| | |
- builtins.object
-
- Alias
- BondInfo
- ExtendedPoseBuilder
- FoldGraph
- IdealAbegoGenerator
- NamedSegment
- PairingType
- PoseFolder
-
- RandomTorsionPoseFolder
- RemodelLoopMoverPoseFolder
- ResidueDihedrals
- Segment
- SegmentPairing
-
- HelixPairing
- StrandPairing
- SheetDB
- StructureData
- rosetta.core.pose.datacache.CacheableObserver(builtins.object)
-
- StructureDataObserver
- rosetta.protocols.forge.components.VarLengthBuild(rosetta.protocols.moves.Mover)
-
- VLBProtected
- rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t(builtins.object)
-
- Picker
- rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t(builtins.object)
-
- StructureDataFactory
- rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution(builtins.object)
-
- NamedSolutions
- rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t(builtins.object)
-
- NamedSolution
- rosetta.utility.excn.EXCN_Base(builtins.object)
-
- EXCN_Fold
- EXCN_PoseInconsistent
class Alias(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.denovo_design.components.Alias) -> NoneType
2. __init__(self : rosetta.protocols.denovo_design.components.Alias, segment : str, resid : int) -> NoneType
3. __init__(self : rosetta.protocols.denovo_design.components.Alias, : rosetta.protocols.denovo_design.components.Alias) -> 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.denovo_design.components.Alias) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.Alias, : rosetta.protocols.denovo_design.components.Alias) -> rosetta.protocols.denovo_design.components.Alias
|
class BondInfo(builtins.object) |
| | |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.denovo_design.components.BondInfo, other : rosetta.protocols.denovo_design.components.BondInfo) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.denovo_design.components.BondInfo) -> NoneType
2. __init__(self : rosetta.protocols.denovo_design.components.BondInfo, s1 : str, s2 : str, r1 : int, r2 : int, a1 : str, a2 : str) -> NoneType
3. __init__(self : rosetta.protocols.denovo_design.components.BondInfo, : rosetta.protocols.denovo_design.components.BondInfo) -> 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.denovo_design.components.BondInfo) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.BondInfo, : rosetta.protocols.denovo_design.components.BondInfo) -> rosetta.protocols.denovo_design.components.BondInfo
Data descriptors defined here:
- atom1
- atom2
- res1
- res2
- seg1
- seg2
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class FoldGraph(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.denovo_design.components.FoldGraph, perm : protocols::denovo_design::components::StructureData) -> NoneType
2. __init__(self : rosetta.protocols.denovo_design.components.FoldGraph, : rosetta.protocols.denovo_design.components.FoldGraph) -> 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.denovo_design.components.FoldGraph, : rosetta.protocols.denovo_design.components.FoldGraph) -> rosetta.protocols.denovo_design.components.FoldGraph
- compute_best_solution(...) from builtins.PyCapsule
- compute_best_solution(self : rosetta.protocols.denovo_design.components.FoldGraph, staple_loops : rosetta.std.vector_std_string) -> rosetta.utility.vector1_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
generates a solution of movable segments to be used in remodel, based on the foldgraph
- create_loops(...) from builtins.PyCapsule
- create_loops(*args, **kwargs)
Overloaded function.
1. create_loops(self : rosetta.protocols.denovo_design.components.FoldGraph, staple_loops : rosetta.std.vector_std_string) -> rosetta.protocols.loops.Loops
generates a loops object to be used in remodel, based on the foldgraph
2. create_loops(self : rosetta.protocols.denovo_design.components.FoldGraph, solution : rosetta.utility.vector1_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> rosetta.protocols.loops.Loops
- fold_tree(...) from builtins.PyCapsule
- fold_tree(self : rosetta.protocols.denovo_design.components.FoldGraph, start_segment : rosetta.std.vector_std_string) -> rosetta.core.kinematics.FoldTree
gives a fold tree based on the segments in the given permutation
- nodeidx(...) from builtins.PyCapsule
- nodeidx(self : rosetta.protocols.denovo_design.components.FoldGraph, segment : str) -> int
given a segment name, returns the associated graph node index
- sd(...) from builtins.PyCapsule
- sd(rosetta.protocols.denovo_design.components.FoldGraph) -> protocols::denovo_design::components::StructureData
const access to StructureData
- segment(...) from builtins.PyCapsule
- segment(self : rosetta.protocols.denovo_design.components.FoldGraph, nodeidx : int) -> str
given a node index, returns the associated segment
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class HelixPairing(SegmentPairing) |
| | |
- Method resolution order:
- HelixPairing
- SegmentPairing
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, h1 : str, h2 : str, is_parallel : bool) -> 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.denovo_design.components.HelixPairing, : rosetta.protocols.denovo_design.components.HelixPairing) -> rosetta.protocols.denovo_design.components.HelixPairing
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.HelixPairing) -> rosetta.protocols.denovo_design.components.SegmentPairing
- pairing_string(...) from builtins.PyCapsule
- pairing_string(self : rosetta.protocols.denovo_design.components.HelixPairing, sd : protocols::denovo_design::components::StructureData) -> str
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.denovo_design.components.HelixPairing) -> rosetta.protocols.denovo_design.components.PairingType
Methods inherited from SegmentPairing:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.denovo_design.components.SegmentPairing) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.protocols.denovo_design.components.SegmentPairing, tag : rosetta.utility.tag.Tag) -> NoneType
- segments(...) from builtins.PyCapsule
- segments(rosetta.protocols.denovo_design.components.SegmentPairing) -> rosetta.std.vector_std_string
- set_segments(...) from builtins.PyCapsule
- set_segments(*args, **kwargs)
Overloaded function.
1. set_segments(self : rosetta.protocols.denovo_design.components.SegmentPairing, segments_str : str) -> NoneType
2. set_segments(self : rosetta.protocols.denovo_design.components.SegmentPairing, segments : rosetta.std.vector_std_string) -> NoneType
|
class NamedSolution(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) |
| | |
- Method resolution order:
- NamedSolution
- rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.denovo_design.components.NamedSolution, fg : rosetta.protocols.denovo_design.components.FoldGraph, solution : rosetta.utility.vector1_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> 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.denovo_design.components.NamedSolution) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.NamedSolution, : rosetta.protocols.denovo_design.components.NamedSolution) -> rosetta.protocols.denovo_design.components.NamedSolution
Methods inherited from rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> bool
Check whether the list is nonempty
- __contains__(...) from builtins.PyCapsule
- __contains__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) -> bool
return true if item in the container
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> bool
- __getitem__(...) from builtins.PyCapsule
- __getitem__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, int) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> bool
- __setitem__(...) from builtins.PyCapsule
- __setitem__(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, int, rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) -> NoneType
- append(...) from builtins.PyCapsule
- append(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) -> NoneType
adds an element to the end
- back(...) from builtins.PyCapsule
- back(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
access the last element
- capacity(...) from builtins.PyCapsule
- capacity(std::vector<std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::allocator<std::set<std::string, std::less<std::string>, std::allocator<std::string> > > >) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(std::vector<std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::allocator<std::set<std::string, std::less<std::string>, std::allocator<std::string> > > >) -> NoneType
clears the contents
- count(...) from builtins.PyCapsule
- count(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) -> int
counts the elements that are equal to value
- erase(...) from builtins.PyCapsule
- erase(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, int) -> NoneType
erases element at index
- extend = _vector_extend_func(vec, othervec)
- # Vector compatibility: Adding 'extend' to all utility.vector* functions
- front(...) from builtins.PyCapsule
- front(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
access the first element
- l(...) from builtins.PyCapsule
- l(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> int
lower index
- max_size(...) from builtins.PyCapsule
- max_size(std::vector<std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::allocator<std::set<std::string, std::less<std::string>, std::allocator<std::string> > > >) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
remove and return last item
2. pop(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, int) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
remove and return item at index
- remove(...) from builtins.PyCapsule
- remove(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) -> NoneType
Remove the first item from the list whose value is x. It is an error if there is no such item.
