| import pyrosetta |
|
|
| from igfold.utils.general import exists |
|
|
|
|
| def init_pyrosetta(init_string=None, silent=True): |
| if not exists(init_string): |
| init_string = "-mute all -ignore_zero_occupancy false -detect_disulf true -detect_disulf_tolerance 1.5 -check_cdr_chainbreaks false" |
| pyrosetta.init(init_string, silent=silent) |
|
|
|
|
| def get_min_mover( |
| max_iter: int = 1000, |
| sf_name: str = "ref2015_cst", |
| coord_cst_weight: float = 1, |
| dih_cst_weight: float = 1, |
| ) -> pyrosetta.rosetta.protocols.moves.Mover: |
| """ |
| Create full-atom minimization mover |
| """ |
|
|
| sf = pyrosetta.create_score_function(sf_name) |
| sf.set_weight( |
| pyrosetta.rosetta.core.scoring.ScoreType.cart_bonded, |
| 1, |
| ) |
| sf.set_weight( |
| pyrosetta.rosetta.core.scoring.ScoreType.pro_close, |
| 0, |
| ) |
| sf.set_weight( |
| pyrosetta.rosetta.core.scoring.ScoreType.coordinate_constraint, |
| coord_cst_weight, |
| ) |
| sf.set_weight( |
| pyrosetta.rosetta.core.scoring.ScoreType.dihedral_constraint, |
| dih_cst_weight, |
| ) |
|
|
| mmap = pyrosetta.rosetta.core.kinematics.MoveMap() |
| mmap.set_bb(True) |
| mmap.set_chi(False) |
| mmap.set_jump(False) |
| min_mover = pyrosetta.rosetta.protocols.minimization_packing.MinMover( |
| mmap, |
| sf, |
| 'lbfgs_armijo_nonmonotone', |
| 0.0001, |
| True, |
| ) |
| min_mover.max_iter(max_iter) |
| min_mover.cartesian(True) |
|
|
| return min_mover |
|
|
|
|
| def get_fa_relax_mover( |
| max_iter: int = 100) -> pyrosetta.rosetta.protocols.moves.Mover: |
| """ |
| Create full-atom relax mover |
| """ |
|
|
| sf = pyrosetta.create_score_function('ref2015_cst') |
|
|
| mmap = pyrosetta.rosetta.core.kinematics.MoveMap() |
| mmap.set_bb(True) |
| mmap.set_chi(True) |
| mmap.set_jump(True) |
|
|
| relax = pyrosetta.rosetta.protocols.relax.FastRelax() |
| relax.set_scorefxn(sf) |
| relax.max_iter(max_iter) |
| relax.set_movemap(mmap) |
|
|
| return relax |
|
|
|
|
| def get_repack_mover(): |
| tf = pyrosetta.rosetta.core.pack.task.TaskFactory() |
| tf.push_back( |
| pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline()) |
| tf.push_back( |
| pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking()) |
|
|
| packer = pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover( |
| ) |
| packer.task_factory(tf) |
|
|
| return packer |
|
|
|
|
| def refine(out_pdb_file, |
| pdb_string, |
| minimization_iter=100, |
| constrain=True, |
| idealize=False): |
| |
| pose = pyrosetta.rosetta.core.pose.Pose() |
| pyrosetta.rosetta.core.import_pose.pose_from_pdbstring( |
| pose, |
| pdb_string, |
| ) |
|
|
| if constrain: |
| cst_mover = pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover() |
| cst_mover.cst_sidechain(False) |
| cst_mover.apply(pose) |
|
|
| min_mover = get_min_mover( |
| max_iter=minimization_iter, |
| coord_cst_weight=1, |
| dih_cst_weight=0, |
| ) |
| min_mover.apply(pose) |
|
|
| if idealize: |
| idealize_mover = pyrosetta.rosetta.protocols.idealize.IdealizeMover() |
| idealize_mover.apply(pose) |
|
|
| packer = get_repack_mover() |
| packer.apply(pose) |
|
|
| min_mover.apply(pose) |
|
|
| pose.dump_pdb(out_pdb_file) |
