Bindings for protocols::jd2::parser namespace

Classes
		builtins.object BluePrint DataLoader FragSetLoader MonteCarloLoader ResidueSelectorLoader ScoreFunctionLoader TaskOperationLoader DataLoaderCreator FragSetLoaderCreator MonteCarloLoaderCreator ResidueSelectorLoaderCreator ScoreFunctionLoaderCreator TaskOperationLoaderCreator DataLoaderFactory FragmentReader   class BluePrint(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.parser.BluePrint) -> NoneType   2. __init__(self : rosetta.protocols.jd2.parser.BluePrint, filename : str) -> NoneType   3. __init__(self : rosetta.protocols.jd2.parser.BluePrint, rval : rosetta.protocols.jd2.parser.BluePrint) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. abego(...) from builtins.PyCapsule abego(*args, **kwargs) Overloaded function.   1. abego(rosetta.protocols.jd2.parser.BluePrint) -> rosetta.utility.vector1_std_string   abego defined in bludprint file   2. abego(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> str   secondary structure at a position in blueprint file assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.BluePrint,  : rosetta.protocols.jd2.parser.BluePrint) -> rosetta.protocols.jd2.parser.BluePrint buildtype(...) from builtins.PyCapsule buildtype(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> str   return build type at each position extra(...) from builtins.PyCapsule extra(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> str   return build type at each position helix_pairings(...) from builtins.PyCapsule helix_pairings(rosetta.protocols.jd2.parser.BluePrint) -> str   helix pairings defined at the line of HHPAIR in blueprint hss_triplets(...) from builtins.PyCapsule hss_triplets(rosetta.protocols.jd2.parser.BluePrint) -> str   strand pairings defined at the line of SSPAIR in blueprint insert_ss_into_pose(...) from builtins.PyCapsule insert_ss_into_pose(self : rosetta.protocols.jd2.parser.BluePrint, pose : rosetta.core.pose.Pose) -> NoneType   set secondary structure into pose insertion(...) from builtins.PyCapsule insertion(self : rosetta.protocols.jd2.parser.BluePrint, i : int) -> str read_blueprint(...) from builtins.PyCapsule read_blueprint(self : rosetta.protocols.jd2.parser.BluePrint,  : str) -> bool   reading blueprint files resnum(...) from builtins.PyCapsule resnum(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> int   residue number at each position in blueprint file resnum_map(...) from builtins.PyCapsule resnum_map(self : rosetta.protocols.jd2.parser.BluePrint, resnum_pose : int) -> int   translate residue number of pose to that of blueprint file secstruct(...) from builtins.PyCapsule secstruct(*args, **kwargs) Overloaded function.   1. secstruct(rosetta.protocols.jd2.parser.BluePrint) -> str   secondary structures defined in blueprint file   2. secstruct(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> str   secondary structure at a position in blueprint file sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.protocols.jd2.parser.BluePrint) -> str   sequence defined in blueprint file   2. sequence(self : rosetta.protocols.jd2.parser.BluePrint, seqpos : int) -> str   a~mino acid type at a position in blueprint file set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.jd2.parser.BluePrint, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   set movemap based on blueprint strand_pairings(...) from builtins.PyCapsule strand_pairings(rosetta.protocols.jd2.parser.BluePrint) -> str   strand pairings defined at the line of SSPAIR in blueprint total_residue(...) from builtins.PyCapsule total_residue(rosetta.protocols.jd2.parser.BluePrint) -> int   total residue number defined in blueprint file total_residue_wolig(...) from builtins.PyCapsule total_residue_wolig(rosetta.protocols.jd2.parser.BluePrint) -> int   total residue number without ligand defined in blueprint file   class DataLoader(builtins.object)     A class for loading arbitrary data into the XML parser's basic::datacache::DataMap.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.parser.DataLoader) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.DataLoader,  : rosetta.protocols.jd2.parser.DataLoader) -> rosetta.protocols.jd2.parser.DataLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.DataLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The DataLoader may load specific information into the basic::datacache::DataMap  object using this interface.   class DataLoaderCreator(builtins.object)     A class for creating new instances of DataLoaders for use in the XML Parser     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.parser.DataLoaderCreator) -> NoneType   2. __init__(rosetta.protocols.jd2.parser.DataLoaderCreator, rosetta.protocols.jd2.parser.DataLoaderCreator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.DataLoaderCreator,  : rosetta.protocols.jd2.parser.DataLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.DataLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.DataLoaderCreator) -> str   class DataLoaderFactory(builtins.object)     A factory for creating DataLoaders, which are able to load arbitrary data into the basic::datacache::DataMap used in the XML-based parser. This factory supports the load-time registration scheme allowing DataLoaders to be defined in libraries outside of protocols.lib     Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.protocols.jd2.parser.DataLoaderFactory, creator : rosetta.protocols.jd2.parser.DataLoaderCreator) -> NoneType get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.parser.DataLoaderFactory newDataLoader(...) from builtins.PyCapsule newDataLoader(self : rosetta.protocols.jd2.parser.DataLoaderFactory,  : str) -> rosetta.protocols.jd2.parser.DataLoader   Create a DataLoader given its identifying string   class FragSetLoader(DataLoader)     A class for loading arbitrary data into the XML parser's basic::datacache::DataMap.     