more convenient but mildly less efficient. Differences are mild all around.

C++: protocols::multistage_rosetta_scripts::cluster::k_medoids_on_the_fly(const class utility::vector1<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>, class std::allocator<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric> > > &, const unsigned short) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.k_medoids_with_edge_precalculation(*args, **kwargs)¶

Overloaded function.

k_medoids_with_edge_precalculation(points: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t, num_medoids: int, medoid_positions: pyrosetta.rosetta.utility.vector1_bool) -> None

Finds “num_medoids” number of clusters from within the “points” vector. If a point becomes the center of a cluster, it’s index in “medoid_positions” is set to true. False otherwise. medoid_positions.size() will equal points.size()

C++: protocols::multistage_rosetta_scripts::cluster::k_medoids_with_edge_precalculation(const class utility::vector1<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>, class std::allocator<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric> > > &, const unsigned short, class utility::vector1<bool, class std::allocator<bool> > &) –> void

k_medoids_with_edge_precalculation(points: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_multistage_rosetta_scripts_cluster_ClusterMetric_t, num_medoids: int) -> pyrosetta.rosetta.utility.vector1_bool

This overload provides you with the vector of results.: It is mildly more convenient but mildly less efficient. Differences are mild all around.

C++: protocols::multistage_rosetta_scripts::cluster::k_medoids_with_edge_precalculation(const class utility::vector1<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>, class std::allocator<class std::shared_ptr<const class protocols::multistage_rosetta_scripts::cluster::ClusterMetric> > > &, const unsigned short) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.vector_has_n_trues(vec: pyrosetta.rosetta.utility.vector1_bool, n: int) → bool¶

This is a simple utility for debugging. Makes sure we have the right number of medoids assigned.

C++: protocols::multistage_rosetta_scripts::cluster::vector_has_n_trues(const class utility::vector1<bool, class std::allocator<bool> > &, int) –> bool

pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, cm_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::multistage_rosetta_scripts::cluster::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void