def get_relaxer_mover(pose,
score_function=DEFAULT.score_function,
no_constraints=DEFAULT.no_constraints,
c_weight=DEFAULT.c_weight):
"""
TO DO
"""
if score_function == "auto":
try:
score_function = get_fa_scorefxn()
except:
import pyrosetta
init()
score_function = get_fa_scorefxn()
else:
from pyrosetta.rosetta.core.scoring import ScoreFunction
assert type(score_function) == ScoreFunction, \
"Score function for relaxer mover must be of type ScoreFunction."
if no_constraints == False:
coordinates_constraint = CoordinateConstraintGenerator()
constraints = AddConstraints()
constraints.add_generator(coordinates_constraint)
constraints.apply(pose)
activate_constraints(score_function, c_weight)
task_factory = standard_task_factory()
task_factory.push_back(ExtraRotamers(0, 2, 1))
task_factory.push_back(RestrictToRepacking())
task_factory.push_back(IncludeCurrent())
fast_relax = FastRelax()
fast_relax.set_scorefxn(score_function)
fast_relax.set_task_factory(task_factory)
return fast_relax
def coord_constrain_peptide(pose, selection=ChainSelector('B')):
""" Applies backbone coordinate constraints to a selection of a pose """
cg = CoordinateConstraintGenerator()
if selection:
cg.set_residue_selector(selection)
ac = AddConstraints()
ac.add_generator(cg)
ac.apply(pose)
return pose
def coord_constrain_pose(pose):
"""
Applies coordinate constraints if needed to selected residues
"""
print_out("Applying Constraints")
ccg = CoordinateConstraintGenerator()
ccg.set_bounded_width(0.2)
ccg.set_bounded(True)
ccg.set_ca_only(True)
ccg.set_sd(0.5)
ac = AddConstraints()
ac.add_generator(ccg)
ac.apply(pose)
return pose
def apply_constraints(pose):
"""
Applies enzdes constraints from the input CST file to a pose
Also applies coordinate constraints to the original substrate peptide
which is assumed correct from the PDB
"""
# Enzdes constraints
cstm = AddOrRemoveMatchCsts()
cstm.set_cst_action(ADD_NEW)
cstm.apply(pose)
# Coordinate constraints
cg = CoordinateConstraintGenerator()
cs = ResidueIndexSelector('213-216')
cg.set_residue_selector(cs)
ac = AddConstraints()
ac.add_generator(cg)
ac.apply(pose)
return
def apply_constraints(pose):
"""
Applies enzdes constraints form the input CST file to a pose
Also applies coordinate constraints to the substrate peptide, assumed to
be chain B
"""
# Enzdes constraints
cstm = AddOrRemoveMatchCsts()
cstm.set_cst_action(ADD_NEW)
cstm.apply(pose)
# Coordinate constraints
cg = CoordinateConstraintGenerator()
cs = ChainSelector('B')
cg.set_residue_selector(cs)
ac = AddConstraints()
ac.add_generator(cg)
ac.apply(pose)
return
def apply_constraints(pose):
"""
Applies enzdes constraints form the input CST file to a pose
Also applies coordinate constraints to the substrate peptide, assumed to
be chain B
"""
# Enzdes constraints
cstm = AddOrRemoveMatchCsts()
cstm.set_cst_action(ADD_NEW)
cstm.apply(pose)
# Coordinate constraints
cg = CoordinateConstraintGenerator()
ors = OrResidueSelector()
ors.add_residue_selector(ChainSelector('A')) # Constrain main backbone
ors.add_residue_selector(
ResidueIndexSelector('113-115')) # Preserving original peptide
cg.set_residue_selector(ors)
ac = AddConstraints()
ac.add_generator(cg)
ac.apply(pose)
return
def apply_coord_constraints(pose,
sidechains=False,
bounded=True,
selection=None):
"""
Applies backbone coordinate constraints to a selection of a pose Returns
constraied pose.