- reserve(...) from builtins.PyCapsule
- reserve(std::vector<std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::allocator<std::set<std::string, std::less<std::string>, std::allocator<std::string> > > >, int) -> NoneType
reserves storage
- resize(...) from builtins.PyCapsule
- resize(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t, int) -> NoneType
changes the number of elements stored
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(std::vector<std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::allocator<std::set<std::string, std::less<std::string>, std::allocator<std::string> > > >) -> NoneType
reduces memory usage by freeing unused memory
- u(...) from builtins.PyCapsule
- u(rosetta.utility.vector1_std_set_std_string_std_less_std_string_std_allocator_std_string_t) -> int
upper index
|
class NamedSolutions(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) |
| | |
- Method resolution order:
- NamedSolutions
- rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution
- 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.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.denovo_design.components.NamedSolutions) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.NamedSolutions, : rosetta.protocols.denovo_design.components.NamedSolutions) -> rosetta.protocols.denovo_design.components.NamedSolutions
Methods inherited from rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> bool
Check whether the list is nonempty
- __contains__(...) from builtins.PyCapsule
- __contains__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, protocols::denovo_design::components::NamedSolution) -> bool
return true if item in the container
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> bool
- __getitem__(...) from builtins.PyCapsule
- __getitem__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, int) -> protocols::denovo_design::components::NamedSolution
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> bool
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> str
- __setitem__(...) from builtins.PyCapsule
- __setitem__(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, int, protocols::denovo_design::components::NamedSolution) -> NoneType
- append(...) from builtins.PyCapsule
- append(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, protocols::denovo_design::components::NamedSolution) -> NoneType
adds an element to the end
- back(...) from builtins.PyCapsule
- back(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> protocols::denovo_design::components::NamedSolution
access the last element
- capacity(...) from builtins.PyCapsule
- capacity(std::vector<protocols::denovo_design::components::NamedSolution, std::allocator<protocols::denovo_design::components::NamedSolution> >) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(std::vector<protocols::denovo_design::components::NamedSolution, std::allocator<protocols::denovo_design::components::NamedSolution> >) -> NoneType
clears the contents
- count(...) from builtins.PyCapsule
- count(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, protocols::denovo_design::components::NamedSolution) -> int
counts the elements that are equal to value
- erase(...) from builtins.PyCapsule
- erase(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, int) -> NoneType
erases element at index
- extend = _vector_extend_func(vec, othervec)
- # Vector compatibility: Adding 'extend' to all utility.vector* functions
- front(...) from builtins.PyCapsule
- front(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> protocols::denovo_design::components::NamedSolution
access the first element
- l(...) from builtins.PyCapsule
- l(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> int
lower index
- max_size(...) from builtins.PyCapsule
- max_size(std::vector<protocols::denovo_design::components::NamedSolution, std::allocator<protocols::denovo_design::components::NamedSolution> >) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> protocols::denovo_design::components::NamedSolution
remove and return last item
2. pop(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, int) -> protocols::denovo_design::components::NamedSolution
remove and return item at index
- remove(...) from builtins.PyCapsule
- remove(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, protocols::denovo_design::components::NamedSolution) -> NoneType
Remove the first item from the list whose value is x. It is an error if there is no such item.
- reserve(...) from builtins.PyCapsule
- reserve(std::vector<protocols::denovo_design::components::NamedSolution, std::allocator<protocols::denovo_design::components::NamedSolution> >, int) -> NoneType
reserves storage
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(std::vector<protocols::denovo_design::components::NamedSolution, std::allocator<protocols::denovo_design::components::NamedSolution> >) -> NoneType
reduces memory usage by freeing unused memory
- u(...) from builtins.PyCapsule
- u(rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> int
upper index
|
class Picker(rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t) |
| |
class used for picking/caching fragments
|
| |
- Method resolution order:
- Picker
- rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.denovo_design.components.Picker) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- create_singleton_instance(...) from builtins.PyCapsule
- create_singleton_instance() -> rosetta.protocols.denovo_design.components.Picker
- fragments_for_permutation(...) from builtins.PyCapsule
- fragments_for_permutation(self : rosetta.protocols.denovo_design.components.Picker, perm : protocols::denovo_design::components::StructureData, comp_ids : rosetta.std.list_std_string_std_allocator_std_string_t, frag_size : int) -> rosetta.core.fragment.ConstantLengthFragSet
picks and caches fragments for the listed components with size frag_size
- fragments_for_permutation_take_X_from_pose(...) from builtins.PyCapsule
- fragments_for_permutation_take_X_from_pose(self : rosetta.protocols.denovo_design.components.Picker, perm : protocols::denovo_design::components::StructureData, pose : rosetta.core.pose.Pose, comp_ids : rosetta.std.vector_std_string, frag_size : int) -> rosetta.core.fragment.ConstantLengthFragSet
picks and caches fragments for the listed components with size frag_size
- pick_and_cache_fragments(...) from builtins.PyCapsule
- pick_and_cache_fragments(*args, **kwargs)
Overloaded function.
1. pick_and_cache_fragments(self : rosetta.protocols.denovo_design.components.Picker, ss : str, abego : str, loops : rosetta.protocols.loops.Loops, chain_endings : rosetta.utility.vector1_unsigned_long, frag_size : int) -> rosetta.core.fragment.ConstantLengthFragSet
picks and caches fragments for the given segments with size frag_size
2. pick_and_cache_fragments(self : rosetta.protocols.denovo_design.components.Picker, complete_ss : str, complete_abego : rosetta.utility.vector1_std_string, chain_endings : rosetta.utility.vector1_unsigned_long, start_res : int, end_res : int, frag_length : int) -> rosetta.core.fragment.ConstantLengthFragSet
pick and cache fragments without considering primary sequence
3. pick_and_cache_fragments(self : rosetta.protocols.denovo_design.components.Picker, complete_aa : str, complete_ss : str, complete_abego : rosetta.utility.vector1_std_string, chain_endings : rosetta.utility.vector1_unsigned_long, start_res : int, end_res : int, frag_length : int) -> rosetta.core.fragment.ConstantLengthFragSet
pick and cache fragments with a primary sequence in mind
- set_nfrags(...) from builtins.PyCapsule
- set_nfrags(self : rosetta.protocols.denovo_design.components.Picker, nfrags : int) -> NoneType
Methods inherited from rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> protocols::denovo_design::components::Picker
|
class PoseFolder(builtins.object) |
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Given a pose with all residues, and a StructureData object,
assign a 3D conformation to the pose
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.denovo_design.components.PoseFolder, type : str) -> NoneType
2. __init__(rosetta.protocols.denovo_design.components.PoseFolder, rosetta.protocols.denovo_design.components.PoseFolder) -> 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.denovo_design.components.PoseFolder, pose : rosetta.core.pose.Pose, movable : rosetta.utility.vector1_bool, loops : rosetta.protocols.loops.Loops) -> NoneType
performs folding
- The pose to be folded, with all residues added. The pose should be prepared with
any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose
should be adjusted, and no residues should be added or removed.
- Subset of residues for which new backbone conformations will be sampled. Residues
specified as 'True' in movable must also be present in one or more Loops in order
to be folded. Movable's size must match pose.total_residue()
- Loops to be folded. Cutpoints specified here must be match the cutpoints found in
the pose. Residues not within any loop should not be folded. Residues contained
in a loop but not in the movable set should not be folded.
EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.PoseFolder, : rosetta.protocols.denovo_design.components.PoseFolder) -> rosetta.protocols.denovo_design.components.PoseFolder
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.PoseFolder) -> rosetta.protocols.denovo_design.components.PoseFolder
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.protocols.denovo_design.components.PoseFolder, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.denovo_design.components.PoseFolder) -> str
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class RemodelLoopMoverPoseFolder(PoseFolder) |
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Folds residues in a pose using RemodelLoopMover
|
| |
- Method resolution order:
- RemodelLoopMoverPoseFolder
- PoseFolder
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) -> 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.denovo_design.components.RemodelLoopMoverPoseFolder, pose : rosetta.core.pose.Pose, movable : rosetta.utility.vector1_bool, loops : rosetta.protocols.loops.Loops) -> NoneType
performs folding
- The pose to be folded, with all residues added. The pose should be prepared with
any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose
should be adjusted, and no residues should be added or removed.
- Subset of residues for which new backbone conformations will be sampled. Residues
specified as 'True' in movable must also be present in one or more Loops in order
to be folded. Movable's size must match pose.total_residue()
- Loops to be folded. Cutpoints specified here must be match the cutpoints found in
the pose. Residues not within any loop should not be folded. Residues contained
in a loop but not in the movable set should not be folded.
EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, : rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) -> rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) -> rosetta.protocols.denovo_design.components.PoseFolder
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Methods inherited from PoseFolder:
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.protocols.denovo_design.components.PoseFolder, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.denovo_design.components.PoseFolder) -> str
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class Segment(builtins.object) |
| |
manages information about segments of residues
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ss_val : str, abego_val : str, start_inc : bool, stop_inc : bool) -> NoneType
3. __init__(handle, rosetta.protocols.denovo_design.components.Segment) -> 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.denovo_design.components.Segment) -> str
- abego(...) from builtins.PyCapsule
- abego(*args, **kwargs)
Overloaded function.
1. abego(rosetta.protocols.denovo_design.components.Segment) -> str
2. abego(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> str
- add_lower_padding(...) from builtins.PyCapsule
- add_lower_padding(rosetta.protocols.denovo_design.components.Segment) -> NoneType
adds "padding" residue before the fixed portion of this segment
- add_upper_padding(...) from builtins.PyCapsule
- add_upper_padding(rosetta.protocols.denovo_design.components.Segment) -> NoneType
adds "padding" residue after the fixed portion of this segment
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.Segment, : rosetta.protocols.denovo_design.components.Segment) -> rosetta.protocols.denovo_design.components.Segment
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.Segment) -> rosetta.protocols.denovo_design.components.Segment
- contains(...) from builtins.PyCapsule
- contains(self : rosetta.protocols.denovo_design.components.Segment, pose_resid : int) -> bool
- cterm_included(...) from builtins.PyCapsule
- cterm_included(rosetta.protocols.denovo_design.components.Segment) -> bool
- cutpoint(...) from builtins.PyCapsule
- cutpoint(rosetta.protocols.denovo_design.components.Segment) -> int
- cutpoint_segment(...) from builtins.PyCapsule
- cutpoint_segment(rosetta.protocols.denovo_design.components.Segment) -> int
segment residue number for cutpoint
- delete_lower_padding(...) from builtins.PyCapsule
- delete_lower_padding(rosetta.protocols.denovo_design.components.Segment) -> NoneType
deletes dummy residues before the fixed portion of this segment
- delete_residue(...) from builtins.PyCapsule
- delete_residue(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> NoneType
given a segment residue number, delete that residue. Resid for start_local() == 1
- delete_upper_padding(...) from builtins.PyCapsule
- delete_upper_padding(rosetta.protocols.denovo_design.components.Segment) -> NoneType
deletes dummy residues after the fixed portion of this segment
- elem_length(...) from builtins.PyCapsule
- elem_length(rosetta.protocols.denovo_design.components.Segment) -> int
- extend(...) from builtins.PyCapsule
- extend(self : rosetta.protocols.denovo_design.components.Segment, secstruct : str, abego : str) -> NoneType
appends segment by the given secstruct and abego
- has_free_lower_terminus(...) from builtins.PyCapsule
- has_free_lower_terminus(rosetta.protocols.denovo_design.components.Segment) -> bool
- has_free_upper_terminus(...) from builtins.PyCapsule
- has_free_upper_terminus(rosetta.protocols.denovo_design.components.Segment) -> bool
- length(...) from builtins.PyCapsule
- length(rosetta.protocols.denovo_design.components.Segment) -> int
- lower(...) from builtins.PyCapsule
- lower(rosetta.protocols.denovo_design.components.Segment) -> int
- lower_dihedrals(...) from builtins.PyCapsule
- lower_dihedrals(rosetta.protocols.denovo_design.components.Segment) -> rosetta.protocols.denovo_design.components.ResidueDihedrals
///////////////////////////////////////
- lower_local(...) from builtins.PyCapsule
- lower_local(rosetta.protocols.denovo_design.components.Segment) -> int
on the chopping block
- lower_padding(...) from builtins.PyCapsule
- lower_padding(rosetta.protocols.denovo_design.components.Segment) -> int
- lower_residue(...) from builtins.PyCapsule
- lower_residue(rosetta.protocols.denovo_design.components.Segment) -> rosetta.core.conformation.Residue
- lower_segment(...) from builtins.PyCapsule
- lower_segment(rosetta.protocols.denovo_design.components.Segment) -> str
- movable_group(...) from builtins.PyCapsule
- movable_group(rosetta.protocols.denovo_design.components.Segment) -> int
- n_residues_after_cutpoint(...) from builtins.PyCapsule
- n_residues_after_cutpoint(rosetta.protocols.denovo_design.components.Segment) -> int
number of residues after the cutpoint, length() if cutpoint not set
- n_residues_before_cutpoint(...) from builtins.PyCapsule
- n_residues_before_cutpoint(rosetta.protocols.denovo_design.components.Segment) -> int
number of residues before the cutpoint, 0 if cutpoint not set
- nterm_included(...) from builtins.PyCapsule
- nterm_included(rosetta.protocols.denovo_design.components.Segment) -> bool
- parse_motif(...) from builtins.PyCapsule
- parse_motif(self : rosetta.protocols.denovo_design.components.Segment, motif_str : str) -> NoneType
construct from motif string (i.e. '1LX-10HA-1LA-1LB')
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.denovo_design.components.Segment, tag : rosetta.utility.tag.Tag) -> NoneType
construct from xml tag
- pose_to_segment(...) from builtins.PyCapsule
- pose_to_segment(self : rosetta.protocols.denovo_design.components.Segment, pose_resid : int) -> int
converts a internal segment resid to a pose resid
segment_start - 1 + 1 --> 1
segment_start - 1 + 2 --> 2
segment_start - 1 + N --> N
- safe(...) from builtins.PyCapsule
- safe(rosetta.protocols.denovo_design.components.Segment) -> int
- safe_segment(...) from builtins.PyCapsule
- safe_segment(rosetta.protocols.denovo_design.components.Segment) -> int
segment residue number for "safe" residue
- segment_to_local(...) from builtins.PyCapsule
- segment_to_local(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> int
converts a segment resid to a "local" resid
- segment_to_pose(...) from builtins.PyCapsule
- segment_to_pose(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> int
converts a internal segment resid to a pose resid
1 --> segment_start - 1 + 1
2 --> segment_start - 1 + 2
N --> segment_start - 1 + N
- set_abego(...) from builtins.PyCapsule
- set_abego(*args, **kwargs)
Overloaded function.
