loops_definers

Bindings for protocols::loops::loops_definers namespace

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner

Bases: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

@ details given a database table with the following schema, defining a single loop per row

CREATE TABLE loops (

tag TEXT, start INTEGER, stop INTEGER, cut INTEGER, skip_rate REAL, extended BOOLEAN);

return all loops associated with the job distributor input tag Note: you can specify a different table using the ‘database_table’ field

Note: if you would like to query the database for loops differently, you can either pre-query the table and store it, or extend, subclass, or create a different LoopsDefiner class.

apply(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::apply(const class core::pose::Pose &) –> class utility::vector1<struct protocols::loops::SerializedLoop, class std::allocator<struct protocols::loops::SerializedLoop> >

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::operator=(const class protocols::loops::loops_definers::LoopsDatabaseDefiner &) –> class protocols::loops::loops_definers::LoopsDatabaseDefiner &

class_name() → str

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

Create another loops definer of the type matching the most-derived

version of the class.

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::clone() const –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.core.pose.Pose) → None

Used to parse an xml-like tag to load parameters and properties.

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsDatabaseDefiner::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator

Bases: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator

creator for the LoopsDatabaseDefiner class

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator

C++: protocols::loops::loops_definers::LoopsDatabaseDefinerCreator::operator=(const class protocols::loops::loops_definers::LoopsDatabaseDefinerCreator &) –> class protocols::loops::loops_definers::LoopsDatabaseDefinerCreator &

create_loops_definer(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

C++: protocols::loops::loops_definers::LoopsDatabaseDefinerCreator::create_loops_definer() const –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsDatabaseDefinerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

type_name(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator) → str

C++: protocols::loops::loops_definers::LoopsDatabaseDefinerCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator

Bases: pybind11_builtins.pybind11_object

creator for the LoopsDefiner class

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator

C++: protocols::loops::loops_definers::LoopsDefinerCreator::operator=(const class protocols::loops::loops_definers::LoopsDefinerCreator &) –> class protocols::loops::loops_definers::LoopsDefinerCreator &

create_loops_definer(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

C++: protocols::loops::loops_definers::LoopsDefinerCreator::create_loops_definer() const –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator, : pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Define the structure of the XML file for the LoopDefiner that this

%LoopDefinerCreator instantiates using the XML Schema language.

C++: protocols::loops::loops_definers::LoopsDefinerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

type_name(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator) → str

C++: protocols::loops::loops_definers::LoopsDefinerCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_loops_loops_definers_LoopsDefinerFactory_t

Create LoopsDefiner Reporters

create_loops_definer(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory, type_name: str) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

C++: protocols::loops::loops_definers::LoopsDefinerFactory::create_loops_definer(const class std::basic_string<char> &) –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

define_loop_definer_xml_schema(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsDefinerFactory::define_loop_definer_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

factory_register(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator) → None

C++: protocols::loops::loops_definers::LoopsDefinerFactory::factory_register(class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefinerCreator>) –> void

get_all_loops_definer_names(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory) → pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::loops::loops_definers::LoopsDefinerFactory::get_all_loops_definer_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_instance() → protocols::loops::loops_definers::LoopsDefinerFactory

C++: utility::SingletonBase<protocols::loops::loops_definers::LoopsDefinerFactory>::get_instance() –> class protocols::loops::loops_definers::LoopsDefinerFactory *

has_type(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory, : str) → bool

C++: protocols::loops::loops_definers::LoopsDefinerFactory::has_type(const class std::basic_string<char> &) const –> bool

loop_definer_xml_schema_group_name() → str

C++: protocols::loops::loops_definers::LoopsDefinerFactory::loop_definer_xml_schema_group_name() –> std::string

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader

Bases: pyrosetta.rosetta.protocols.parser.DataLoader

A class for loading Loops data into the XML parser’s basic::datacache::DataMap.

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader

C++: protocols::loops::loops_definers::LoopsDefinerLoader::operator=(const class protocols::loops::loops_definers::LoopsDefinerLoader &) –> class protocols::loops::loops_definers::LoopsDefinerLoader &

load_data(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader, pose: pyrosetta.rosetta.core.pose.Pose, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The LoopsDefinerLoader will load named task operations into the basic::datacache::DataMap

C++: protocols::loops::loops_definers::LoopsDefinerLoader::load_data(const class core::pose::Pose &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

loader_name() → str

C++: protocols::loops::loops_definers::LoopsDefinerLoader::loader_name() –> std::string

loop_def_loader_ct_namer(element_name: str) → str

C++: protocols::loops::loops_definers::LoopsDefinerLoader::loop_def_loader_ct_namer(const class std::basic_string<char> &) –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsDefinerLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator

Bases: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator

creator for the LoopsExplicitDefiner class

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator

C++: protocols::loops::loops_definers::LoopsExplicitDefinerCreator::operator=(const class protocols::loops::loops_definers::LoopsExplicitDefinerCreator &) –> class protocols::loops::loops_definers::LoopsExplicitDefinerCreator &

create_loops_definer(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

C++: protocols::loops::loops_definers::LoopsExplicitDefinerCreator::create_loops_definer() const –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsExplicitDefinerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

type_name(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator) → str

C++: protocols::loops::loops_definers::LoopsExplicitDefinerCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator

Bases: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator

creator for the LoopsFileDefiner class

assign(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator, : pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator

C++: protocols::loops::loops_definers::LoopsFileDefinerCreator::operator=(const class protocols::loops::loops_definers::LoopsFileDefinerCreator &) –> class protocols::loops::loops_definers::LoopsFileDefinerCreator &

create_loops_definer(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator) → pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner

C++: protocols::loops::loops_definers::LoopsFileDefinerCreator::create_loops_definer() const –> class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loops::loops_definers::LoopsFileDefinerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

type_name(self: pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator) → str

C++: protocols::loops::loops_definers::LoopsFileDefinerCreator::type_name() const –> std::string

pyrosetta.rosetta.protocols.loops.loops_definers.attributes_for_load_loop_definitions(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Appends the attributes read by load_loop_definitions

C++: protocols::loops::loops_definers::attributes_for_load_loop_definitions(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.loops.loops_definers.complex_type_name_for_loop_definer(element_name: str) → str

C++: protocols::loops::loops_definers::complex_type_name_for_loop_definer(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.loops.loops_definers.load_loop_definitions(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::loops::loops_definers::load_loop_definitions(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const class core::pose::Pose &) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.loops.loops_definers.xsd_type_definition_w_attributes(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, loop_definer_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::loops::loops_definers::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void