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- rosetta.core.pack.rotamer_set.RotamerSetFactory(builtins.object)
-
- SymmetricRotamerSetFactory
- rosetta.core.pack.rotamer_set.RotamerSet_(rosetta.core.pack.rotamer_set.RotamerSet)
-
- SymmetricRotamerSet_
- rosetta.core.pack.rotamer_set.RotamerSets(rosetta.core.pack.rotamer_set.FixbbRotamerSets)
-
- SymmetricRotamerSets
class SymmetricRotamerSet_(rosetta.core.pack.rotamer_set.RotamerSet_) |
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Container for a set of rotamers for use in packing.
Rotamers are sorted into groups of the same residue type.
Offsets into these rotamer groups are maintained by this class, as is
information concerning the "original rotamer" -- the rotamer
present on the input pose before packing began.
symmetrical version of RotamerSet_
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- Method resolution order:
- SymmetricRotamerSet_
- rosetta.core.pack.rotamer_set.RotamerSet_
- rosetta.core.pack.rotamer_set.RotamerSet
- rosetta.core.conformation.RotamerSetBase
- builtins.object
Methods defined here:
- PackerEnergyAdd(...) from builtins.PyCapsule
- PackerEnergyAdd(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies : rosetta.utility.vector1_float, add : rosetta.utility.vector1_float) -> NoneType
- PackerEnergyMultiply(...) from builtins.PyCapsule
- PackerEnergyMultiply(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies : rosetta.utility.vector1_float, factor : int) -> NoneType
- PackerEnergySubtract(...) from builtins.PyCapsule
- PackerEnergySubtract(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies : rosetta.utility.vector1_float, subtract : rosetta.utility.vector1_float) -> NoneType
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- compute_one_body_energies(...) from builtins.PyCapsule
- compute_one_body_energies(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, energies : rosetta.utility.vector1_float) -> NoneType
Computes the packers "one body energies" for the set of rotamers.
- initialize_pose_for_rotset_creation(...) from builtins.PyCapsule
- initialize_pose_for_rotset_creation(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose : rosetta.core.pose.Pose) -> NoneType
- orient_rotamer_set_to_symmetric_partner(...) from builtins.PyCapsule
- orient_rotamer_set_to_symmetric_partner(*args, **kwargs)
Overloaded function.
1. orient_rotamer_set_to_symmetric_partner(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose : rosetta.core.pose.Pose, residue_in : rosetta.core.conformation.Residue, sympos : int, rotset_in : rosetta.core.pack.rotamer_set.RotamerSet) -> rosetta.core.pack.rotamer_set.RotamerSet
2. orient_rotamer_set_to_symmetric_partner(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose : rosetta.core.pose.Pose, residue_in : rosetta.core.conformation.Residue, sympos : int, rotset_in : rosetta.core.pack.rotamer_set.RotamerSet, set_up_mirror_types_if_has_mirror_symmetry : bool) -> rosetta.core.pack.rotamer_set.RotamerSet
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSet_:
- add_rotamer(...) from builtins.PyCapsule
- add_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, rotamer : rosetta.core.conformation.Residue) -> NoneType
- begin(...) from builtins.PyCapsule
- begin(rosetta.core.pack.rotamer_set.RotamerSet_) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::conformation::Residue> const*, std::vector<std::shared_ptr<core::conformation::Residue>, std::allocator<std::shared_ptr<core::conformation::Residue> > > >
- build_dependent_rotamers(...) from builtins.PyCapsule
- build_dependent_rotamers(self : rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_sets : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph) -> NoneType
Build rotamers that depend on positions of rotamers built in a previous pass
- build_rotamers(...) from builtins.PyCapsule
- build_rotamers(*args, **kwargs)
Overloaded function.