1. set_abego(self : rosetta.protocols.denovo_design.components.Segment, abego_str : str) -> NoneType
2. set_abego(self : rosetta.protocols.denovo_design.components.Segment, abego : rosetta.utility.vector1_std_string) -> NoneType
- set_cutpoint(...) from builtins.PyCapsule
- set_cutpoint(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> NoneType
sets cutpoint for this segment to be the ith residue in the segment
cut = segment_start - 1 + cut_res
- set_lower_segment(...) from builtins.PyCapsule
- set_lower_segment(self : rosetta.protocols.denovo_design.components.Segment, comp : str) -> NoneType
- set_movable_group(...) from builtins.PyCapsule
- set_movable_group(self : rosetta.protocols.denovo_design.components.Segment, mg : int) -> NoneType
- set_pose_start(...) from builtins.PyCapsule
- set_pose_start(self : rosetta.protocols.denovo_design.components.Segment, pose_resid : int) -> NoneType
///////////////////////////////////////
- set_safe(...) from builtins.PyCapsule
- set_safe(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int) -> NoneType
sets safe residue for this segment to be the ith residue in the segment
safe = segment_start - 1 + cut_res
- set_ss(...) from builtins.PyCapsule
- set_ss(self : rosetta.protocols.denovo_design.components.Segment, segment_resid : int, ss_type : str) -> NoneType
- set_template_pose(...) from builtins.PyCapsule
- set_template_pose(self : rosetta.protocols.denovo_design.components.Segment, template_pose : rosetta.core.pose.Pose, start_resid : int, stop_resid : int) -> NoneType
sets template pose to be the given residues from template_pose
- set_upper_segment(...) from builtins.PyCapsule
- set_upper_segment(self : rosetta.protocols.denovo_design.components.Segment, comp : str) -> NoneType
- ss(...) from builtins.PyCapsule
- ss(rosetta.protocols.denovo_design.components.Segment) -> str
///////////////////////////////////////
- start(...) from builtins.PyCapsule
- start(rosetta.protocols.denovo_design.components.Segment) -> int
- start_local(...) from builtins.PyCapsule
- start_local(rosetta.protocols.denovo_design.components.Segment) -> int
- stop(...) from builtins.PyCapsule
- stop(rosetta.protocols.denovo_design.components.Segment) -> int
- stop_local(...) from builtins.PyCapsule
- stop_local(rosetta.protocols.denovo_design.components.Segment) -> int
- template_pose(...) from builtins.PyCapsule
- template_pose(rosetta.protocols.denovo_design.components.Segment) -> rosetta.core.pose.Pose
returns template pose
- upper(...) from builtins.PyCapsule
- upper(rosetta.protocols.denovo_design.components.Segment) -> int
- upper_dihedrals(...) from builtins.PyCapsule
- upper_dihedrals(rosetta.protocols.denovo_design.components.Segment) -> rosetta.protocols.denovo_design.components.ResidueDihedrals
- upper_local(...) from builtins.PyCapsule
- upper_local(rosetta.protocols.denovo_design.components.Segment) -> int
- upper_padding(...) from builtins.PyCapsule
- upper_padding(rosetta.protocols.denovo_design.components.Segment) -> int
- upper_residue(...) from builtins.PyCapsule
- upper_residue(rosetta.protocols.denovo_design.components.Segment) -> rosetta.core.conformation.Residue
- upper_segment(...) from builtins.PyCapsule
- upper_segment(rosetta.protocols.denovo_design.components.Segment) -> str
///////////////////////////////////////
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class SheetDB(builtins.object) |
| |
class used to create/manipulate a database of sheets using a list of pdb files
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.denovo_design.components.SheetDB) -> NoneType
2. __init__(self : rosetta.protocols.denovo_design.components.SheetDB, : rosetta.protocols.denovo_design.components.SheetDB) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_sheet(...) from builtins.PyCapsule
- add_sheet(self : rosetta.protocols.denovo_design.components.SheetDB, pose : rosetta.core.pose.Pose, nstrands : int, orientations : str, lengths_shifts : str, check_descriptor_against_pose : bool) -> NoneType
add a sheet to the database
- add_sheets_from_pose(...) from builtins.PyCapsule
- add_sheets_from_pose(self : rosetta.protocols.denovo_design.components.SheetDB, pose : rosetta.core.pose.Pose) -> int
adds sheet(s) based on a pose -- returns # of sheets added
- add_sheets_from_spairs(...) from builtins.PyCapsule
- add_sheets_from_spairs(self : rosetta.protocols.denovo_design.components.SheetDB, pose : rosetta.core.pose.Pose, spairs : rosetta.protocols.fldsgn.topology.StrandPairingSet, ss_info : protocols::fldsgn::topology::SS_Info2) -> int
adds sheet(s) based on a strand pairing set and pose -- returns # of sheets added
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.SheetDB, : rosetta.protocols.denovo_design.components.SheetDB) -> rosetta.protocols.denovo_design.components.SheetDB
- has_data(...) from builtins.PyCapsule
- has_data(self : rosetta.protocols.denovo_design.components.SheetDB, lengths : rosetta.utility.vector1_unsigned_long, orientations : rosetta.utility.vector1_protocols_denovo_design_architects_StrandOrientation, shifts : rosetta.utility.vector1_long) -> bool
query the database, returns whether data exists
- lengths_shifts(...) from builtins.PyCapsule
- lengths_shifts(self : rosetta.protocols.denovo_design.components.SheetDB, nstrands : int, orientations : str) -> rosetta.utility.vector1_std_string
queries the database for all lengths/shifts with nstrands strands and given orientations
- nstrand_values(...) from builtins.PyCapsule
- nstrand_values(rosetta.protocols.denovo_design.components.SheetDB) -> rosetta.utility.vector1_unsigned_long
queries the database for all strand lengths
- orientations(...) from builtins.PyCapsule
- orientations(self : rosetta.protocols.denovo_design.components.SheetDB, nstrands : int) -> rosetta.utility.vector1_std_string
queries the database for all orientations with nstrands strands
- set_db_path(...) from builtins.PyCapsule
- set_db_path(self : rosetta.protocols.denovo_design.components.SheetDB, db_path : str) -> NoneType
set location of sheet database files
- set_idealize(...) from builtins.PyCapsule
- set_idealize(self : rosetta.protocols.denovo_design.components.SheetDB, idealize_val : bool) -> NoneType
- set_sheetlist(...) from builtins.PyCapsule
- set_sheetlist(self : rosetta.protocols.denovo_design.components.SheetDB, list : rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands : int, in_orientations : str, in_lengths : str) -> NoneType
add a sheet to the database
- set_sheetlist_as_is(...) from builtins.PyCapsule
- set_sheetlist_as_is(self : rosetta.protocols.denovo_design.components.SheetDB, list : rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands : int, orientations : str, lengths : str) -> NoneType
adds a sheet list as it is presented
- sheet_list(...) from builtins.PyCapsule
- sheet_list(self : rosetta.protocols.denovo_design.components.SheetDB, lengths : rosetta.utility.vector1_unsigned_long, orientations : rosetta.utility.vector1_protocols_denovo_design_architects_StrandOrientation, shifts : rosetta.utility.vector1_long) -> rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t
query the database for a sheet and retrieve the list -- if not found, tries to read from disk
- sheet_list_const(...) from builtins.PyCapsule
- sheet_list_const(self : rosetta.protocols.denovo_design.components.SheetDB, lengths : rosetta.utility.vector1_unsigned_long, orientations : rosetta.utility.vector1_protocols_denovo_design_architects_StrandOrientation, shifts : rosetta.utility.vector1_long) -> rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t
query the database for a sheet and retrieve the list -- if not found, tries to read from disk
|
class StrandPairing(SegmentPairing) |
| | |
- Method resolution order:
- StrandPairing
- SegmentPairing
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, s1 : str, s2 : str, orient1 : rosetta.protocols.denovo_design.architects.StrandOrientation, orient2 : rosetta.protocols.denovo_design.architects.StrandOrientation, shift : int) -> 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.denovo_design.components.StrandPairing, : rosetta.protocols.denovo_design.components.StrandPairing) -> rosetta.protocols.denovo_design.components.StrandPairing
- class_name(...) from builtins.PyCapsule
- class_name() -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.StrandPairing) -> rosetta.protocols.denovo_design.components.SegmentPairing
- pairing_string(...) from builtins.PyCapsule
- pairing_string(self : rosetta.protocols.denovo_design.components.StrandPairing, sd : protocols::denovo_design::components::StructureData) -> str
- parallel(...) from builtins.PyCapsule
- parallel(rosetta.protocols.denovo_design.components.StrandPairing) -> bool
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.denovo_design.components.StrandPairing) -> rosetta.protocols.denovo_design.components.PairingType
Methods inherited from SegmentPairing:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.denovo_design.components.SegmentPairing) -> str
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.protocols.denovo_design.components.SegmentPairing, tag : rosetta.utility.tag.Tag) -> NoneType
- segments(...) from builtins.PyCapsule
- segments(rosetta.protocols.denovo_design.components.SegmentPairing) -> rosetta.std.vector_std_string
- set_segments(...) from builtins.PyCapsule
- set_segments(*args, **kwargs)
Overloaded function.
1. set_segments(self : rosetta.protocols.denovo_design.components.SegmentPairing, segments_str : str) -> NoneType
2. set_segments(self : rosetta.protocols.denovo_design.components.SegmentPairing, segments : rosetta.std.vector_std_string) -> NoneType
|
class StructureData(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, id_val : str) -> NoneType
3. __init__(handle, rosetta.protocols.denovo_design.components.StructureData) -> 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.denovo_design.components.StructureData) -> str
- abego(...) from builtins.PyCapsule
- abego(*args, **kwargs)
Overloaded function.