"""
cg = CoordinateConstraintGenerator()
cg.set_sidechain(sidechains)
if bounded:
cg.set_bounded(True)
cg.set_bounded_width(0.1)
cg.set_sd(0.5)
if selection:
cg.set_residue_selector(selection)
ac = AddConstraints()
ac.add_generator(cg)
ac.apply(pose)
return pose
pdb_info, args.pdb, args.symmetry)
match_indexes = match_substrate_pose_indexes.union(
match_res_pose_indexes)
active_site_positions.update(match_index
for match_index in match_indexes)
if args.substrates:
active_site_positions.update(args.substrates)
# coordinate constraint
if args.reference_pose:
coord_cst_gen = create_coord_cst(
ref_pose=ref_pose
) #, ligand_res_indexes=match_substrate_pose_indexes)
else:
coord_cst_gen = create_coord_cst(
) #ligand_res_indexes=match_substrate_pose_indexes)
add_csts = AddConstraints()
add_csts.add_generator(coord_cst_gen)
add_csts.apply(pose)
# constraint
if args.constraints:
add_fa_constraints_from_cmdline(pose, sfxn)
# enzyme design constraint
if args.enzyme_design_constraints:
enzdes_cst = create_enzdes_cst()
enzdes_cst.apply(pose)
# declare movers
movers = list()
if not args.rmsd:
rmsdm = RMSDMetric(pose)
else:
rmsdm = RMSDMetric(
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)
# Creating symmetry setup
if args.symmetry:
sfsm = SetupForSymmetryMover(args.symmetry)
# Setting up the scorefunction with the desired constraint weights
if args.symmetry:
sf = SymmetricScoreFunction()
sf.add_weights_from_file(args.score_function)
else:
sf = create_score_function(args.score_function)
if args.coord_wt:
sf.set_weight(st.coordinate_constraint, args.coord_wt)
if args.enzdes_wt:
sf.set_weight(st.atom_pair_constraint, args.enzdes_wt)
sf.set_weight(st.angle_constraint, args.enzdes_wt)
sf.set_weight(st.dihedral_constraint, args.enzdes_wt)
# Creating FastRelax protocol with the given score function
fr = FastRelax()
fr.set_scorefxn(sf)
# Packer tasks
tf = standard_task_factory()
tf.push_back(RestrictToRepacking())
tf.push_back(IncludeCurrent())
tf.push_back(ExtraRotamers(0, 1, 1))
tf.push_back(ExtraRotamers(0, 2, 1))
fr.set_task_factory(tf)
# Determining file name
if args.name:
file_name = args.name
else:
file_name = basename(args.pdb_file).replace('.pdb', '').replace('.gz', '')
file_name += '_relaxed'
out_name = join(dir_name, file_name)
# Loading PDB file, applying constraints
pose = pose_from_pdb(args.pdb_file)
ac.apply(pose)
if args.constraints:
enz_cst.apply(pose)
if args.symmetry:
sfsm.apply(pose)
# RMSD metric
rmsdm = RMSDMetric()
rmsdm.set_comparison_pose(pose)
# Running relax set
jd = PyJobDistributor(out_name, args.n_decoys, sf)
while not jd.job_complete:
pp = Pose()
pp.assign(pose)
fr.apply(pp)
rmsdm.apply(pp)
jd.output_decoy(pp)
args = parser.parse_args()
validate_arguments(args)
init()
# Define the starting Pose:
pose = pose_from_pdb(args.input_file)
# Define the Score Function:
score_function = get_fa_scorefxn()
if args.no_constraints == False:
# Create the Generator
coordinates_constraint = CoordinateConstraintGenerator()
# Add the Generate to a new AddConstraints object
constraints = AddConstraints()
constraints.add_generator(coordinates_constraint)
# Apply the defined AddConstraints object to a Pose
constraints.apply(pose)
# Enable all constraint weights on the score function
activate_constraints(score_function, args.c_weight)
# An optinal but recommended Task is to include extra rotamers (away from
# the regular optimums) for both chi1 (ex1) and chi2 (ex2)
task_factory = standard_task_factory()
# It seems that Ex1 is enabled by default.
# Ex. task_factory.push_back(ExtraRotamers(0, 1, 1)) # ex1
task_factory.push_back(ExtraRotamers(0, 2, 1)) # ex2
# FastRelax, by default, blocks 'design' on the regular rotamers. However,
# when adding the ExtraRotamers, new 'designable' rotamers are included
# and considered during the sampling. Therefore, the TaskFactory must
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)