| | |
- builtins.object
-
- HotspotStub
- HotspotStubSet
- SearchPattern
-
- CartesianSearchPattern
- ComposeSearchPatterns
- ConstPattern
- LSMSearchPattern
- PartitionedSearchPattern
- RotationSearchPattern
- SICPatternAtTransform
- SearchPatternExpansion
- SearchPatternTransform
- SphericalRotationSearchPattern
- SurfaceSearchPattern
- TestPattern
- StubGenerator
- StubStatus
- VectorPair
- rosetta.core.pack.task.operation.TaskOperation(builtins.object)
-
- AddSearchPatternRotSetOp
- rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO(rosetta.core.pack.rotamer_set.RotamerSetOperation)
-
- SearchPatternRotSetOp
class CartesianSearchPattern(SearchPattern) |
| | |
- Method resolution order:
- CartesianSearchPattern
- SearchPattern
- builtins.object
Methods defined here:
- Searchpoints(...) from builtins.PyCapsule
- Searchpoints(rosetta.protocols.hotspot_hashing.CartesianSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, x_sampling : float, y_sampling : float, z_sampling : float, x_min : float, x_max : float, y_min : float, y_max : float, z_min : float, z_max : float) -> 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.hotspot_hashing.CartesianSearchPattern, : rosetta.protocols.hotspot_hashing.CartesianSearchPattern) -> rosetta.protocols.hotspot_hashing.CartesianSearchPattern
- generate_search_points(...) from builtins.PyCapsule
- generate_search_points(rosetta.protocols.hotspot_hashing.CartesianSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
Data descriptors defined here:
- searchpoints_
- x_max
- x_min
- x_sampling
- y_max
- y_min
- y_sampling
- z_max
- z_min
- z_sampling
|
class HotspotStub(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.hotspot_hashing.HotspotStub) -> NoneType
2. __init__(self : rosetta.protocols.hotspot_hashing.HotspotStub, residue : rosetta.core.conformation.Residue, bonus_value : float, pose : rosetta.core.pose.Pose, chain_to_design : int, filter : rosetta.protocols.filters.Filter) -> NoneType
3. __init__(self : rosetta.protocols.hotspot_hashing.HotspotStub, src : rosetta.protocols.hotspot_hashing.HotspotStub) -> 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.hotspot_hashing.HotspotStub, src : rosetta.protocols.hotspot_hashing.HotspotStub) -> rosetta.protocols.hotspot_hashing.HotspotStub
- bonus_value(...) from builtins.PyCapsule
- bonus_value(rosetta.protocols.hotspot_hashing.HotspotStub) -> float
Return this potential hotspot's bonus value
- get_nearest_residue(...) from builtins.PyCapsule
- get_nearest_residue(self : rosetta.protocols.hotspot_hashing.HotspotStub, pose : rosetta.core.pose.Pose) -> int
find the residue that's closest to the stub on chain_to_design_
- get_scaffold_status(...) from builtins.PyCapsule
- get_scaffold_status(self : rosetta.protocols.hotspot_hashing.HotspotStub, seqpos : int) -> bool
Get status at position (setting status if not set)
- residue(...) from builtins.PyCapsule
- residue(rosetta.protocols.hotspot_hashing.HotspotStub) -> rosetta.core.conformation.Residue
Return the residue associated with this potential hotspot
- set_filter(...) from builtins.PyCapsule
- set_filter(self : rosetta.protocols.hotspot_hashing.HotspotStub, filter : rosetta.protocols.filters.Filter) -> NoneType
- set_scaffold_status(...) from builtins.PyCapsule
- set_scaffold_status(self : rosetta.protocols.hotspot_hashing.HotspotStub, seqpos : int, status : rosetta.protocols.hotspot_hashing.StubStatus) -> NoneType
Set status at position
|
class HotspotStubSet(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> NoneType
2. __init__(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, init : rosetta.protocols.hotspot_hashing.HotspotStubSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_hotspot_constraints_to_pose(...) from builtins.PyCapsule
- add_hotspot_constraints_to_pose(*args, **kwargs)
Overloaded function.