1. abego(rosetta.protocols.denovo_design.components.StructureData) -> str
return abego string
2. abego(self : rosetta.protocols.denovo_design.components.StructureData, resid : int) -> str
abego of residue resid
- add_covalent_bond(...) from builtins.PyCapsule
- add_covalent_bond(self : rosetta.protocols.denovo_design.components.StructureData, res1 : int, atom1 : str, res2 : int, atom2 : str) -> NoneType
- add_pairing(...) from builtins.PyCapsule
- add_pairing(self : rosetta.protocols.denovo_design.components.StructureData, pairing : rosetta.protocols.denovo_design.components.SegmentPairing) -> NoneType
- add_prefix_to_segments(...) from builtins.PyCapsule
- add_prefix_to_segments(self : rosetta.protocols.denovo_design.components.StructureData, prefix : str) -> NoneType
renames a residue segment and updates all connections
- add_segment(...) from builtins.PyCapsule
- add_segment(*args, **kwargs)
Overloaded function.
1. add_segment(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str, resis : rosetta.protocols.denovo_design.components.Segment) -> NoneType
adds a residues segment to the end of the list
2. add_segment(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str, resis : rosetta.protocols.denovo_design.components.Segment, insert_before_segment : str) -> NoneType
adds a residues segment -- will be ordered before the given segment
3. add_segment(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str, resis : rosetta.protocols.denovo_design.components.Segment, insert_pos : std::_List_iterator<std::string>) -> NoneType
adds a residues segment -- will be inserted just before at given iterator
- alias(...) from builtins.PyCapsule
- alias(self : rosetta.protocols.denovo_design.components.StructureData, alias : str) -> int
given a residue alias, returns a pose residue number
- aliases(...) from builtins.PyCapsule
- aliases(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.map_std_string_protocols_denovo_design_components_Alias
gets all alias data
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.denovo_design.components.StructureData, : rosetta.protocols.denovo_design.components.StructureData) -> rosetta.protocols.denovo_design.components.StructureData
- available_lower_termini(...) from builtins.PyCapsule
- available_lower_termini(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.vector_std_string
returns segments which have free lower termini
- available_upper_termini(...) from builtins.PyCapsule
- available_upper_termini(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.vector_std_string
returns segments which have free upper termini
- check_consistency(...) from builtins.PyCapsule
- check_consistency(rosetta.protocols.denovo_design.components.StructureData) -> NoneType
checks consistency of the data
EXCN_PoseInconsistent if there is a problem
- check_pose_consistency(...) from builtins.PyCapsule
- check_pose_consistency(self : rosetta.protocols.denovo_design.components.StructureData, pose : rosetta.core.pose.Pose) -> NoneType
checks the permutation for internal consistency vs a pose
EXCN_PoseInconsistent if there is a problem
- choose_new_movable_group(...) from builtins.PyCapsule
- choose_new_movable_group(rosetta.protocols.denovo_design.components.StructureData) -> int
chooses a new movable group which doesn't conflict with existing ones
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.protocols.denovo_design.components.StructureData
- connect_segments(...) from builtins.PyCapsule
- connect_segments(self : rosetta.protocols.denovo_design.components.StructureData, segment1 : str, segment2 : str) -> NoneType
connects the given chains together, doesn't update anything -- don't call this on its own unless you know what you're doing
- connected_segments(...) from builtins.PyCapsule
- connected_segments(self : rosetta.protocols.denovo_design.components.StructureData, seg : str, stop_at_cutpoint : bool) -> rosetta.std.list_std_string_std_allocator_std_string_t
returns an ordered list of segments which are all connected containing seg
- if true, segments past a cutpoint will not be counted as connected
- copy_data(...) from builtins.PyCapsule
- copy_data(self : rosetta.protocols.denovo_design.components.StructureData, perm : rosetta.protocols.denovo_design.components.StructureData) -> NoneType
copies user data fields from one permutation to this one -- overwrites existing data
- covalent_bonds_begin(...) from builtins.PyCapsule
- covalent_bonds_begin(rosetta.protocols.denovo_design.components.StructureData) -> __gnu_cxx::__normal_iterator<protocols::denovo_design::components::BondInfo const*, std::vector<protocols::denovo_design::components::BondInfo, std::allocator<protocols::denovo_design::components::BondInfo> > >
start/end of covalent bonds list
- covalent_bonds_end(...) from builtins.PyCapsule
- covalent_bonds_end(rosetta.protocols.denovo_design.components.StructureData) -> __gnu_cxx::__normal_iterator<protocols::denovo_design::components::BondInfo const*, std::vector<protocols::denovo_design::components::BondInfo, std::allocator<protocols::denovo_design::components::BondInfo> > >
end of covalent bonds list
- cutpoints(...) from builtins.PyCapsule
- cutpoints(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.utility.vector1_unsigned_long
returns list of all cutpoints, in N-->C order
- data_int(...) from builtins.PyCapsule
- data_int(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.map_std_string_int
gets all real number data
- data_real(...) from builtins.PyCapsule
- data_real(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.map_std_string_double
gets all real number data
- data_str(...) from builtins.PyCapsule
- data_str(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.std.map_std_string_std_string
gets all string data
- declare_covalent_bond(...) from builtins.PyCapsule
- declare_covalent_bond(*args, **kwargs)
Overloaded function.
1. declare_covalent_bond(self : rosetta.protocols.denovo_design.components.StructureData, seg1 : str, res1 : int, atom1 : str, seg2 : str, res2 : int, atom2 : str) -> NoneType
declares a covalent bond between the specified atoms
2. declare_covalent_bond(self : rosetta.protocols.denovo_design.components.StructureData, res1 : int, atom1 : str, res2 : int, atom2 : str) -> NoneType
declares a covalent bond using pose residues
- delete_jump_and_intervening_cutpoint(...) from builtins.PyCapsule
- delete_jump_and_intervening_cutpoint(self : rosetta.protocols.denovo_design.components.StructureData, segment1 : str, segment2 : str) -> NoneType
removes jump and cutpoint between the two segments to create a single polymer chain
- delete_leading_residues(...) from builtins.PyCapsule
- delete_leading_residues(self : rosetta.protocols.denovo_design.components.StructureData, seg : str) -> NoneType
deletes the residues between the segment N terminus and the N anchor point
- delete_residue(...) from builtins.PyCapsule
- delete_residue(self : rosetta.protocols.denovo_design.components.StructureData, pose_resid : int) -> NoneType
- delete_segment(...) from builtins.PyCapsule
- delete_segment(self : rosetta.protocols.denovo_design.components.StructureData, segment : str) -> NoneType
removes all traces of the given segment from the object
- delete_trailing_residues(...) from builtins.PyCapsule
- delete_trailing_residues(self : rosetta.protocols.denovo_design.components.StructureData, seg : str) -> NoneType
deletes the residues between the segment C terminus and the C anchor point
- disconnect_segments(...) from builtins.PyCapsule
- disconnect_segments(self : rosetta.protocols.denovo_design.components.StructureData, segment1 : str, segment2 : str) -> NoneType
connects the given chains together, doesn't update anything -- don't call this on its own unless you know what you're doing
- find_non_polymer_bond(...) from builtins.PyCapsule
- find_non_polymer_bond(self : rosetta.protocols.denovo_design.components.StructureData, seg1 : str, seg2 : str) -> __gnu_cxx::__normal_iterator<protocols::denovo_design::components::BondInfo const*, std::vector<protocols::denovo_design::components::BondInfo, std::allocator<protocols::denovo_design::components::BondInfo> > >
finds a non-peptide bond between two segments, returns end() if there isn't one
- find_segment(...) from builtins.PyCapsule
- find_segment(self : rosetta.protocols.denovo_design.components.StructureData, segname : str) -> std::_Rb_tree_const_iterator<std::pair<std::string const, protocols::denovo_design::components::Segment> >
finds a segment in the segment map and returns an iterator to it
- find_segment_name(...) from builtins.PyCapsule
- find_segment_name(self : rosetta.protocols.denovo_design.components.StructureData, segname : str) -> std::_List_const_iterator<std::string>
finds a segment in the segment_order list and returns an iterator to it
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.protocols.denovo_design.components.StructureData
- get_data_int(...) from builtins.PyCapsule
- get_data_int(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> int
gets integer data
- get_data_real(...) from builtins.PyCapsule
- get_data_real(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> float
gets real number data
- get_data_str(...) from builtins.PyCapsule
- get_data_str(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> str
gets real number data
- has_alias(...) from builtins.PyCapsule
- has_alias(self : rosetta.protocols.denovo_design.components.StructureData, alias : str) -> bool
given a residue alias, returns a pose residue number
- has_data_int(...) from builtins.PyCapsule
- has_data_int(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> bool
check for integer data
- has_data_real(...) from builtins.PyCapsule
- has_data_real(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> bool
check for real number data
- has_data_str(...) from builtins.PyCapsule
- has_data_str(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str) -> bool
gets real number data
- has_free_lower_terminus(...) from builtins.PyCapsule
- has_free_lower_terminus(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str) -> bool
tells if the segment given has an available lower terminus
- has_free_upper_terminus(...) from builtins.PyCapsule
- has_free_upper_terminus(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str) -> bool
tells if the segment given has an available lower terminus
- has_segment(...) from builtins.PyCapsule
- has_segment(self : rosetta.protocols.denovo_design.components.StructureData, seg : str) -> bool
true if this permutation contains a residue segment named seg
- has_segment_group(...) from builtins.PyCapsule
- has_segment_group(self : rosetta.protocols.denovo_design.components.StructureData, sname : str) -> bool
returns true if this object has a group of segments with the given name
- id(...) from builtins.PyCapsule
- id(rosetta.protocols.denovo_design.components.StructureData) -> str
returns the id of this permutation
- length(...) from builtins.PyCapsule
- length(rosetta.protocols.denovo_design.components.StructureData) -> int
returns the length of this permutation
- lower_anchor(...) from builtins.PyCapsule
- lower_anchor(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str) -> int
returns n-terminal residue of the chain represented by given string
- mark_connected(...) from builtins.PyCapsule
- mark_connected(self : rosetta.protocols.denovo_design.components.StructureData, lower_seg : str, upper_seg : str) -> NoneType
marks the given segments as covanlently connected
- mark_disconnected(...) from builtins.PyCapsule
- mark_disconnected(self : rosetta.protocols.denovo_design.components.StructureData, seg1 : str, seg2 : str) -> NoneType
unmarks the given segments as covalently connected
- merge(...) from builtins.PyCapsule
- merge(*args, **kwargs)
Overloaded function.
