def test():
acl = Egor.from_pdbfile(
pdbfile='output/PAU-WEI-b9b-8_NIT2/pre_PAU-WEI-b9b-8_NIT2.pdb',
params_file='output/PAU-WEI-b9b-8_NIT2/PAU-WEI-b9b-8_NIT2.params',
constraint_file='cysBound.noCY.cst')
acl.coordinate_constraint = 100
print('initial')
print(acl.ligand_score())
print(acl.ligand_residue) # AtomPair SG 145A HE2 41A HARMONIC 1.8 0.2
print(acl.key_residues)
r = acl.pose.pdb_info().pdb2pose(res=41, chain='A')
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
MutateResidue(target=r, new_res='HIS_D').apply(acl.pose)
MutateResidue(target=r, new_res='HIS').apply(acl.pose)
pymover = pyrosetta.PyMOLMover()
pymover.pymol_name(f'initial')
native = acl.pose.clone()
pymover.apply(native)
acl.pose = native.clone()
acl.minimise(10)
pymover.pymol_name(f'relaxed')
pymover.apply(acl.pose)
print('cartesian relaxed')
print(acl.ligand_score())
acl.pose.dump_pdb('egor_test.pdb')
def __init__(
self,
pose:
object = None, # pyrosetta.rosetta.core.pose.Pose, Pose of starting structure
score:
object = None, # pyrosetta.ScoreFunction, # scorefunction from pyrosetta
seq_mover:
object = None, # pyrosetta.rosetta.protocols.moves.SequenceMover, # sequence of moves between MC evaluations
n_steps: int = 1000000,
kT: float = 1,
output: bool = True,
out_freq: int = 500,
):
super().__init__()
# initialize input values
self.pose = pose
self._score = score
self.seq_mover = seq_mover
self._kT = kT
self.n_steps = n_steps
self._output = output
self._out_freq = out_freq
if self._output is False:
self._out_freq = n_steps
# Build MC Object
self.mc = pyrosetta.MonteCarlo(self.pose, self._score, self._kT)
self.mc_trial = pyrosetta.TrialMover(self.seq_mover, self.mc)
if self._output:
self.pymol = pyrosetta.PyMOLMover()
print("Initial Energy :", self.get_energy())
def test_CGSmallAngleMover():
pymol = pyrosetta.PyMOLMover()
pose = pyrosetta.pose_from_sequence(
'X[CG11x3:CGLower]X[CG11x3]X[CG11x3][CG11x3:CGUpper]')
conf = pose.conformation()
small_mover = cg_pyrosetta.CG_movers.CGSmallAngleMover(pose)
# print(small_mover.bond_angles)
assert len(small_mover.bond_angles) != 0
pymol.apply(pose)
for angle in small_mover.bond_angles:
print("Changing Angle:", angle[0], angle[1], angle[2])
old_angle = conf.bond_angle(angle[0], angle[1], angle[2])
conf.set_bond_angle(angle[0], angle[1], angle[2],
old_angle + 10 * np.pi / 180)
pymol.apply(pose)
assert conf.bond_angle(angle[0], angle[1],
angle[2]) == pytest.approx(old_angle +
10 * np.pi / 180)
#!/usr/bin/env python
# :noTabs=true:
from __future__ import print_function
import rosetta, pyrosetta
pyrosetta.init(
extra_options="-constant_seed"
) # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT IN PRODUCTION RUNS!!!!!
