Bindings for protocols::farna::libraries namespace

Classes
		builtins.object BasePairStepLibrary BasePairStepSequence BasePairType ChunkSet RNA_ChunkLibrary RNA_JumpLibrary RNA_PairingTemplate rosetta.utility.SingletonBase_protocols_farna_libraries_RNA_LibraryManager_t(builtins.object) RNA_LibraryManager   class BasePairStepLibrary(builtins.object)     /////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.farna.libraries.BasePairStepLibrary) -> NoneType   doc   2. __init__(self : rosetta.protocols.farna.libraries.BasePairStepLibrary, canonical : bool) -> NoneType   3. __init__(self : rosetta.protocols.farna.libraries.BasePairStepLibrary,  : rosetta.protocols.farna.libraries.BasePairStepLibrary) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. canonical(...) from builtins.PyCapsule canonical(rosetta.protocols.farna.libraries.BasePairStepLibrary) -> bool database_dir(...) from builtins.PyCapsule database_dir(rosetta.protocols.farna.libraries.BasePairStepLibrary) -> str has_value(...) from builtins.PyCapsule has_value(self : rosetta.protocols.farna.libraries.BasePairStepLibrary, base_pair_step_sequence : rosetta.protocols.farna.libraries.BasePairStepSequence) -> bool mini_pose_list(...) from builtins.PyCapsule mini_pose_list(self : rosetta.protocols.farna.libraries.BasePairStepLibrary, base_pair_step_sequence : rosetta.protocols.farna.libraries.BasePairStepSequence) -> rosetta.utility.vector1_std_shared_ptr_core_pose_MiniPose_t scratch_pose(...) from builtins.PyCapsule scratch_pose(self : rosetta.protocols.farna.libraries.BasePairStepLibrary, base_pair_step_sequence : rosetta.protocols.farna.libraries.BasePairStepSequence) -> rosetta.core.pose.Pose   class BasePairStepSequence(builtins.object)     /////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.farna.libraries.BasePairStepSequence, str, str, str, str) -> NoneType   doc   2. __init__(self : rosetta.protocols.farna.libraries.BasePairStepSequence, nt_i : str, nt_i_next : str, nt_j : str, nt_j_next : str, num_bulge : int) -> NoneType   3. __init__(self : rosetta.protocols.farna.libraries.BasePairStepSequence, sequence : str, i : int, i_next : int, j : int, j_next : int) -> NoneType   4. __init__(self : rosetta.protocols.farna.libraries.BasePairStepSequence, sequence : str, base_pair_step : rosetta.protocols.farna.base_pairs.BasePairStep) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.farna.libraries.BasePairStepSequence) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.farna.libraries.BasePairStepSequence,  : rosetta.protocols.farna.libraries.BasePairStepSequence) -> rosetta.protocols.farna.libraries.BasePairStepSequence num_bulge(...) from builtins.PyCapsule num_bulge(rosetta.protocols.farna.libraries.BasePairStepSequence) -> int subdir(...) from builtins.PyCapsule subdir(rosetta.protocols.farna.libraries.BasePairStepSequence) -> str tag(...) from builtins.PyCapsule tag(rosetta.protocols.farna.libraries.BasePairStepSequence) -> str   class BasePairType(builtins.object)     ////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.farna.libraries.BasePairType, aa1_in : str, aa2_in : str, edge1_in : rosetta.core.chemical.rna.BaseEdge, edge2_in : rosetta.core.chemical.rna.BaseEdge, orientation_in : rosetta.core.chemical.rna.BaseDoubletOrientation) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. tag(...) from builtins.PyCapsule tag(rosetta.protocols.farna.libraries.BasePairType) -> str Data descriptors defined here: aa1 aa2 edge1 edge2 orientation   class ChunkSet(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.farna.libraries.ChunkSet, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, res_map : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType   2. __init__(self : rosetta.protocols.farna.libraries.ChunkSet, mini_pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_MiniPose_t, example_pose : rosetta.core.pose.Pose, res_map : rosetta.std.map_unsigned_long_unsigned_long) -> 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.farna.libraries.ChunkSet,  : rosetta.protocols.farna.libraries.ChunkSet) -> rosetta.protocols.farna.libraries.ChunkSet check_fold_tree_OK(...) from builtins.PyCapsule check_fold_tree_OK(self : rosetta.protocols.farna.libraries.ChunkSet, pose : rosetta.core.pose.Pose) -> bool get_atom_id_map(...) from builtins.PyCapsule get_atom_id_map(self : rosetta.protocols.farna.libraries.ChunkSet, pose : rosetta.core.pose.Pose, atom_id_mapper_to_target_vanilla_pose : protocols::toolbox::AtomID_Mapper) -> rosetta.std.map_core_id_AtomID_core_id_AtomID insert_chunk_into_pose(...) from builtins.PyCapsule insert_chunk_into_pose(*args, **kwargs) Overloaded function.   