1. merge(self : rosetta.protocols.denovo_design.components.StructureData, other : rosetta.protocols.denovo_design.components.StructureData) -> NoneType
merge all data and segments from "other" into this StructureData
2. merge(self : rosetta.protocols.denovo_design.components.StructureData, other : rosetta.protocols.denovo_design.components.StructureData, segments : rosetta.std.vector_std_string) -> NoneType
merge given data and segments from "other" into this StructureData
- merge_before(...) from builtins.PyCapsule
- merge_before(*args, **kwargs)
Overloaded function.
1. merge_before(self : rosetta.protocols.denovo_design.components.StructureData, other : rosetta.protocols.denovo_design.components.StructureData, position : str) -> NoneType
merge all data and segments from "other" into this StructureData before the given position
2. merge_before(self : rosetta.protocols.denovo_design.components.StructureData, other : rosetta.protocols.denovo_design.components.StructureData, position : str, segments : rosetta.std.vector_std_string) -> NoneType
merge all data and given segments from "other" into this StructureData before the given position
- merge_segments(...) from builtins.PyCapsule
- merge_segments(self : rosetta.protocols.denovo_design.components.StructureData, segment1 : str, segment2 : str, new_name : str) -> NoneType
merges two segments into one that has the name new_name. They must be next to each other in sequence.
- movable_group(...) from builtins.PyCapsule
- movable_group(self : rosetta.protocols.denovo_design.components.StructureData, resid : int) -> int
movable group of segment which contains residue resid
- movable_groups(...) from builtins.PyCapsule
- movable_groups(rosetta.protocols.denovo_design.components.StructureData) -> rosetta.utility.vector1_unsigned_long
computes and returns a set of movable groups
- move_segment(...) from builtins.PyCapsule
- move_segment(self : rosetta.protocols.denovo_design.components.StructureData, segment1 : str, segment2 : str) -> NoneType
re-arranges segments suchs that segment2 follows segment1 in sequence
- non_polymer_bond(...) from builtins.PyCapsule
- non_polymer_bond(self : rosetta.protocols.denovo_design.components.StructureData, seg1 : str, seg2 : str) -> rosetta.protocols.denovo_design.components.BondInfo
finds a non-peptide bond between two segments, returns end() if there isn't one
- non_polymer_bond_exists(...) from builtins.PyCapsule
- non_polymer_bond_exists(self : rosetta.protocols.denovo_design.components.StructureData, seg1 : str, seg2 : str) -> bool
tells whether a non-polymer bond exists between the given segments
- num_chains(...) from builtins.PyCapsule
- num_chains(rosetta.protocols.denovo_design.components.StructureData) -> int
Total number of chains WARNING: This is an O(n) operation, where n is number of residue segments
- pairings_begin(...) from builtins.PyCapsule
- pairings_begin(rosetta.protocols.denovo_design.components.StructureData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const> const*, std::vector<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const>, std::allocator<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const> > > >
- pairings_end(...) from builtins.PyCapsule
- pairings_end(rosetta.protocols.denovo_design.components.StructureData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const> const*, std::vector<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const>, std::allocator<std::shared_ptr<protocols::denovo_design::components::SegmentPairing const> > > >
- parse_subtag(...) from builtins.PyCapsule
- parse_subtag(self : rosetta.protocols.denovo_design.components.StructureData, tag : rosetta.utility.tag.Tag) -> NoneType
Retrieves data from an XML subtag
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.denovo_design.components.StructureData, tag : rosetta.utility.tag.Tag) -> NoneType
Retrieves data from an XML tag
- pose_length(...) from builtins.PyCapsule
- pose_length(rosetta.protocols.denovo_design.components.StructureData) -> int
returns the total length of this permutation, including n-, c-terminal loop residues which are basically for show
- pose_residue(...) from builtins.PyCapsule
- pose_residue(self : rosetta.protocols.denovo_design.components.StructureData, segment_name : str, local_res : int) -> int
returns the actual residue number of the given name and res #
- rename_segment(...) from builtins.PyCapsule
- rename_segment(self : rosetta.protocols.denovo_design.components.StructureData, old_name : str, new_name : str) -> NoneType
renames a residue segment and updates all connections
- renumber_movable_group(...) from builtins.PyCapsule
- renumber_movable_group(self : rosetta.protocols.denovo_design.components.StructureData, oldg : int, newg : int) -> NoneType
renumbers movable group "oldg" to have new number "newg"
- replace_segment(...) from builtins.PyCapsule
- replace_segment(self : rosetta.protocols.denovo_design.components.StructureData, seg_name : str, segment : rosetta.protocols.denovo_design.components.Segment) -> NoneType
replace segment named seg_name with the given new segment
- retrieve_remarks(...) from builtins.PyCapsule
- retrieve_remarks(self : rosetta.protocols.denovo_design.components.StructureData, pose : rosetta.core.pose.Pose) -> rosetta.core.io.Remarks
retrieves saved remarks, makes any enzdes residues specific to the given pose
- save_remarks(...) from builtins.PyCapsule
- save_remarks(self : rosetta.protocols.denovo_design.components.StructureData, remarks : rosetta.core.io.Remarks) -> NoneType
Saves given remarks changes enzdes residues to generic segment name/number
- segment(...) from builtins.PyCapsule
- segment(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str) -> rosetta.protocols.denovo_design.components.Segment
returns segment represented by given string
- segment_group(...) from builtins.PyCapsule
- segment_group(self : rosetta.protocols.denovo_design.components.StructureData, sname : str) -> rosetta.std.vector_std_string
returns true if this object has a group of segments with the given name
- segment_name(...) from builtins.PyCapsule
- segment_name(self : rosetta.protocols.denovo_design.components.StructureData, res : int) -> str
returns segment which includes residue number res
- segments_begin(...) from builtins.PyCapsule
- segments_begin(rosetta.protocols.denovo_design.components.StructureData) -> std::_List_const_iterator<std::string>
start of segments list
- segments_end(...) from builtins.PyCapsule
- segments_end(rosetta.protocols.denovo_design.components.StructureData) -> std::_List_const_iterator<std::string>
end of segment list
- segments_in_movable_group(...) from builtins.PyCapsule
- segments_in_movable_group(self : rosetta.protocols.denovo_design.components.StructureData, group : int) -> rosetta.std.vector_std_string
computes and returns a set of segments which are in the given movable group
- set_abego(...) from builtins.PyCapsule
- set_abego(*args, **kwargs)
Overloaded function.