import os
os.chdir('.test.output')
pose = pyrosetta.pose_from_sequence('EVAAAVAT')
pymol = pyrosetta.PyMOLMover()
pymol.apply(pose)
scorefxn = pyrosetta.get_fa_scorefxn(
) # rosetta.create_score_function('standard')
scorefxn(pose)
pymol.send_energy(pose)
#pymol.send_energy(pose, label=True) DEPRECATED: needed to be ported to C++ version
#pymol.send_colors(pose, {}, default_color="orange")
pymol.send_colors(pose,
rosetta.std.map_int_int(),
default_color=rosetta.protocols.moves.XC_orange)
while offset < 3:
phi, psi, omega, description = fragment[offset]
frag_description += description + "\n"
pose.set_phi(position + offset, phi)
pose.set_psi(position + offset, psi)
pose.set_omega(position + offset, omega)
offset += 1
return frag_description
seq = 'MIKVTVTNSFFEVTGHAPDKTLCASVSLLTQHVANFLKAEKKAKIKKESGYLKVKFEELENCEVKVLAAMVRSLKELEQKFPSQIRVEVIDNGS'
three_mer_file = '../Projects/homework/homework_folding/structure_prediction/1S12/1S12.200.3mers'
nine_mer_file = '../Projects/homework/homework_folding/structure_prediction/1S12/1S12.200.9mers'
fragments = angles_from_file(three_mer_file)
pose = pyrosetta.pose_from_sequence(seq)
pmm = pyrosetta.PyMOLMover()
pmm.apply(pose)
accepted = 0
rejected = 0
scorefxn = pyrosetta.teaching.get_fa_scorefxn()
score = scorefxn(pose)
best_score = score
best_pose = pyrosetta.pose_from_sequence(seq)
best_pose.assign(pose)
new_pose = pyrosetta.pose_from_sequence(seq)
frag_mover = fragment_mover_init(frag_file=three_mer_file, frag_length=3)
def __init__(self,
sequence,
BBB_angle=120,
BBBB_dihe=180,
file_name='outputs/traj.pdb',
energy_graph_output=False):
"""
folding object used for easily implementing different
movers into a single folding algorithm.
Arguments
---------
sequence : str
Sequence of CG residues
BBB_angle : float
Desired angle of all B-B-B angles. Generalizes to all backbone models (not working)
BBBB_angle : float
Desired dihedral of all B-B-B-B torsion angles. Generalizes to all backbone models (not working)
"""
# Build CG model and set desired initial angles
self.pose = pyrosetta.pose_from_sequence(sequence, auto_termini=False)
self.energy_graph_output = energy_graph_output
# self.pose = self.set_BBB_angles(self.pose, BBB_angle)
# self.pose = self.set_BBBB_dihe(self.pose, BBBB_dihe)
# PyMOL mover, if wanting to visualize
self.pymol = pyrosetta.PyMOLMover()
self.pymol.apply(self.pose)
# randomizer = CG_movers.randomizeBackBone(self.pose)
# randomizer.apply(self.pose)
self.pymol.apply(self.pose)
# Building PDBTrajWriter object, used for writing multiple structures
# to a single file
self.PDB_writer = pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder(
)
# self.PDB_writer.apply(self.pose) # write initial structure
self.PDB_writer.file_name('outputs/traj.pdb')
self.PDB_writer.stride(100)
# Define scorefunction terms
self.scorefxn = pyrosetta.ScoreFunction()
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_atr,
1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_rep,
1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_bend, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_rep, 1) # segfaults beware!
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_atr, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_rep, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_atr, 1)
# Build standard CG 1-1 movers
self.small = CG_movers.CGSmallMover(self.pose)
# self.shear = CG_movers.CGShearMover(self.pose)
self.small_angle = CG_movers.CGSmallAngleMover(self.pose)
# Build minimization movers
self.mini = pyrosetta.rosetta.protocols.minimization_packing.MinMover()
self.mini.min_type('lbfgs_armijo_nonmonotone')
self.movemap = pyrosetta.MoveMap()
self.mini.score_function(self.scorefxn)
# for atom in self.small_angle.bb_atoms:
# self.movemap.set(pyrosetta.rosetta.core.id.DOF_ID(atom , pyrosetta.rosetta.core.id.THETA), True)
self.movemap.set_bb_true_range(1, self.pose.size())
self.mini.movemap(self.movemap)
# Build MC object + Trial Mover (empty for now)
self.mc = pyrosetta.MonteCarlo(self.pose, self.scorefxn, 1)
self.trial_mc = pyrosetta.TrialMover()
# Building variable to store various folding algorithms
self.folding_protocols = {}
# Adding a default mover
self.build_fold_alg('default')
self.add_folding_move('default', pyrosetta.RepeatMover(self.small, 10))
# self.add_folding_move('default', pyrosetta.RepeatMover(self.shear, 10))
self.add_folding_move('default', pyrosetta.RepeatMover(self.mini, 10))