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- builtins.object
-
- RNA_DeNovoParameters
- RNA_DeNovoPoseInitializer
- RNA_DeNovoSetup
class RNA_DeNovoParameters(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, filename : str) -> NoneType
2. __init__(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> NoneType
3. __init__(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, : rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_insert_res(...) from builtins.PyCapsule
- allow_insert_res(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_unsigned_long
- chain_connections(...) from builtins.PyCapsule
- chain_connections(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
- cutpoints_closed(...) from builtins.PyCapsule
- cutpoints_closed(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_unsigned_long
- cutpoints_open(...) from builtins.PyCapsule
- cutpoints_open(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_unsigned_long
- obligate_pairing_sets(...) from builtins.PyCapsule
- obligate_pairing_sets(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
- rna_pairing_list(...) from builtins.PyCapsule
- rna_pairing_list(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_core_pose_rna_BasePair
- set_allow_insert_res(...) from builtins.PyCapsule
- set_allow_insert_res(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
- set_chain_connections(...) from builtins.PyCapsule
- set_chain_connections(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- set_cutpoints_closed(...) from builtins.PyCapsule
- set_cutpoints_closed(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
- set_cutpoints_open(...) from builtins.PyCapsule
- set_cutpoints_open(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
- set_obligate_pairing_sets(...) from builtins.PyCapsule
- set_obligate_pairing_sets(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- set_rna_pairing_list(...) from builtins.PyCapsule
- set_rna_pairing_list(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_core_pose_rna_BasePair) -> NoneType
- set_stem_pairing_sets(...) from builtins.PyCapsule
- set_stem_pairing_sets(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- set_virtual_anchor_attachment_points(...) from builtins.PyCapsule
- set_virtual_anchor_attachment_points(self : rosetta.protocols.farna.setup.RNA_DeNovoParameters, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
- stem_pairing_sets(...) from builtins.PyCapsule
- stem_pairing_sets(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
- virtual_anchor_attachment_points(...) from builtins.PyCapsule
- virtual_anchor_attachment_points(rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> rosetta.utility.vector1_unsigned_long
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class RNA_DeNovoPoseInitializer(builtins.object) |
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///////////////////////////////////////////////////////////////////////////////////////////
Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and
jump changes.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, rna_params_file_info : rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> NoneType
2. __init__(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- initialize_for_de_novo_protocol(...) from builtins.PyCapsule
- initialize_for_de_novo_protocol(*args, **kwargs)
Overloaded function.
1. initialize_for_de_novo_protocol(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, pose : rosetta.core.pose.Pose) -> NoneType
"classic" setup, used in denovo protocol. Note: changes pose (virtualizes phosphate).
and requires later call of setup_fold_tree_and_jumps_and_variants
2. initialize_for_de_novo_protocol(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, pose : rosetta.core.pose.Pose, ignore_secstruct : bool) -> NoneType
"classic" setup, used in denovo protocol. Note: changes pose (virtualizes phosphate).
and requires later call of setup_fold_tree_and_jumps_and_variants
- rna_params(...) from builtins.PyCapsule
- rna_params(rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer) -> rosetta.protocols.farna.setup.RNA_DeNovoParameters
- set_bps_moves(...) from builtins.PyCapsule
- set_bps_moves(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, setting : bool) -> NoneType
- set_root_at_first_rigid_body(...) from builtins.PyCapsule
- set_root_at_first_rigid_body(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, setting : bool) -> NoneType
- setup_fold_tree_and_jumps_and_variants(...) from builtins.PyCapsule
- setup_fold_tree_and_jumps_and_variants(*args, **kwargs)
Overloaded function.
1. setup_fold_tree_and_jumps_and_variants(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, pose : rosetta.core.pose.Pose, rna_jump_mover : protocols::farna::movers::RNA_JumpMover, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> NoneType
2. setup_fold_tree_and_jumps_and_variants(self : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer, pose : rosetta.core.pose.Pose) -> NoneType
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