1. insert_chunk_into_pose(self : rosetta.protocols.farna.libraries.ChunkSet, pose : rosetta.core.pose.Pose, chunk_pose_index : int, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> NoneType   2. insert_chunk_into_pose(self : rosetta.protocols.farna.libraries.ChunkSet, pose : rosetta.core.pose.Pose, chunk_pose_index : int, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap, do_rosetta_library_domain_check : bool) -> NoneType mini_pose(...) from builtins.PyCapsule mini_pose(self : rosetta.protocols.farna.libraries.ChunkSet, idx : int) -> rosetta.core.pose.MiniPose num_chunks(...) from builtins.PyCapsule num_chunks(rosetta.protocols.farna.libraries.ChunkSet) -> int set_user_input(...) from builtins.PyCapsule set_user_input(self : rosetta.protocols.farna.libraries.ChunkSet, setting : bool) -> NoneType user_input(...) from builtins.PyCapsule user_input(rosetta.protocols.farna.libraries.ChunkSet) -> bool   class RNA_ChunkLibrary(builtins.object)     ////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> NoneType   2. __init__(rosetta.protocols.farna.libraries.RNA_ChunkLibrary, rosetta.utility.vector1_std_string, rosetta.utility.vector1_std_string, rosetta.core.pose.Pose, rosetta.utility.vector1_unsigned_long) -> NoneType   doc   3. __init__(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pdb_files : rosetta.utility.vector1_std_string, silent_files : rosetta.utility.vector1_std_string, pose : rosetta.core.pose.Pose, input_res : rosetta.utility.vector1_unsigned_long, allow_insert_res : rosetta.utility.vector1_unsigned_long) -> NoneType   4. __init__(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, silent_files : rosetta.utility.vector1_std_string, pose : rosetta.core.pose.Pose, input_res : rosetta.utility.vector1_unsigned_long) -> NoneType   5. __init__(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose) -> NoneType   6. __init__(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary,  : rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_chunk_set(...) from builtins.PyCapsule add_chunk_set(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, silent_file : str, res_map : rosetta.std.map_unsigned_long_unsigned_long, big_pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary,  : rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> rosetta.protocols.farna.libraries.RNA_ChunkLibrary atom_level_domain_map(...) from builtins.PyCapsule atom_level_domain_map(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> rosetta.protocols.toolbox.AtomLevelDomainMap check_fold_tree_OK(...) from builtins.PyCapsule check_fold_tree_OK(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose) -> bool chunk_coverage(...) from builtins.PyCapsule chunk_coverage(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> float chunk_set(...) from builtins.PyCapsule chunk_set(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, n : int) -> rosetta.protocols.farna.libraries.ChunkSet clone(...) from builtins.PyCapsule clone(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> rosetta.protocols.farna.libraries.RNA_ChunkLibrary   clone the ChunkLibrary get_indices_of_moving_chunks(...) from builtins.PyCapsule get_indices_of_moving_chunks(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> rosetta.utility.vector1_unsigned_long initialize_random_chunks(...) from builtins.PyCapsule initialize_random_chunks(*args, **kwargs) Overloaded function.   1. initialize_random_chunks(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose) -> NoneType   2. initialize_random_chunks(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose, dump_pdb : bool) -> NoneType initialize_rna_chunk_library(...) from builtins.PyCapsule initialize_rna_chunk_library(*args, **kwargs) Overloaded function.   1. initialize_rna_chunk_library(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pdb_files : rosetta.utility.vector1_std_string, silent_files : rosetta.utility.vector1_std_string, pose : rosetta.core.pose.Pose, input_res : rosetta.utility.vector1_unsigned_long) -> NoneType   2. initialize_rna_chunk_library(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pdb_files : rosetta.utility.vector1_std_string, silent_files : rosetta.utility.vector1_std_string, pose : rosetta.core.pose.Pose, input_res : rosetta.utility.vector1_unsigned_long, allow_insert_res : rosetta.utility.vector1_unsigned_long) -> NoneType insert_chunk_into_pose(...) from builtins.PyCapsule insert_chunk_into_pose(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose, chunk_list_index : int, chunk_pose_index : int) -> NoneType num_chunk_sets(...) from builtins.PyCapsule num_chunk_sets(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> int num_chunks(...) from builtins.PyCapsule num_chunks(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, n : int) -> int num_moving_chunks(...) from builtins.PyCapsule num_moving_chunks(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> int random_chunk_insertion(...) from builtins.PyCapsule random_chunk_insertion(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose) -> bool set_atom_level_domain_map(...) from builtins.PyCapsule set_atom_level_domain_map(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> NoneType single_user_input_chunk(...) from builtins.PyCapsule single_user_input_chunk(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> int superimpose_to_single_user_input_chunk(...) from builtins.PyCapsule superimpose_to_single_user_input_chunk(self : rosetta.protocols.farna.libraries.RNA_ChunkLibrary, pose : rosetta.core.pose.Pose) -> bool update_to_move_rosetta_library_chunks(...) from builtins.PyCapsule update_to_move_rosetta_library_chunks(rosetta.protocols.farna.libraries.RNA_ChunkLibrary) -> NoneType   class RNA_JumpLibrary(builtins.object)     ////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, filename : str) -> NoneType   2. __init__(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary,  : rosetta.protocols.farna.libraries.RNA_JumpLibrary) -> 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.farna.libraries.RNA_JumpLibrary,  : rosetta.protocols.farna.libraries.RNA_JumpLibrary) -> rosetta.protocols.farna.libraries.RNA_JumpLibrary check_forward_backward(...) from builtins.PyCapsule check_forward_backward(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, atom_name : str, forward : bool, j : rosetta.core.kinematics.Jump, t : rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> NoneType get_random_base_pair_jump(...) from builtins.PyCapsule get_random_base_pair_jump(*args, **kwargs) Overloaded function.   1. get_random_base_pair_jump(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, aa1 : str, aa2 : str, edge1 : rosetta.core.chemical.rna.BaseEdge, edge2 : rosetta.core.chemical.rna.BaseEdge, orientation : rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1 : str, atom_name2 : str, success : bool) -> rosetta.core.kinematics.Jump   2. get_random_base_pair_jump(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, aa1 : str, aa2 : str, edge1 : rosetta.core.chemical.rna.BaseEdge, edge2 : rosetta.core.chemical.rna.BaseEdge, orientation : rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1 : str, atom_name2 : str, success : bool, forward1 : bool) -> rosetta.core.kinematics.Jump   3. get_random_base_pair_jump(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, aa1 : str, aa2 : str, edge1 : rosetta.core.chemical.rna.BaseEdge, edge2 : rosetta.core.chemical.rna.BaseEdge, orientation : rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1 : str, atom_name2 : str, success : bool, forward1 : bool, forward2 : bool) -> rosetta.core.kinematics.Jump has_template(...) from builtins.PyCapsule has_template(self : rosetta.protocols.farna.libraries.RNA_JumpLibrary, base_pair_type : rosetta.protocols.farna.libraries.BasePairType) -> bool   class RNA_LibraryManager(rosetta.utility.SingletonBase_protocols_farna_libraries_RNA_LibraryManager_t)     Holds all libraries relevant to FARFAR as CONST copies:            JumpLibrary          FullAtomRNA_Fragments          BasePairStepLibrary, ...   However, those const libraries include some mutable data to allow for efficient, lazy loading -- need to put mutexes around those functions that update those data.     Method resolution order: RNA_LibraryManager rosetta.utility.SingletonBase_protocols_farna_libraries_RNA_LibraryManager_t builtins.object 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. canonical_base_pair_step_library(...) from builtins.PyCapsule canonical_base_pair_step_library(rosetta.protocols.farna.libraries.RNA_LibraryManager) -> rosetta.protocols.farna.libraries.BasePairStepLibrary general_base_pair_step_library(...) from builtins.PyCapsule general_base_pair_step_library(rosetta.protocols.farna.libraries.RNA_LibraryManager) -> rosetta.protocols.farna.libraries.BasePairStepLibrary rna_fragment_library(...) from builtins.PyCapsule rna_fragment_library(self : rosetta.protocols.farna.libraries.RNA_LibraryManager, tag : str) -> rosetta.protocols.farna.fragments.RNA_Fragments rna_jump_library(...) from builtins.PyCapsule rna_jump_library(self : rosetta.protocols.farna.libraries.RNA_LibraryManager, tag : str) -> rosetta.protocols.farna.libraries.RNA_JumpLibrary rna_jump_library_cop(...) from builtins.PyCapsule rna_jump_library_cop(*args, **kwargs) Overloaded function.   1. rna_jump_library_cop(self : rosetta.protocols.farna.libraries.RNA_LibraryManager, tag : str) -> rosetta.protocols.farna.libraries.RNA_JumpLibrary   2. rna_jump_library_cop(rosetta.protocols.farna.libraries.RNA_LibraryManager) -> rosetta.protocols.farna.libraries.RNA_JumpLibrary Methods inherited from rosetta.utility.SingletonBase_protocols_farna_libraries_RNA_LibraryManager_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::farna::libraries::RNA_LibraryManager   class RNA_PairingTemplate(builtins.object)     ////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.farna.libraries.RNA_PairingTemplate, j : rosetta.core.kinematics.Jump, atom_name1 : str, atom_name2 : str) -> NoneType   2. __init__(self : rosetta.protocols.farna.libraries.RNA_PairingTemplate, j1 : rosetta.core.kinematics.Jump, j2 : rosetta.core.kinematics.Jump, atom_name1 : str, atom_name2 : str) -> NoneType   3. __init__(self : rosetta.protocols.farna.libraries.RNA_PairingTemplate,  : rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. atom_name1(...) from builtins.PyCapsule atom_name1(rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> str atom_name2(...) from builtins.PyCapsule atom_name2(rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> str jump(...) from builtins.PyCapsule jump(rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> rosetta.core.kinematics.Jump jump_backward(...) from builtins.PyCapsule jump_backward(rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> rosetta.core.kinematics.Jump jump_forward(...) from builtins.PyCapsule jump_forward(rosetta.protocols.farna.libraries.RNA_PairingTemplate) -> rosetta.core.kinematics.Jump