def dock_one(enum_tuple):
""" Docks one smiles. Input = tuple from enumerate iterator"""
identifier, smiles = enum_tuple
return dock(smiles,
identifier,
PYTHONSH,
VINA,
parallel=False,
exhaustiveness=16)
def one_slurm(list_smiles,
server,
unique_id,
name,
target='drd3',
parallel=True,
exhaustiveness=16,
mean=False,
load=False):
"""
:param list_smiles:
:param server:
:param unique_id:
:param name:
:param parallel:
:param exhaustiveness:
:param mean:
:param load:
:return:
"""
pythonsh, vina = set_path(server)
dirname = os.path.join(script_dir, 'results', name,
'docking_small_results')
dump_path = os.path.join(dirname, f"{unique_id}.csv")
header = ['smile', 'score']
with open(dump_path, 'w', newline='') as csvfile:
csv.writer(csvfile).writerow(header)
for smile in list_smiles:
score_smile = dock(smile,
target='drd3',
unique_id=unique_id,
parallel=parallel,
exhaustiveness=exhaustiveness,
mean=mean,
pythonsh=pythonsh,
vina=vina,
load=load)
# score_smile = 0
with open(dump_path, 'a', newline='') as csvfile:
list_to_write = [smile, score_smile]
csv.writer(csvfile).writerow(list_to_write)
def one_dock(smile,
server,
parallel=False,
exhaustiveness=16,
mean=False,
load=False,
target='drd3'):
pythonsh, vina = set_path(server)
score_smile = dock(smile,
unique_id=smile,
parallel=parallel,
exhaustiveness=exhaustiveness,
mean=mean,
pythonsh=pythonsh,
vina=vina,
load=load,
target=target)
return score_smile
"-i",
"--input",
default='O=CC=C(C1C2=NC=C(C=NC3=CC=CC=C3N=C2)C=C1F)NC=C',
help="Smiles to dock")
parser.add_argument('--target',
type=str,
default='drd3',
help='target to dock')
parser.add_argument(
"-s",
"--server",
default='pasteur',
help="Server to run the docking on, for path and configs.")
parser.add_argument("-e",
"--ex",
default=16,
help="exhaustiveness parameter for vina")
args, _ = parser.parse_known_args()
PYTHONSH, VINA = set_path(args.server)
sc = dock(smile=args.input,
target=args.target,
unique_id=1,
pythonsh=PYTHONSH,
vina=VINA,
parallel=True,
exhaustiveness=args.ex)
print('Score :', sc)