Method resolution order: FragSetLoader DataLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.FragSetLoader,  : rosetta.protocols.jd2.parser.FragSetLoader) -> rosetta.protocols.jd2.parser.FragSetLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.FragSetLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The FragSetLoader will create named FragSets and load them into the basic::datacache::DataMap   class FragSetLoaderCreator(DataLoaderCreator)       Method resolution order: FragSetLoaderCreator DataLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.FragSetLoaderCreator,  : rosetta.protocols.jd2.parser.FragSetLoaderCreator) -> rosetta.protocols.jd2.parser.FragSetLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.FragSetLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.FragSetLoaderCreator) -> str   class FragmentReader(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.parser.FragmentReader) -> NoneType   2. __init__(self : rosetta.protocols.jd2.parser.FragmentReader, tag : rosetta.utility.tag.Tag) -> NoneType   3. __init__(self : rosetta.protocols.jd2.parser.FragmentReader,  : rosetta.protocols.jd2.parser.FragmentReader) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.jd2.parser.FragmentReader, fragset : rosetta.core.fragment.FragSet) -> NoneType   main opeartion assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.FragmentReader,  : rosetta.protocols.jd2.parser.FragmentReader) -> rosetta.protocols.jd2.parser.FragmentReader   class MonteCarloLoader(DataLoader)     The MonteCarloLoader will create named MonteCarlo objects and load them into the basic::datacache::DataMap     Method resolution order: MonteCarloLoader DataLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.MonteCarloLoader,  : rosetta.protocols.jd2.parser.MonteCarloLoader) -> rosetta.protocols.jd2.parser.MonteCarloLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.MonteCarloLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The MonteCarloLoader will create named MonteCarlo objects and load them into the basic::datacache::DataMap   class MonteCarloLoaderCreator(DataLoaderCreator)       Method resolution order: MonteCarloLoaderCreator DataLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.MonteCarloLoaderCreator,  : rosetta.protocols.jd2.parser.MonteCarloLoaderCreator) -> rosetta.protocols.jd2.parser.MonteCarloLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.MonteCarloLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.MonteCarloLoaderCreator) -> str   class ResidueSelectorLoader(DataLoader)     A class for loading arbitrary data into the XML parser's basic::datacache::DataMap.     Method resolution order: ResidueSelectorLoader DataLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.ResidueSelectorLoader,  : rosetta.protocols.jd2.parser.ResidueSelectorLoader) -> rosetta.protocols.jd2.parser.ResidueSelectorLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.ResidueSelectorLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The ResidueSelectorLoader will create named ResidueSelectors and load them into the basic::datacache::DataMap   class ResidueSelectorLoaderCreator(DataLoaderCreator)       Method resolution order: ResidueSelectorLoaderCreator DataLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.ResidueSelectorLoaderCreator,  : rosetta.protocols.jd2.parser.ResidueSelectorLoaderCreator) -> rosetta.protocols.jd2.parser.ResidueSelectorLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.ResidueSelectorLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.ResidueSelectorLoaderCreator) -> str   class ScoreFunctionLoader(DataLoader)     A class for loading arbitrary data into the XML parser's basic::datacache::DataMap.     Method resolution order: ScoreFunctionLoader DataLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.ScoreFunctionLoader,  : rosetta.protocols.jd2.parser.ScoreFunctionLoader) -> rosetta.protocols.jd2.parser.ScoreFunctionLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.ScoreFunctionLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The ScoreFunctionLoader will create named ScoreFunctions and load them into the basic::datacache::DataMap loader_name(...) from builtins.PyCapsule loader_name() -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType score_function_loader_ct_namer(...) from builtins.PyCapsule score_function_loader_ct_namer(element_name : str) -> str   class ScoreFunctionLoaderCreator(DataLoaderCreator)       Method resolution order: ScoreFunctionLoaderCreator DataLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.ScoreFunctionLoaderCreator,  : rosetta.protocols.jd2.parser.ScoreFunctionLoaderCreator) -> rosetta.protocols.jd2.parser.ScoreFunctionLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.ScoreFunctionLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.ScoreFunctionLoaderCreator) -> str   class TaskOperationLoader(DataLoader)     A class for loading arbitrary data into the XML parser's basic::datacache::DataMap.     Method resolution order: TaskOperationLoader DataLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.TaskOperationLoader,  : rosetta.protocols.jd2.parser.TaskOperationLoader) -> rosetta.protocols.jd2.parser.TaskOperationLoader load_data(...) from builtins.PyCapsule load_data(self : rosetta.protocols.jd2.parser.TaskOperationLoader, pose : rosetta.core.pose.Pose, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType   The TaskOperationLoader will load named task operations into the basic::datacache::DataMap loader_name(...) from builtins.PyCapsule loader_name() -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType task_op_loader_ct_namer(...) from builtins.PyCapsule task_op_loader_ct_namer(element_name : str) -> str   class TaskOperationLoaderCreator(DataLoaderCreator)       Method resolution order: TaskOperationLoaderCreator DataLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.parser.TaskOperationLoaderCreator,  : rosetta.protocols.jd2.parser.TaskOperationLoaderCreator) -> rosetta.protocols.jd2.parser.TaskOperationLoaderCreator create_loader(...) from builtins.PyCapsule create_loader(rosetta.protocols.jd2.parser.TaskOperationLoaderCreator) -> rosetta.protocols.jd2.parser.DataLoader keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.parser.TaskOperationLoaderCreator) -> str