1. add_hotspot_constraints_to_pose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, partner : int, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float) -> NoneType
Sets up constraints using a given partner (auto choose packer task and fixed reference atom)
2. add_hotspot_constraints_to_pose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, partner : int, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float, apply_ambiguous_constraints : bool) -> NoneType
Sets up constraints using a given partner (auto choose packer task and fixed reference atom)
3. add_hotspot_constraints_to_pose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, fixed_atom : rosetta.core.id.AtomID, packer_task : rosetta.core.pack.task.PackerTask, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float) -> NoneType
Sets up constraints with user-supplied packer task and fixed reference atom
4. add_hotspot_constraints_to_pose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, fixed_atom : rosetta.core.id.AtomID, packer_task : rosetta.core.pack.task.PackerTask, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float, apply_ambiguous_constraints : bool) -> NoneType
Sets up constraints with user-supplied packer task and fixed reference atom
- add_hotspot_constraints_to_wholepose(...) from builtins.PyCapsule
- add_hotspot_constraints_to_wholepose(*args, **kwargs)
Overloaded function.
1. add_hotspot_constraints_to_wholepose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, partner : int, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float) -> NoneType
2. add_hotspot_constraints_to_wholepose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, partner : int, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float, apply_ambiguous_constraints : bool) -> NoneType
3. add_hotspot_constraints_to_wholepose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, fixed_atom : rosetta.core.id.AtomID, packer_task : rosetta.core.pack.task.PackerTask, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float) -> NoneType
Sets up constraints with user-supplied packer task and fixed reference atom
4. add_hotspot_constraints_to_wholepose(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, fixed_atom : rosetta.core.id.AtomID, packer_task : rosetta.core.pack.task.PackerTask, hotspot_stub_set : rosetta.protocols.hotspot_hashing.HotspotStubSet, CB_force_constant : float, worst_allowed_stub_bonus : float, apply_self_energies : bool, bump_cutoff : float, apply_ambiguous_constraints : bool) -> NoneType
Sets up constraints with user-supplied packer task and fixed reference atom
- add_stub_(...) from builtins.PyCapsule
- add_stub_(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, stub : rosetta.protocols.hotspot_hashing.HotspotStub) -> NoneType
- add_stub_set(...) from builtins.PyCapsule
- add_stub_set(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, stubset : rosetta.protocols.hotspot_hashing.HotspotStubSet) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, : rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
- autofill(...) from builtins.PyCapsule
- autofill(*args, **kwargs)
Overloaded function.
1. autofill(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, n_stubs : int) -> NoneType
fill the stub set with n_stubs each of A, R, N, D, E, Q, H, I, L, K, M, P, F, S, T, W, Y, and V
2. autofill(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, target : int, distance : float, n_stubs : int) -> NoneType
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> __gnu_cxx::__normal_iterator<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > > const*, std::vector<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > >, std::allocator<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > > > > >
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> NoneType
- cluster(...) from builtins.PyCapsule
- cluster(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
cluster stubs, returning a new stubset of cluster centers for each residue
- colonyE(...) from builtins.PyCapsule
- colonyE(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002)
- constraints(...) from builtins.PyCapsule
- constraints(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
return bbcst's associatied with this stub set
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> __gnu_cxx::__normal_iterator<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > > const*, std::vector<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > >, std::allocator<std::pair<std::string, std::pair<double, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > > > > >
- fill(...) from builtins.PyCapsule
- fill(*args, **kwargs)
Overloaded function.
1. fill(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, reference_pose : rosetta.core.pose.Pose, scorefxn_in : rosetta.core.scoring.ScoreFunction, residue_name3 : str, n_stubs : int) -> NoneType
fill the stub set with n_stubs by Rosetta residue name
2. fill(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, reference_pose : rosetta.core.pose.Pose, scorefxn_in : rosetta.core.scoring.ScoreFunction, target : int, distance : float, residue_name3 : str, n_stubs : int) -> NoneType
only keep stubs within a certain distance of a residue on the target pose.
