pose_inputters¶

Bindings for protocols::jd3::pose_inputters namespace

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter¶

Bases: PoseInputter

This is the simplest implementation of PoseInputter, which reads from -s/-l and PDB files. These can be any Protein Data Bank file type: .pdb, .cif, .mmtf

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter, : pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter¶: C++: protocols::jd3::pose_inputters::PDBPoseInputter::operator=(const class protocols::jd3::pose_inputters::PDBPoseInputter &) –> class protocols::jd3::pose_inputters::PDBPoseInputter &

job_available_on_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter) → bool¶: C++: protocols::jd3::pose_inputters::PDBPoseInputter::job_available_on_command_line() const –> bool

static keyname() → str¶

returns the name for the element that will be used in a job-definition: file for a structure originating from a .pdb file: “PDB”

C++: protocols::jd3::pose_inputters::PDBPoseInputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::PDBPoseInputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

pose_from_input_source(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter, : protocols::jd3::pose_inputters::PoseInputSource, : pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.core.pose.Pose¶

Takes a PoseInputSource object previously initialized in the: call to initialize_pose_input_sources()

C++: protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source(const class protocols::jd3::pose_inputters::PoseInputSource &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) –> class std::shared_ptr<class core::pose::Pose>

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

returns the schema for the PDB element used in a job-definition file: including all options that govern how a PDB is loaded.

C++: protocols::jd3::pose_inputters::PDBPoseInputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator¶

Bases: PoseInputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator¶: C++: protocols::jd3::pose_inputters::PDBPoseInputterCreator::operator=(const class protocols::jd3::pose_inputters::PDBPoseInputterCreator &) –> class protocols::jd3::pose_inputters::PDBPoseInputterCreator &

create_inputter(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶: C++: protocols::jd3::pose_inputters::PDBPoseInputterCreator::create_inputter() const –> class std::shared_ptr<class protocols::jd3::pose_inputters::PoseInputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator) → str¶: C++: protocols::jd3::pose_inputters::PDBPoseInputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::PDBPoseInputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_inputters::PDBPoseInputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource¶

Bases: InputSource

The %PoseInputSource is a small class for holding data about the starting Pose for a Job and where it comes from (i.e. which of the PoseInputters claims responsibility for creating a Pose for this instance). The “input_tag” is a string description of the input source and will be used as the “job_tag” to control output – the input tag should not include the file extension. It is perfectly reasonable for complex PoseInputters to subclass from PoseInputSource to tuck more complex data in the PoseInputSource, though, the string-string map ought to provide considerable flexibility in storing data without deriving new subclasses.

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource, : pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource¶: C++: protocols::jd3::pose_inputters::PoseInputSource::operator=(const class protocols::jd3::pose_inputters::PoseInputSource &) –> class protocols::jd3::pose_inputters::PoseInputSource &

input_tag(*args, **kwargs)¶

Overloaded function.

input_tag(self: pyrosetta.rosetta.protocols.jd3.InputSource) -> str

C++: protocols::jd3::InputSource::input_tag() const –> const std::string &

input_tag(self: pyrosetta.rosetta.protocols.jd3.InputSource, setting: str) -> None

C++: protocols::jd3::InputSource::input_tag(const std::string &) –> void

origin(*args, **kwargs)¶

Overloaded function.

origin(self: pyrosetta.rosetta.protocols.jd3.InputSource) -> str

C++: protocols::jd3::InputSource::origin() const –> const std::string &

origin(self: pyrosetta.rosetta.protocols.jd3.InputSource, setting: str) -> None

C++: protocols::jd3::InputSource::origin(const std::string &) –> void

source_id(*args, **kwargs)¶

Overloaded function.

source_id(self: pyrosetta.rosetta.protocols.jd3.InputSource) -> int

C++: protocols::jd3::InputSource::source_id() const –> unsigned long

source_id(self: pyrosetta.rosetta.protocols.jd3.InputSource, setting: int) -> None

C++: protocols::jd3::InputSource::source_id(unsigned long) –> void

store_string_pair(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource, key: str, value: str) → None¶: C++: protocols::jd3::pose_inputters::PoseInputSource::store_string_pair(const std::string &, const std::string &) –> void

string_string_map(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: protocols::jd3::pose_inputters::PoseInputSource::string_string_map() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶

Bases: pybind11_object

The %PoseInputter is responsible for reading from the command line a set of structures that are each to be run through a protocol, where each input struture will be the starting point for some number of jobs (where that number is at the JobQueen’s discretion). The %PoseInputter is responsible for two things: - for creating a list of PoseInputSource objects - for turning a PoseInputSource object into a Pose on demand.

In addition to the virtual functions, each derived PoseInputter should define two static methods that will be invoked by its corresponding PoseInputterCreator: - static std::string keyname(); - static void provide_xml_schema( utility::tag::XMLSchemaDefinition & xsd );

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter, : pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶: C++: protocols::jd3::pose_inputters::PoseInputter::operator=(const class protocols::jd3::pose_inputters::PoseInputter &) –> class protocols::jd3::pose_inputters::PoseInputter &

job_available_on_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter) → bool¶: C++: protocols::jd3::pose_inputters::PoseInputter::job_available_on_command_line() const –> bool

pose_from_input_source(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter, input_source: protocols::jd3::pose_inputters::PoseInputSource, options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.core.pose.Pose¶

Convert a single PoseInputSource into a Pose that will be used to: initialize a Job. The PoseInputSource object must have originated from this %PoseInputter in the prior call to initialize_pose_input_sources.