1. build_rotamers(self : rosetta.core.pack.rotamer_set.RotamerSet_, the_pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph) -> NoneType
2. build_rotamers(self : rosetta.core.pack.rotamer_set.RotamerSet_, the_pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, use_neighbor_context : bool) -> NoneType
- bump_check(...) from builtins.PyCapsule
- bump_check(self : rosetta.core.pack.rotamer_set.RotamerSet_, rotamer : rosetta.core.conformation.Residue, sf : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph) -> float
Computes the "bump energy" of a rotamer: the bump energy is the
sum of rotamer's interactions with 1) the backbone-and-side chains of
neighboring residues that are held fixed during this repacking optimization
and 2) the backbones of neighboring residues that are changable during this
repacking optimization.
- compute_one_body_energy_maps(...) from builtins.PyCapsule
- compute_one_body_energy_maps(self : rosetta.core.pack.rotamer_set.RotamerSet_, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, energies : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType
for OPTE
- drop_rotamer(...) from builtins.PyCapsule
- drop_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, rot_id : int) -> NoneType
removes a single rotamer and causes a rotamer index update
- drop_rotamers(...) from builtins.PyCapsule
- drop_rotamers(self : rosetta.core.pack.rotamer_set.RotamerSet_, rotamers_to_delete : rosetta.utility.vector1_bool) -> NoneType
rotamers_to_delete must be of size nrotmaers -- each position
in the array that's "true" is removed from the set of rotamers
- drop_rotamers_by_index(...) from builtins.PyCapsule
- drop_rotamers_by_index(self : rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_indices_to_delete : rosetta.utility.vector1_unsigned_long) -> NoneType
deletes the rotamers in the list with the given indices.
The indices of these rotamers is presumed to be those before any delete operation.
e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3,
then the rotamers that will remain are the rotamers originally indexed as 2 and 4,
even though their new indices will be 1 & 2.
- end(...) from builtins.PyCapsule
- end(rosetta.core.pack.rotamer_set.RotamerSet_) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::conformation::Residue> const*, std::vector<std::shared_ptr<core::conformation::Residue>, std::allocator<std::shared_ptr<core::conformation::Residue> > > >
- get_n_residue_groups(...) from builtins.PyCapsule
- get_n_residue_groups(rosetta.core.pack.rotamer_set.RotamerSet_) -> int
- get_n_residue_types(...) from builtins.PyCapsule
- get_n_residue_types(rosetta.core.pack.rotamer_set.RotamerSet_) -> int
- get_n_rotamers_for_residue_group(...) from builtins.PyCapsule
- get_n_rotamers_for_residue_group(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup : int) -> int
- get_n_rotamers_for_residue_type(...) from builtins.PyCapsule
- get_n_rotamers_for_residue_type(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup : int) -> int
- get_residue_group_begin(...) from builtins.PyCapsule
- get_residue_group_begin(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup : int) -> int
- get_residue_group_index_for_rotamer(...) from builtins.PyCapsule
- get_residue_group_index_for_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer : int) -> int
- get_residue_type_begin(...) from builtins.PyCapsule
- get_residue_type_begin(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_restype : int) -> int
- get_residue_type_index_for_rotamer(...) from builtins.PyCapsule
- get_residue_type_index_for_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer : int) -> int
- get_trie(...) from builtins.PyCapsule
- get_trie(self : rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id : int) -> rosetta.core.conformation.AbstractRotamerTrie
- id_for_current_rotamer(...) from builtins.PyCapsule
- id_for_current_rotamer(rosetta.core.pack.rotamer_set.RotamerSet_) -> int
- nonconst_rotamer(...) from builtins.PyCapsule
- nonconst_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, rot_id : int) -> rosetta.core.conformation.Residue
- num_rotamers(...) from builtins.PyCapsule
- num_rotamers(rosetta.core.pack.rotamer_set.RotamerSet_) -> int
- rotamer(...) from builtins.PyCapsule
- rotamer(self : rosetta.core.pack.rotamer_set.RotamerSet_, rot_id : int) -> rosetta.core.conformation.Residue
- rotamer_ref(...) from builtins.PyCapsule
- rotamer_ref(self : rosetta.core.pack.rotamer_set.RotamerSet_, rot_id : int) -> rosetta.core.conformation.Residue
- set_extra_samples(...) from builtins.PyCapsule
- set_extra_samples(self : rosetta.core.pack.rotamer_set.RotamerSet_, task : rosetta.core.pack.task.PackerTask, num_10A_neighbors : int, chi : int, concrete_residue : rosetta.core.chemical.ResidueType, extra_chi_steps : rosetta.utility.vector1_double) -> NoneType
Pushes standard-deviation multiples that should be sampled
for this residue -- if this residue has more neighbors within 10A
than the task-specified cutoff for buriedness, then extra rotamer
samples are added to the extra_chi_steps vector, otherwise, the
vector is not modified.