- filter(...) from builtins.PyCapsule
- filter(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, filter : rosetta.protocols.filters.Filter) -> NoneType
set the filter to use for scaffold matching within this set
- get_best_energy_stub(...) from builtins.PyCapsule
- get_best_energy_stub(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.protocols.hotspot_hashing.HotspotStub
gets the best energy stub in the set
- get_nearest_stub(...) from builtins.PyCapsule
- get_nearest_stub(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, stub : rosetta.core.conformation.Residue) -> rosetta.protocols.hotspot_hashing.HotspotStub
get the stub that's nearest to a residue
- get_stub(...) from builtins.PyCapsule
- get_stub(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, residue_name3 : str, score : float) -> std::_Rb_tree_const_iterator<std::pair<double const, std::shared_ptr<protocols::hotspot_hashing::HotspotStub> > >
gets a stub from the stub_set_. A version returning an OP is private
- hotspot_length(...) from builtins.PyCapsule
- hotspot_length(*args, **kwargs)
Overloaded function.
1. hotspot_length(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> int
set length of hotspot peptide used for finding stubs. Default=1, Hotspot stored in set will always be only 1 residue
2. hotspot_length(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, length : int) -> NoneType
- pair_with_scaffold(...) from builtins.PyCapsule
- pair_with_scaffold(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, partner : int, filter : rosetta.protocols.filters.Filter) -> NoneType
associate all stubs in the set with a scaffold partner
- prepare_hashing_packer_task_(...) from builtins.PyCapsule
- prepare_hashing_packer_task_(*args, **kwargs)
Overloaded function.
1. prepare_hashing_packer_task_(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
2. prepare_hashing_packer_task_(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, chain_to_redesign : int) -> rosetta.core.pack.task.PackerTask
- random_stub(...) from builtins.PyCapsule
- random_stub(*args, **kwargs)
Overloaded function.
1. random_stub(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> rosetta.protocols.hotspot_hashing.HotspotStub
returns a random stub either from the entire set or based on residue name
2. random_stub(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, resname : str) -> rosetta.protocols.hotspot_hashing.HotspotStub
- read_data(...) from builtins.PyCapsule
- read_data(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, filename : str) -> NoneType
add to stubset by reading from a file
- remove_all_hotspot_constraints(...) from builtins.PyCapsule
- remove_all_hotspot_constraints(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose) -> bool
remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose
- remove_random_stubs_from_set(...) from builtins.PyCapsule
- remove_random_stubs_from_set(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, num_to_remove : int) -> NoneType
- remove_stub(...) from builtins.PyCapsule
- remove_stub(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, stub : rosetta.protocols.hotspot_hashing.HotspotStub) -> bool
removes a single stub. Reports false if stub is not found
- rescore(...) from builtins.PyCapsule
- rescore(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
rescore all stubs in this set based on current flags (eg - sc_only() )
- retrieve(...) from builtins.PyCapsule
- retrieve(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, residue_name3 : str) -> rosetta.std.multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_std_less_double_std_allocator_std_pair_const_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t
retrieve all stubs with a given residue name
- sc_only(...) from builtins.PyCapsule
- sc_only(*args, **kwargs)
Overloaded function.
1. sc_only(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> bool
true if these stubs are sidechain-only (defaults true)
2. sc_only(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, sc_switch : bool) -> NoneType
set whether or not sidechains are included
- score_threshold(...) from builtins.PyCapsule
- score_threshold(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, threshold : float) -> NoneType
only accept stubs that score better than this threshold (default is -1.0)
- set_chain_to_design(...) from builtins.PyCapsule
- set_chain_to_design(*args, **kwargs)
Overloaded function.
1. set_chain_to_design(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> NoneType
2. set_chain_to_design(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, chain_to_design : int) -> NoneType
- size(...) from builtins.PyCapsule
- size(*args, **kwargs)
Overloaded function.
1. size(rosetta.protocols.hotspot_hashing.HotspotStubSet) -> int
how many total stubs are in the set (all residues)?
2. size(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, resname : str) -> int
how many stubs are in the set by residue?
