def apply_constraints(pose, cst_file='protease_design/ly104.cst'):
""" Applies the constraints form the input CST file to a pose """
cstm = AddOrRemoveMatchCsts()
cstm.set_cst_action(ADD_NEW)
cstm.cstfile(cst_file)
cstm.apply(pose)
return pose
def apply_enzdes_constraints(pose, cst_file):
"""
Applies the constraints form the input CST file to a pose. Returns
constraied pose.
"""
from pyrosetta.rosetta.protocols.enzdes import ADD_NEW, AddOrRemoveMatchCsts
cstm = AddOrRemoveMatchCsts()
cstm.set_cst_action(ADD_NEW)
cstm.cstfile(cst_file)
cstm.apply(pose)
return pose
def main(args):
# Destination folder for PDB files
if args.out_dir:
dir_name = args.out_dir
if not isdir(dir_name):
makedirs(dir_name)
else:
dir_name = ""
# Creating coordinate constraints for the entire molecule
cg = CoordinateConstraintGenerator()
ac = AddConstraints()
ac.add_generator(cg)
# Create enzdes constraints
if args.constraints:
enz_cst = AddOrRemoveMatchCsts()
enz_cst.set_cst_action(ADD_NEW)
''' Declare the score function. '''
if args.symmetry: # Declare symmetric score functions
score_function = SymmetricScoreFunction()
if args.repulsive_type == 'hard':
if args.membrane:
score_function.add_weights_from_file('franklin2019')
else:
score_function.add_weights_from_file('ref2015')
elif args.repulsive_type == 'soft':
if args.membrane: # Set up a soft-rep version of franklin2019 manually
score_function.add_weights_from_file('ref2015_soft')
score_function.set_weight(ScoreType.fa_water_to_bilayer, 1.0)
else:
score_function.add_weights_from_file('ref2015_soft')
else: # Declare ordinary score functions
if args.repulsive_type == 'hard':
if args.membrane:
score_function = create_score_function('franklin2019')
else:
score_function = create_score_function('ref2015')
elif args.repulsive_type == 'soft':
if args.membrane: # Set up a soft-rep version of franklin2019 manually
score_function = create_score_function('ref2015_soft')
score_function.set_weight(ScoreType.fa_water_to_bilayer, 1.0)
else:
score_function = create_score_function('ref2015_soft')
if args.coord_wt:
score_function.set_weight(ScoreType.coordinate_constraint,
args.coord_wt)
if args.enzdes_wt:
score_function.set_weight(ScoreType.atom_pair_constraint,
args.enzdes_wt)
score_function.set_weight(ScoreType.angle_constraint, args.enzdes_wt)
score_function.set_weight(ScoreType.dihedral_constraint,
args.enzdes_wt)
# Loading PDB file
pose = pose_from_pdb(args.pdb_file)
if args.symmetry: # Applying symmetry if specified
sfsm = SetupForSymmetryMover(args.symmetry)
sfsm.apply(pose)
if args.membrane: # Set up membrane for membrane protein
add_memb = SymmetricAddMembraneMover(args.span_file)
add_memb.apply(pose)
else:
if args.membrane: # Set up membrane for membrane protein
add_memb = AddMembraneMover(args.span_file)
add_memb.apply(pose)
# Creating FastRelax protocol with the given score function
fr = FastRelax()
fr.set_scorefxn(score_function)
# Packer tasks
tf = standard_task_factory()
tf.push_back(IncludeCurrent())
tf.push_back(ExtraRotamers(0, 1, 1))
tf.push_back(ExtraRotamers(0, 2, 1))
protein_selector = ResiduePropertySelector(ResidueProperty.PROTEIN)
repack = RestrictToRepackingRLT()
tf.push_back(OperateOnResidueSubset(repack, protein_selector))
prevent = PreventRepackingRLT()
tf.push_back(OperateOnResidueSubset(prevent, protein_selector, True))
fr.set_task_factory(tf)
move_map = MoveMap()
if args.repulsive_type == 'hard':
move_map.set_bb(True)
elif args.repulsive_type == 'soft':
''' When using the soft-rep score function, backbone should be fixed. '''
move_map.set_bb(False)
protein_res_true_vector = protein_selector.apply(pose)
move_map.set_chi(protein_res_true_vector)
fr.set_movemap(move_map)
# Determining file name
if args.name:
file_name = args.name
else:
file_name = basename(args.pdb_file).replace('.pdb', '_relaxed')
out_name = join(dir_name, file_name)
# Applying constraints
ac.apply(pose)
if args.constraints:
enz_cst.apply(pose)
# RMSD metric
rmsdm = RMSDMetric()
rmsdm.set_comparison_pose(pose)
print(tf.create_task_and_apply_taskoperations(pose))
# Running relax set
jd = PyJobDistributor(out_name, args.n_decoys, score_function)
while not jd.job_complete:
pp = Pose()
pp.assign(pose)
fr.apply(pp)
rmsdm.apply(pp)
jd.output_decoy(pp)