C++: protocols::jd3::pose_inputters::PoseInputter::pose_from_input_source(const class protocols::jd3::pose_inputters::PoseInputSource &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) –> class std::shared_ptr<class core::pose::Pose>

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator¶: C++: protocols::jd3::pose_inputters::PoseInputterCreator::operator=(const class protocols::jd3::pose_inputters::PoseInputterCreator &) –> class protocols::jd3::pose_inputters::PoseInputterCreator &

create_inputter(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶: C++: protocols::jd3::pose_inputters::PoseInputterCreator::create_inputter() const –> class std::shared_ptr<class protocols::jd3::pose_inputters::PoseInputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator) → str¶: C++: protocols::jd3::pose_inputters::PoseInputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::PoseInputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_inputters::PoseInputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory¶

Bases: SingletonBase_protocols_jd3_pose_inputters_PoseInputterFactory_t

static complex_type_name_for_pose_inputter(inputter_key: str) → str¶: C++: protocols::jd3::pose_inputters::PoseInputterFactory::complex_type_name_for_pose_inputter(const std::string &) –> std::string

define_pose_inputter_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶

The %ResidueSelectorFactory is the point of entry for the definition of the XML Schemas: for every ResidueSelector that may be instantiated from a file. It is responsible for defining an xs:group named “residue_selector” listing each of the residue-selector-complex types that may be initialized using the %ResidueSelectorFactory and to iterate across each of the ResidueSelectorCreators it contains asking them for the XML schema of the ResidueSelector they are responsible for creating.

C++: protocols::jd3::pose_inputters::PoseInputterFactory::define_pose_inputter_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory, creator: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator) → None¶: C++: protocols::jd3::pose_inputters::PoseInputterFactory::factory_register(class std::shared_ptr<class protocols::jd3::pose_inputters::PoseInputterCreator>) –> void

static get_instance() → protocols::jd3::pose_inputters::PoseInputterFactory¶: C++: utility::SingletonBase<protocols::jd3::pose_inputters::PoseInputterFactory>::get_instance() –> class protocols::jd3::pose_inputters::PoseInputterFactory *

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::PoseInputterFactory::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

new_pose_inputter(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory, : str) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶

Create a pose inputter given its identifying string, e.g. the name of an XML element.

C++: protocols::jd3::pose_inputters::PoseInputterFactory::new_pose_inputter(const std::string &) const –> class std::shared_ptr<class protocols::jd3::pose_inputters::PoseInputter>

pose_inputter_creators(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory) → pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t¶: C++: protocols::jd3::pose_inputters::PoseInputterFactory::pose_inputter_creators() const –> const class std::list<class std::shared_ptr<const class protocols::jd3::pose_inputters::PoseInputterCreator>, class std::allocator<class std::shared_ptr<const class protocols::jd3::pose_inputters::PoseInputterCreator> > > &

static pose_inputter_xml_schema_group_name() → str¶: C++: protocols::jd3::pose_inputters::PoseInputterFactory::pose_inputter_xml_schema_group_name() –> std::string

set_throw_on_double_registration(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory) → None¶

Should the Factory throw an exception or call utility::exit when it encounters the: second of two PoseInputterCreators 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::jd3::pose_inputters::PoseInputterFactory::set_throw_on_double_registration() –> void

class pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter¶

Bases: PoseInputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter, : pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter) → pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::operator=(const class protocols::jd3::pose_inputters::SilentFilePoseInputter &) –> class protocols::jd3::pose_inputters::SilentFilePoseInputter &

job_available_on_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter) → bool¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::job_available_on_command_line() const –> bool

static keyname() → str¶

returns the name for the element that will be used in a job-definition: file for a structure originating from a silent file: “Silent”

C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

pose_from_input_source(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter, input_source: pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource, options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::pose_from_input_source(const class protocols::jd3::pose_inputters::PoseInputSource &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) –> class std::shared_ptr<class core::pose::Pose>

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

returns the schema for the PDB element used in a job-definition file: including all options that govern how a silent struct is loaded.

C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

silent_file_data(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter) → pyrosetta.rosetta.core.io.silent.SilentFileData¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputter::silent_file_data() const –> const class core::io::silent::SilentFileData &

class pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator¶

Bases: PoseInputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::operator=(const class protocols::jd3::pose_inputters::SilentFilePoseInputterCreator &) –> class protocols::jd3::pose_inputters::SilentFilePoseInputterCreator &

create_inputter(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::create_inputter() const –> class std::shared_ptr<class protocols::jd3::pose_inputters::PoseInputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator) → str¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.jd3.pose_inputters.pose_inputter_xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, inputter_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶

Define the XML schema definition for a PoseInputter that contains: no subtags but may contain any number of attributes (aka options).

C++: protocols::jd3::pose_inputters::pose_inputter_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