- subset(...) from builtins.PyCapsule
- subset(*args, **kwargs)
Overloaded function.
1. subset(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, residue_name3 : str, scorecut : float) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
2. subset(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, scorecut : float) -> rosetta.protocols.hotspot_hashing.HotspotStubSet
build a new stubset containing stubs that pass a score cutoff
- write_all(...) from builtins.PyCapsule
- write_all(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, filename : str) -> NoneType
write all stubs contained in this set to filename
- write_stub(...) from builtins.PyCapsule
- write_stub(self : rosetta.protocols.hotspot_hashing.HotspotStubSet, outstream : rosetta.utility.io.ozstream, stub : rosetta.protocols.hotspot_hashing.HotspotStub, tag : str) -> NoneType
write one stub with a user-supplied tag
|
class RotationSearchPattern(SearchPattern) |
| | |
- Method resolution order:
- RotationSearchPattern
- SearchPattern
- builtins.object
Methods defined here:
- Searchpoints(...) from builtins.PyCapsule
- Searchpoints(rosetta.protocols.hotspot_hashing.RotationSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, float, float) -> NoneType
doc
2. __init__(handle, float, float, float) -> NoneType
doc
3. __init__(handle, float, float, float, float) -> NoneType
doc
4. __init__(handle, float, float, float, float, float) -> NoneType
doc
5. __init__(self : handle, x_sampling : float, y_sampling : float, x_min : float, x_max : float, y_min : float, y_max : float) -> 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.hotspot_hashing.RotationSearchPattern, : rosetta.protocols.hotspot_hashing.RotationSearchPattern) -> rosetta.protocols.hotspot_hashing.RotationSearchPattern
- generate_search_points(...) from builtins.PyCapsule
- generate_search_points(rosetta.protocols.hotspot_hashing.RotationSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
Data descriptors defined here:
- searchpoints_
- x_max
- x_min
- x_sampling
- y_max
- y_min
- y_sampling
|
class SICPatternAtTransform(SearchPattern) |
| | |
- Method resolution order:
- SICPatternAtTransform
- SearchPattern
- builtins.object
Methods defined here:
- Searchpoints(...) from builtins.PyCapsule
- Searchpoints(rosetta.protocols.hotspot_hashing.SICPatternAtTransform) -> rosetta.utility.vector1_core_kinematics_Stub
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.core.pose.Pose, rosetta.core.pose.Pose, rosetta.protocols.hotspot_hashing.SearchPattern, rosetta.protocols.hotspot_hashing.SearchPattern) -> NoneType
doc
2. __init__(self : handle, source_pose : rosetta.core.pose.Pose, placed_pose : rosetta.core.pose.Pose, slide_pattern : rosetta.protocols.hotspot_hashing.SearchPattern, source_pattern : rosetta.protocols.hotspot_hashing.SearchPattern, starting_displacement : float) -> NoneType
3. __init__(handle, rosetta.core.pose.Pose, rosetta.core.pose.Pose, rosetta.protocols.hotspot_hashing.SearchPattern) -> NoneType
doc
4. __init__(self : handle, source_pose : rosetta.core.pose.Pose, placed_pose : rosetta.core.pose.Pose, slide_pattern : rosetta.protocols.hotspot_hashing.SearchPattern, starting_displacement : float) -> 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.hotspot_hashing.SICPatternAtTransform, : rosetta.protocols.hotspot_hashing.SICPatternAtTransform) -> rosetta.protocols.hotspot_hashing.SICPatternAtTransform
|
class SearchPatternRotSetOp(rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO) |
| | |
- Method resolution order:
- SearchPatternRotSetOp
- rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, pattern : rosetta.protocols.hotspot_hashing.SearchPattern) -> NoneType
2. __init__(handle, rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- get_rigid_body_confs(...) from builtins.PyCapsule
- get_rigid_body_confs(self : rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask, residue_index : int) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, residue_index : int) -> float
Methods inherited from rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO:
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
Adds additional rotamers at each rb conf.
fairly simple: iterate over the rotamers in the rotamer_set, superimpose
each of them onto all the internally stored rigid body confs, and then
add the newly generated rotamers to the rotamer_set
Recalculates chi-angle expansion via call to RotamerSet::extra_chi_samples
and then generate candidate rotamers from each rb conf via
SingleResidueRotamerLibrary::fill_rotamer_vector if rotamer library is
available for the residue type, else just adds the alternate confs.