1. set_abego(self : rosetta.protocols.denovo_design.components.StructureData, segment : str, abego : str) -> NoneType
2. set_abego(self : rosetta.protocols.denovo_design.components.StructureData, segment : str, abego : rosetta.utility.vector1_std_string) -> NoneType
- set_alias(...) from builtins.PyCapsule
- set_alias(*args, **kwargs)
Overloaded function.
1. set_alias(self : rosetta.protocols.denovo_design.components.StructureData, alias_name : str, segment_name : str, resi : int) -> NoneType
sets an "alias" for a particular residue inside a segment which allows for it to be easily accessed
2. set_alias(self : rosetta.protocols.denovo_design.components.StructureData, alias_name : str, resi : int) -> NoneType
sets an "alias" for a particular residue which allows for it to be easily accessed
- set_cutpoint(...) from builtins.PyCapsule
- set_cutpoint(*args, **kwargs)
Overloaded function.
1. set_cutpoint(self : rosetta.protocols.denovo_design.components.StructureData, resid : int) -> NoneType
marks the ith residue as a cutpoint
2. set_cutpoint(self : rosetta.protocols.denovo_design.components.StructureData, seg : str, resi : int) -> NoneType
marks the resi-th residue of segment as a cutpoint
- set_data_int(...) from builtins.PyCapsule
- set_data_int(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str, val : int) -> NoneType
sets real number data
- set_data_real(...) from builtins.PyCapsule
- set_data_real(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str, val : float) -> NoneType
sets real number data
- set_data_str(...) from builtins.PyCapsule
- set_data_str(self : rosetta.protocols.denovo_design.components.StructureData, segment_id : str, data_name : str, val : str) -> NoneType
sets real number data
- set_id(...) from builtins.PyCapsule
- set_id(self : rosetta.protocols.denovo_design.components.StructureData, id_str : str) -> NoneType
sets id name
- set_movable_group(...) from builtins.PyCapsule
- set_movable_group(self : rosetta.protocols.denovo_design.components.StructureData, id : str, mg : int) -> NoneType
sets movable group of a segment
- set_ss(...) from builtins.PyCapsule
- set_ss(self : rosetta.protocols.denovo_design.components.StructureData, resid : int, ss_type : str) -> NoneType
sets secondary structure for residue resid
- set_template_pose(...) from builtins.PyCapsule
- set_template_pose(self : rosetta.protocols.denovo_design.components.StructureData, segment : str, template_pose : rosetta.core.pose.Pose, start_resid : int, stop_resid : int) -> NoneType
attaches a template pose to the given segment
- slice(...) from builtins.PyCapsule
- slice(self : rosetta.protocols.denovo_design.components.StructureData, segments : rosetta.std.vector_std_string) -> rosetta.protocols.denovo_design.components.StructureData
Returns a StructureData containing only the given segments
The resulting StructureData will contain all data from the current
- ss(...) from builtins.PyCapsule
- ss(*args, **kwargs)
Overloaded function.
1. ss(rosetta.protocols.denovo_design.components.StructureData) -> str
return secondary structure string
2. ss(self : rosetta.protocols.denovo_design.components.StructureData, resid : int) -> str
abego of residue resid
- termini(...) from builtins.PyCapsule
- termini(self : rosetta.protocols.denovo_design.components.StructureData, seg : str) -> (str, str)
returns n and c terminal segments of the chain which includes seg
- update_numbering(...) from builtins.PyCapsule
- update_numbering(rosetta.protocols.denovo_design.components.StructureData) -> NoneType
updates numbering based on the saved order of Segment objects
- upper_anchor(...) from builtins.PyCapsule
- upper_anchor(self : rosetta.protocols.denovo_design.components.StructureData, id_val : str) -> int
returns c-terminal residue of the chain represented by given string
|
class StructureDataFactory(rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t) |
| |
Singleton for creating StructureData objects
|
| |
- Method resolution order:
- StructureDataFactory
- rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.denovo_design.components.StructureDataFactory) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- attach_observer(...) from builtins.PyCapsule
- attach_observer(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose, sd : rosetta.protocols.denovo_design.components.StructureData) -> NoneType
attaches cacheable observer. Overwrites whatever was there before
- clear_from_pose(...) from builtins.PyCapsule
- clear_from_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> NoneType
clears all structuredata information (including cached xml) from
this pose.
- create_from_pose(...) from builtins.PyCapsule
- create_from_pose(*args, **kwargs)
Overloaded function.
1. create_from_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache
Creates a StructureData using the pose (but doesn't attach it) if
the cached StructureData could not be retrieved properly
2. create_from_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose, newid : str) -> rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache
Creates a StructureData using the pose (but doesn't attach it) if
the cached StructureData could not be retrieved properly
- create_singleton_instance(...) from builtins.PyCapsule
- create_singleton_instance() -> rosetta.protocols.denovo_design.components.StructureDataFactory
- detach_observer(...) from builtins.PyCapsule
- detach_observer(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> NoneType
detaches cacheable observer and removes from observable cache
- get_from_const_pose(...) from builtins.PyCapsule
- get_from_const_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache
Creates a StructureData using the pose (but doesn't attach it) if
the cached StructureData could not be retrieved properly
- get_from_pose(...) from builtins.PyCapsule
- get_from_pose(*args, **kwargs)
Overloaded function.
1. get_from_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache
creates one if necessary
2. get_from_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose, newid : str) -> rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from observable cache
creates one if necessary, and sets it in the pose
- has_cached_string(...) from builtins.PyCapsule
- has_cached_string(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> bool
stores a string in the pose's datacache
- observer_attached(...) from builtins.PyCapsule
- observer_attached(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> bool
checks for a StructureData in the pose observer cache
Returns true if one is found, false otherwise
- retrieve_cached_string(...) from builtins.PyCapsule
- retrieve_cached_string(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> str
stores a string in the pose's datacache
- retrieve_observer(...) from builtins.PyCapsule
- retrieve_observer(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose) -> protocols::denovo_design::components::StructureDataObserver
returns observer pointer if the pose has one cached
pointer returned can be null if no StructureData is present in the cache
- save_into_pose(...) from builtins.PyCapsule
- save_into_pose(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose, sd : rosetta.protocols.denovo_design.components.StructureData) -> NoneType
stores the data of this permutation into a pose for later retrieval
StructureData stored in a pose this way can be retrieved by calling
get_from_pose(), or get_from_const_pose()
- set_cached_string(...) from builtins.PyCapsule
- set_cached_string(self : rosetta.protocols.denovo_design.components.StructureDataFactory, pose : rosetta.core.pose.Pose, ssorig : str) -> NoneType
stores a string in the pose's datacache
Methods inherited from rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> protocols::denovo_design::components::StructureDataFactory
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class VLBProtected(rosetta.protocols.forge.components.VarLengthBuild) |
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- Method resolution order:
- VLBProtected
- rosetta.protocols.forge.components.VarLengthBuild
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.denovo_design.components.VLBProtected) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- pick_fragments_public(...) from builtins.PyCapsule
- pick_fragments_public(self : rosetta.protocols.denovo_design.components.VLBProtected, complete_ss : str, complete_aa : str, complete_abego : rosetta.utility.vector1_std_string, interval : protocols::forge::build::Interval, frag_length : int, n_frags : int) -> rosetta.core.fragment.FrameList
pick fragments of a given length, padding when necessary
The complete secondary structure string, typically from a Pose.
The complete amino acid string, typically from a Pose;
can be empty. If empty, sequence bias is not used to pick fragments.
The complete abego string, typically from a setter, set_abego
The interval [left, right] to pick fragments from; Pose
numbering (i.e. 1-based indexing).
The desired length of the fragments
The number of fragments to pick per position.
