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- create_packer_graph(...) method of builtins.PyCapsule instance
- create_packer_graph(*args, **kwargs)
Overloaded function.
1. create_packer_graph(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.graph.Graph
2. create_packer_graph(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, total_nodes : int, residue_radii : rosetta.utility.vector1_double) -> rosetta.core.graph.Graph
- figure_out_repackable_residues(...) method of builtins.PyCapsule instance
- figure_out_repackable_residues(pose : rosetta.core.pose.Pose, to_repack : rosetta.core.id.AtomID_Map_bool_t, repackable : rosetta.utility.vector1_bool) -> bool
return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb
- find_residue_max_radii(...) method of builtins.PyCapsule instance
- find_residue_max_radii(pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.utility.vector1_double
- get_rotamer_angle_diffs(...) method of builtins.PyCapsule instance
- get_rotamer_angle_diffs(pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t
Get rotamer angle differences
Outer vector is pose length, inner vector is different chi's
- make_new_symmetric_PackerTask_by_requested_method(...) method of builtins.PyCapsule instance
- make_new_symmetric_PackerTask_by_requested_method(pose : rosetta.core.pose.Pose, non_symmetric_task : rosetta.core.pack.task.PackerTask) -> rosetta.core.pack.task.PackerTask
- make_symmetric_PackerTask_by_truncation(...) method of builtins.PyCapsule instance
- make_symmetric_PackerTask_by_truncation(pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- min_pack(...) method of builtins.PyCapsule instance
- min_pack(*args, **kwargs)
Overloaded function.
1. min_pack(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> NoneType
Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.
2. min_pack(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, cartesian : bool) -> NoneType
Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.
3. min_pack(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, cartesian : bool, nonideal : bool) -> NoneType
Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.
- min_pack_optimize(...) method of builtins.PyCapsule instance
- min_pack_optimize(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, scminmap : core::pack::scmin::SCMinMinimizerMap, mingraph : core::scoring::MinimizationGraph, atc : core::pack::scmin::AtomTreeCollection, min_options : rosetta.core.optimization.MinimizerOptions, best_state : core::pack::scmin::SidechainStateAssignment) -> NoneType
- min_pack_place_opt_rotamers_on_pose(...) method of builtins.PyCapsule instance
- min_pack_place_opt_rotamers_on_pose(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, atc : core::pack::scmin::AtomTreeCollection, best_state : core::pack::scmin::SidechainStateAssignment, start_score : float) -> NoneType
- min_pack_setup(...) method of builtins.PyCapsule instance
- min_pack_setup(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, cartesian : bool, nonideal : bool, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, scminmap : core::pack::scmin::SCMinMinimizerMap, mingraph : core::scoring::MinimizationGraph, atc : core::pack::scmin::AtomTreeCollection, min_options : rosetta.core.optimization.MinimizerOptions) -> NoneType
- off_rotamer_pack(...) method of builtins.PyCapsule instance
- off_rotamer_pack(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> NoneType
Interface to a version of the packer that uses very little memory
and simultaneously is able to go off rotamer and explore more of sidechain
conformation space. Quite a bit faster than the min-packer.
- off_rotamer_pack_optimize(...) method of builtins.PyCapsule instance
- off_rotamer_pack_optimize(rotsets : core::pack::rotamer_set::ContinuousRotamerSets, atc : core::pack::scmin::AtomTreeCollection, ig : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, best_state : core::pack::scmin::SidechainStateAssignment) -> NoneType
- off_rotamer_pack_setup(...) method of builtins.PyCapsule instance
- off_rotamer_pack_setup(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, rotsets : core::pack::rotamer_set::ContinuousRotamerSets, atc : core::pack::scmin::AtomTreeCollection, ig : rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> NoneType
- off_rotamer_pack_update_pose(...) method of builtins.PyCapsule instance
- off_rotamer_pack_update_pose(pose : rosetta.core.pose.Pose, rotsets : core::pack::rotamer_set::ContinuousRotamerSets, atc : core::pack::scmin::AtomTreeCollection, best_state : core::pack::scmin::SidechainStateAssignment) -> NoneType
- optimizeH(...) method of builtins.PyCapsule instance
- optimizeH(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
This function will optimize the placement of all movable
hydrogen atoms. This includes the hydroxyl hydrogens as well as
the HIS protonation state. If the -flip_HNQ flag is on the command
line, then it will also consider the flip states of histadine,
asparagine and glutamine, (nearly) as described by Word et al. 1999.