Does not have full safety checks to make sure all the rotamers in the set are
of the same residue type as the internally stored ones, i.e. that no user sets this
position to designing in the task
- determine_largest_nbr_atom_distance(...) from builtins.PyCapsule
- determine_largest_nbr_atom_distance(target_res : rosetta.core.conformation.Residue, alternate_confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> float
returns the largest observed distance between the nbr atom
in the target res and the nbr atom in any of the candidate rb confs
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, : rosetta.core.pack.rotamer_set.RotamerSetOperation) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
|
class SphericalRotationSearchPattern(SearchPattern) |
| | |
- Method resolution order:
- SphericalRotationSearchPattern
- SearchPattern
- builtins.object
Methods defined here:
- Searchpoints(...) from builtins.PyCapsule
- Searchpoints(rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, float, float, float) -> NoneType
doc
2. __init__(handle, float, float, float, float) -> NoneType
doc
3. __init__(handle, float, float, float, float, float) -> NoneType
doc
4. __init__(handle, float, float, float, float, float, float) -> NoneType
doc
5. __init__(handle, float, float, float, float, float, float, float) -> NoneType
doc
6. __init__(handle, float, float, float, float, float, float, float, float) -> NoneType
doc
7. __init__(self : handle, polar_rotation_sampling : float, altitude_rotation_sampling : float, azmiuth_rotation_sampling : float, polar_min : float, polar_max : float, altitude_min : float, altitude_max : float, azmiuth_min : float, azmiuth_max : float) -> 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.hotspot_hashing.SphericalRotationSearchPattern, : rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern) -> rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern
- generate_search_points(...) from builtins.PyCapsule
- generate_search_points(rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern) -> rosetta.utility.vector1_core_kinematics_Stub
Data descriptors defined here:
- altitude_max
- altitude_min
- altitude_rotation_sampling
- azmiuth_max
- azmiuth_min
- azmiuth_rotation_sampling
- polar_max
- polar_min
- polar_rotation_sampling
- searchpoints_
|
class StubGenerator(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.
- getStubByName(...) from builtins.PyCapsule
- getStubByName(name : str) -> rosetta.core.conformation.Residue
- moveFromStubFrame(...) from builtins.PyCapsule
- moveFromStubFrame(residue : rosetta.core.conformation.Residue, transform : rosetta.core.kinematics.Stub) -> NoneType
- moveIntoStubFrame(...) from builtins.PyCapsule
- moveIntoStubFrame(residue : rosetta.core.conformation.Residue, transform : rosetta.core.kinematics.Stub) -> NoneType
- placeResidueAtTransform(...) from builtins.PyCapsule
- placeResidueAtTransform(pose : rosetta.core.pose.Pose, sourceResidue : rosetta.core.conformation.Residue, transform : rosetta.core.kinematics.Stub, residuejumpindex : int, residueindex : int) -> NoneType
- placeResidueOnPose(...) from builtins.PyCapsule
- placeResidueOnPose(pose : rosetta.core.pose.Pose, residue : rosetta.core.conformation.Residue) -> NoneType
- residueStubCentroid(...) from builtins.PyCapsule
- residueStubCentroid(residue : rosetta.core.conformation.Residue) -> rosetta.numeric.xyzVector_double_t
- residueStubCentroidFrame(...) from builtins.PyCapsule
- residueStubCentroidFrame(residue : rosetta.core.conformation.Residue) -> rosetta.core.kinematics.Stub
- residueStubOrientFrame(...) from builtins.PyCapsule
- residueStubOrientFrame(residue : rosetta.core.conformation.Residue) -> rosetta.core.kinematics.Stub
|
|