- store_trie(...) from builtins.PyCapsule
- store_trie(self : rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id : int, trie : rosetta.core.conformation.AbstractRotamerTrie) -> NoneType
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSet:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.pack.rotamer_set.RotamerSet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamer_set.RotamerSet, : rosetta.core.pack.rotamer_set.RotamerSet) -> rosetta.core.pack.rotamer_set.RotamerSet
- resid(...) from builtins.PyCapsule
- resid(rosetta.core.pack.rotamer_set.RotamerSet) -> int
- set_resid(...) from builtins.PyCapsule
- set_resid(self : rosetta.core.pack.rotamer_set.RotamerSet, resid : int) -> NoneType
Methods inherited from rosetta.core.conformation.RotamerSetBase:
- data(...) from builtins.PyCapsule
- data(*args, **kwargs)
Overloaded function.
1. data(rosetta.core.conformation.RotamerSetBase) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
2. data(rosetta.core.conformation.RotamerSetBase) -> rosetta.basic.datacache.BasicDataCache
BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
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class SymmetricRotamerSets(rosetta.core.pack.rotamer_set.RotamerSets) |
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- Method resolution order:
- SymmetricRotamerSets
- rosetta.core.pack.rotamer_set.RotamerSets
- rosetta.core.pack.rotamer_set.FixbbRotamerSets
- rosetta.core.pack.rotamer_set.RotamerSetsBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets) -> rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets
- compute_energies(...) from builtins.PyCapsule
- compute_energies(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph, ig : rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType
- compute_one_body_energies(...) from builtins.PyCapsule
- compute_one_body_energies(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph, ig : rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType
- initialize_pose_for_rotsets_creation(...) from builtins.PyCapsule
- initialize_pose_for_rotsets_creation(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose : rosetta.core.pose.Pose) -> NoneType
- precompute_two_body_energies(...) from builtins.PyCapsule
- precompute_two_body_energies(*args, **kwargs)
Overloaded function.
1. precompute_two_body_energies(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph, pig : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph) -> NoneType
precomputes all rotamer pair energies between neighboring RotamerSets( residues )
and stores those energies in an intereaction graph capable of storing them
public so it can be used by the GreenPacker.
2. precompute_two_body_energies(self : rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph, pig : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, finalize_edges : bool) -> NoneType
precomputes all rotamer pair energies between neighboring RotamerSets( residues )
and stores those energies in an intereaction graph capable of storing them
public so it can be used by the GreenPacker.