Methods inherited from rosetta.protocols.forge.components.VarLengthBuild:
- add_rcg(...) from builtins.PyCapsule
- add_rcg(self : rosetta.protocols.forge.components.VarLengthBuild, rcg : protocols::forge::remodel::RemodelConstraintGenerator) -> NoneType
- add_setup_mover(...) from builtins.PyCapsule
- add_setup_mover(self : rosetta.protocols.forge.components.VarLengthBuild, mover_in : rosetta.protocols.moves.Mover) -> NoneType
- add_user_provided_mover(...) from builtins.PyCapsule
- add_user_provided_mover(self : rosetta.protocols.forge.components.VarLengthBuild, mover_in : rosetta.protocols.moves.Mover) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.forge.components.VarLengthBuild, pose : rosetta.core.pose.Pose) -> NoneType
run protocol on given Pose
if procedure successful, return Pose with modifications and a
sealed fold tree, otherwise return Pose with modifications and the
in-progress cut fold tree
Before invoking this function it's best to make sure
the secondary structure in the Pose is marked via the method
that you would prefer, e.g. by Dssp (protocols::jumping::Dssp),
by the old Rosetta++ binning method (core::pose::set_ss_from_phipsi)
or by external method such as reading in a file.
- cache_fragments(...) from builtins.PyCapsule
- cache_fragments(*args, **kwargs)
Overloaded function.
1. cache_fragments(rosetta.protocols.forge.components.VarLengthBuild) -> bool
cache fragments after picking? (default true)
If true, will cache fragments and reuse them upon each
apply() call instead of repicking every time.
2. cache_fragments(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
cache fragments after picking?
If true, will cache fragments and reuse them upon each
apply() call instead of repicking every time.
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
clear any currently cached fragments
- clear_rcgs(...) from builtins.PyCapsule
- clear_rcgs(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clear_setup_movers(...) from builtins.PyCapsule
- clear_setup_movers(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clear_user_provided_movers(...) from builtins.PyCapsule
- clear_user_provided_movers(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.moves.Mover
clone this object
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.moves.Mover
create a new instance of this type of object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.forge.components.VarLengthBuild) -> str
- ignore_cmdline_enzdes_cstfile(...) from builtins.PyCapsule
- ignore_cmdline_enzdes_cstfile(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
- loop_mover_fold_tree_constant(...) from builtins.PyCapsule
- loop_mover_fold_tree_constant(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
- loop_mover_str(...) from builtins.PyCapsule
- loop_mover_str(*args, **kwargs)
Overloaded function.
1. loop_mover_str(rosetta.protocols.forge.components.VarLengthBuild) -> str
the string id of the loop mover to use
(default "RemodelLoopMover")
"RemodelLoopMover" for the forge RemodelLoopMover, otherwise a
string recognized by create_loop_mover() in the "LoopMoverFactory".
2. loop_mover_str(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
set the loop mover to use via string
use "RemodelLoopMover" for the forge RemodelLoopMover,
otherwise set it to a string recognized by
create_loop_mover() in the "LoopMoverFactory".
- manager(...) from builtins.PyCapsule
- manager(*args, **kwargs)
Overloaded function.
1. manager(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.forge.build.BuildManager
build manager
2. manager(self : rosetta.protocols.forge.components.VarLengthBuild, manager : rosetta.protocols.forge.build.BuildManager) -> NoneType
set build manager; also clears any cached fragments
- max_linear_chainbreak(...) from builtins.PyCapsule
- max_linear_chainbreak(*args, **kwargs)
Overloaded function.
1. max_linear_chainbreak(rosetta.protocols.forge.components.VarLengthBuild) -> float
return the highest linear chainbreak score a chainbreak can have
and still be considered closed
default 0.07
2. max_linear_chainbreak(self : rosetta.protocols.forge.components.VarLengthBuild, tol : float) -> NoneType
set the highest linear chainbreak score a chainbreak can have
and still be considered closed
- new_secondary_structure_override(...) from builtins.PyCapsule
- new_secondary_structure_override(*args, **kwargs)
Overloaded function.
1. new_secondary_structure_override(rosetta.protocols.forge.components.VarLengthBuild) -> str
full sequence string with length corresponding to the *new*
modified pose used to pick secondary structure biased fragments.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick secondary structure biased
fragments without modification. All secondary structure settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
2. new_secondary_structure_override(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
full sequence string with length corresponding to the *new*
modified pose used to pick secondary structure biased fragments.
String with length equals to the *new* modified pose.
See remarks for help on how to determine this. String is allowed
to be empty, in which case it will clear the setting.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick secondary structure biased
fragments without modification. All secondary structure settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
- new_sequence_override(...) from builtins.PyCapsule
- new_sequence_override(*args, **kwargs)
Overloaded function.
1. new_sequence_override(rosetta.protocols.forge.components.VarLengthBuild) -> str
full amino acid string with length corresponding to the *new*
modified pose used to pick sequence biased fragments.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick sequence biased
fragments without modification. All sequence settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
2. new_sequence_override(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
full amino acid string with length corresponding to the *new*
modified pose used to pick sequence biased fragments.
String with length equals to the *new* modified pose.
See remarks for help on how to determine this. String is allowed
to be empty, in which case it will clear the setting.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick sequence biased
fragments without modification. All sequence settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
- num_fragpick(...) from builtins.PyCapsule
- num_fragpick(*args, **kwargs)
Overloaded function.
1. num_fragpick(rosetta.protocols.forge.components.VarLengthBuild) -> int
the number of fragments to pick at each position
(default 200)
2. num_fragpick(self : rosetta.protocols.forge.components.VarLengthBuild, num : int) -> NoneType
the number of fragments to pick at each position (default 200)
- original_sequence(...) from builtins.PyCapsule
- original_sequence(*args, **kwargs)
Overloaded function.
1. original_sequence(rosetta.protocols.forge.components.VarLengthBuild) -> str
full sequence string corresponding to original input pose
used to pick sequence biased fragments; if empty, sequence bias
is not used when picking fragments
2. original_sequence(self : rosetta.protocols.forge.components.VarLengthBuild, seq : str) -> NoneType
full sequence string corresponding to original input pose
used to pick sequence biased fragments; if empty, sequence bias
is not used when picking fragments
- recover_original_on_failure(...) from builtins.PyCapsule
- recover_original_on_failure(*args, **kwargs)
Overloaded function.
1. recover_original_on_failure(rosetta.protocols.forge.components.VarLengthBuild) -> bool
at the end of apply(), reset the Pose to the original Pose if
mover was not successful? (default true)
2. recover_original_on_failure(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
at the end of apply(), reset the Pose to the original Pose if
mover was not successful?
- restart_mode(...) from builtins.PyCapsule
- restart_mode(*args, **kwargs)
Overloaded function.
1. restart_mode(rosetta.protocols.forge.components.VarLengthBuild) -> bool
Flag to turn on restart mode, in which VLB assumes that the Pose
fed to it during apply() has already been modified by the manager.
(default False)
In restart mode, VLB only runs the manager's dummy modify
capability during apply() to get the mapping info.
2. restart_mode(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
Flag to turn on restart mode, in which VLB assumes that the Pose
fed to it during apply() has already been modified by the manager.
(default False)
In restart mode, VLB only runs the manager's dummy modify
capability during apply() to get the mapping info.
- scorefunction(...) from builtins.PyCapsule
- scorefunction(*args, **kwargs)
Overloaded function.
1. scorefunction(self : rosetta.protocols.forge.components.VarLengthBuild, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set ScoreFunction used during build
2. scorefunction(self : rosetta.protocols.forge.components.VarLengthBuild, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set ScoreFunction used during build
- set_abego(...) from builtins.PyCapsule
- set_abego(self : rosetta.protocols.forge.components.VarLengthBuild, abego : rosetta.utility.vector1_std_string) -> NoneType
set abego definition for fragments
- use_fullmer(...) from builtins.PyCapsule
- use_fullmer(*args, **kwargs)
Overloaded function.
1. use_fullmer(rosetta.protocols.forge.components.VarLengthBuild) -> bool
also use fragments spanning the entire length of a loop?
(default false)
2. use_fullmer(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
also use fragments spanning the entire length of a loop?
- vall_memory_usage(...) from builtins.PyCapsule
- vall_memory_usage(*args, **kwargs)
Overloaded function.
1. vall_memory_usage(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum
option dictating whether to keep VallLibrary in memory or clear
it under certain circumstances after picking fragments.
(default KEEP_IN_MEMORY)
2. vall_memory_usage(self : rosetta.protocols.forge.components.VarLengthBuild, level : rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum) -> NoneType
option dictating whether to keep VallLibrary in memory or clear
it under certain circumstances after picking fragments.
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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