- optimize_H_and_notify(...) method of builtins.PyCapsule instance
- optimize_H_and_notify(pose : rosetta.core.pose.Pose, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType
Call optimizeH and tell the user what chi angles have changed
- pack_missing_sidechains(...) method of builtins.PyCapsule instance
- pack_missing_sidechains(pose : rosetta.core.pose.Pose, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType
This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask)
- pack_rotamers(...) method of builtins.PyCapsule instance
- pack_rotamers(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> NoneType
- pack_rotamers_loop(...) method of builtins.PyCapsule instance
- pack_rotamers_loop(*args, **kwargs)
Overloaded function.
1. pack_rotamers_loop(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, nloop : int, results : rosetta.utility.vector1_std_pair_double_std_string_t) -> NoneType
2. pack_rotamers_loop(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, nloop : int, results : rosetta.utility.vector1_std_pair_double_std_string_t, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> NoneType
3. pack_rotamers_loop(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, nloop : int) -> NoneType
- pack_rotamers_run(...) method of builtins.PyCapsule instance
- pack_rotamers_run(*args, **kwargs)
Overloaded function.
1. pack_rotamers_run(pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> float
Run simulated annealing, return the energy of the best rotamer assignment
found, and place the best rotamers onto the input pose.
2. pack_rotamers_run(pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig : rosetta.core.pack.interaction_graph.AnnealableGraphBase, rot_to_pack : rosetta.utility.vector0_int) -> float
Run simulated annealing, return the energy of the best rotamer assignment
found, and place the best rotamers onto the input pose.
3. pack_rotamers_run(pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig : rosetta.core.pack.interaction_graph.AnnealableGraphBase, rot_to_pack : rosetta.utility.vector0_int, bestrotamer_at_seqpos : ObjexxFCL::FArray1D<int>, bestenergy : float) -> NoneType
Run simulated annealing and return the best rotamer assignment
found. This function does not modify the input pose.
- pack_rotamers_setup(...) method of builtins.PyCapsule instance
- pack_rotamers_setup(*args, **kwargs)
Overloaded function.
1. pack_rotamers_setup(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, ig : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> NoneType
2. pack_rotamers_setup(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase
- pack_scorefxn_pose_handshake(...) method of builtins.PyCapsule instance
- pack_scorefxn_pose_handshake(pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- reinitialize_mingraph_neighborhood_for_residue(...) method of builtins.PyCapsule instance
- reinitialize_mingraph_neighborhood_for_residue(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, bgres : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, scminmap : core::pack::scmin::SCMinMinimizerMap, rsd : rosetta.core.conformation.Residue, mingraph : core::scoring::MinimizationGraph) -> NoneType
- repackable_residues(...) method of builtins.PyCapsule instance
- repackable_residues(the_task : rosetta.core.pack.task.PackerTask) -> rosetta.utility.vector1_unsigned_long
- residue_rotamer_recovery(...) method of builtins.PyCapsule instance
- residue_rotamer_recovery(*args, **kwargs)
Overloaded function.
1. residue_rotamer_recovery(pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose) -> float
Percentage of residues which have same rotamers
2. residue_rotamer_recovery(pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, difference : float) -> float
Percentage of residues which have same rotamers
- rotamer_recovery(...) method of builtins.PyCapsule instance
- rotamer_recovery(*args, **kwargs)
Overloaded function.
1. rotamer_recovery(pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose) -> float
Percentage of rotamers recovered
2. rotamer_recovery(pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, difference : float) -> float
Percentage of rotamers recovered
- rotamer_trials(...) method of builtins.PyCapsule instance
- rotamer_trials(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, input_task : rosetta.core.pack.task.PackerTask) -> NoneType
- symmetric_rotamer_trials(...) method of builtins.PyCapsule instance
- symmetric_rotamer_trials(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, input_task : rosetta.core.pack.task.PackerTask) -> NoneType
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