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSets:
- begin(...) from builtins.PyCapsule
- begin(rosetta.core.pack.rotamer_set.RotamerSets) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> const*, std::vector<std::shared_ptr<core::pack::rotamer_set::RotamerSet>, std::allocator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> > > >
- build_rotamers(...) from builtins.PyCapsule
- build_rotamers(self : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph) -> NoneType
- dump_pdb(...) from builtins.PyCapsule
- dump_pdb(self : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, filename : str) -> NoneType
- end(...) from builtins.PyCapsule
- end(rosetta.core.pack.rotamer_set.RotamerSets) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> const*, std::vector<std::shared_ptr<core::pack::rotamer_set::RotamerSet>, std::allocator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> > > >
- get_bb_bbE(...) from builtins.PyCapsule
- get_bb_bbE(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue) -> float
- get_sc_bbE(...) from builtins.PyCapsule
- get_sc_bbE(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue) -> float
- moltenres_2_resid(...) from builtins.PyCapsule
- moltenres_2_resid(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- moltenres_2_resid_vector(...) from builtins.PyCapsule
- moltenres_2_resid_vector(rosetta.core.pack.rotamer_set.RotamerSets) -> rosetta.utility.vector1_unsigned_long
- moltenres_for_rotamer(...) from builtins.PyCapsule
- moltenres_for_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- moltenres_rotid_2_rotid(...) from builtins.PyCapsule
- moltenres_rotid_2_rotid(self : rosetta.core.pack.rotamer_set.RotamerSets, moltenres : int, moltenresrotid : int) -> int
convert moltenres rotid to id in full rotamer enumeration
- nmoltenres(...) from builtins.PyCapsule
- nmoltenres(rosetta.core.pack.rotamer_set.RotamerSets) -> int
- nrotamer_offset_for_moltenres(...) from builtins.PyCapsule
- nrotamer_offset_for_moltenres(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- nrotamers(...) from builtins.PyCapsule
- nrotamers(rosetta.core.pack.rotamer_set.RotamerSets) -> int
- nrotamers_for_moltenres(...) from builtins.PyCapsule
- nrotamers_for_moltenres(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- prepare_sets_for_packing(...) from builtins.PyCapsule
- prepare_sets_for_packing(self : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
- res_for_rotamer(...) from builtins.PyCapsule
- res_for_rotamer(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- resid_2_moltenres(...) from builtins.PyCapsule
- resid_2_moltenres(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> int
- resid_2_moltenres_vector(...) from builtins.PyCapsule
- resid_2_moltenres_vector(rosetta.core.pack.rotamer_set.RotamerSets) -> rosetta.utility.vector1_unsigned_long
- rotamer(...) from builtins.PyCapsule
- rotamer(self : rosetta.core.pack.rotamer_set.RotamerSets, : int) -> rosetta.core.conformation.Residue
- rotamer_for_moltenres(...) from builtins.PyCapsule
- rotamer_for_moltenres(self : rosetta.core.pack.rotamer_set.RotamerSets, moltenres_id : int, rotamerid : int) -> rosetta.core.conformation.Residue
- rotamer_set_for_moltenresidue(...) from builtins.PyCapsule
- rotamer_set_for_moltenresidue(*args, **kwargs)
Overloaded function.
1. rotamer_set_for_moltenresidue(self : rosetta.core.pack.rotamer_set.RotamerSets, moltenresid : int) -> core::pack::rotamer_set::RotamerSet
2. rotamer_set_for_moltenresidue(self : rosetta.core.pack.rotamer_set.RotamerSets, moltenresid : int) -> core::pack::rotamer_set::RotamerSet
- rotamer_set_for_residue(...) from builtins.PyCapsule
- rotamer_set_for_residue(*args, **kwargs)
Overloaded function.
1. rotamer_set_for_residue(self : rosetta.core.pack.rotamer_set.RotamerSets, resid : int) -> core::pack::rotamer_set::RotamerSet
2. rotamer_set_for_residue(self : rosetta.core.pack.rotamer_set.RotamerSets, resid : int) -> core::pack::rotamer_set::RotamerSet
- rotid_on_moltenresidue(...) from builtins.PyCapsule
- rotid_on_moltenresidue(self : rosetta.core.pack.rotamer_set.RotamerSets, rotid : int) -> int
convert rotid in full rotamer enumeration into rotamer id on its source residue
- set_task(...) from builtins.PyCapsule
- set_task(self : rosetta.core.pack.rotamer_set.RotamerSets, task : core::pack::task::PackerTask) -> NoneType
- task(...) from builtins.PyCapsule
- task(rosetta.core.pack.rotamer_set.RotamerSets) -> core::pack::task::PackerTask
access to packer_task_
- total_residue(...) from builtins.PyCapsule
- total_residue(rosetta.core.pack.rotamer_set.RotamerSets) -> int
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetsBase:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.pack.rotamer_set.RotamerSetsBase) -> str
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