def dockStructure(data):
pos, smiles, ligand_name, pdb_name, force_flipper = data
score, res, ligand = interface_functions.RunDocking_(
smiles,
dock_obj=docker,
pos=pos,
name=ligand_name,
target_name=pdb_name,
force_flipper=force_flipper)
# print(oechem.OEWriteMolToBytes(".smi", ligand))
return score, res, ligand
def worker(df):
struct = "input/"
start_pos = rank * 100
for pos in range(start_pos, 100 + start_pos):
path = "test" + str(pos) + "/"
smiles = df.iloc[pos, 0]
# pipline
comm.send([smiles], dest=0, tag=11)
r = comm.recv(source=0, tag=11)
print("Rank", rank, "should I run docking on", smiles, "?",
"\t my model says", bool(r))
# pipeline
if r:
print("Rank", rank, "running docking...")
score = interface_functions.RunDocking_(smiles, struct, path)
comm.send([smiles, score], dest=0, tag=11)
r = comm.recv(source=0, tag=11)
print("Rank", rank,
"should I run minimize, given the docking score", score, "?",
"\t my model says", bool(r))
# pipeline
if r:
print("Rank", rank, "running param and mini")
interface_functions.ParameterizeOE(path)
mscore = interface_functions.RunMinimization_(path, path)
comm.send([smiles, score, mscore], dest=0, tag=11)
r = comm.recv(source=0, tag=11)
print(
"Rank", rank,
"should I run mmgbsa for 1 ns given a energy minmization result of",
mscore, "?\t my model says", bool(r))
if r:
print("Rank", rank, "running simulation")
escore = interface_functions.RunMMGBSA_(path, path)
print("Rank", rank, "ran simulation and got", escore)
def dock_one_smile(smile, target_oeb_file, license_file, module_dir=None):
import os
import sys
if module_dir is not None:
sys.path.append(module_dir)
os.environ['OE_LICENSE'] = license_file
from openeye import oechem, oedocking
from impress_md import interface_functions
docker, _ = interface_functions.get_receptor(target_oeb_file,
use_hybrid=True,
high_resolution=True)
score, _, _ = interface_functions.RunDocking_(smile,
dock_obj=docker,
pos=0,
name="",
target_name="",
force_flipper=True)
return score
def slave():
docker, receptor = interface_functions.get_receptor(
target_file, use_hybrid=use_hybrid, high_resolution=high_resolution)
comm.send([], dest=0, tag=11)
poss = comm.recv(source=0, tag=MPI.ANY_TAG)
while True:
for (pos, smiles, ligand_name) in poss:
try:
with timeout(seconds=180):
score, res, ligand = interface_functions.RunDocking_(
smiles,
dock_obj=docker,
pos=pos,
name=ligand_name,
target_name=pdb_name,
force_flipper=force_flipper)
if args.v:
print("RANK {}:".format(rank), res, end='')
if ofs and ligand is not None:
oechem.OEWriteMolecule(ofs, ligand)
except TimeoutError:
print("TIMEOUT", smiles, ligand_name)
continue
comm.send([], dest=0, tag=11)
status = MPI.Status()
poss = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
if status.Get_tag() == DIETAG:
break
if ofs is not None:
ofs.close()
comm.Barrier()
itmap = p.imap(dockStructure, data_run)
for (score, res, ligand) in itmap:
if args.v:
print(res, end='')
if ligand is not None:
oechem.OEWriteMolecule(ofs, ligand)
else:
for pos in range(smiles_file.shape[0]):
smiles = smiles_file.iloc[pos, smiles_col]
ligand_name = smiles_file.iloc[pos, name_col]
score, res, ligand = interface_functions.RunDocking_(
smiles,
dock_obj=docker,
pos=pos,
name=ligand_name,
target_name=pdb_name,
force_flipper=force_flipper)
if args.v:
print(res, end='')
if ofs and ligand is not None:
for i, col in enumerate(columns):
value = str(smiles_file.iloc[pos, i]).strip()
if col.lower() != 'smiles' and 'na' not in value.lower(
) and len(value) > 1:
try:
oechem.OESetSDData(ligand, col, value)
except ValueError:
pass
assert ('OE_LICENSE' in os.environ)
smiles_files = pd.read_csv(sys.argv[1], sep=' ', header=None)
target_filoe = sys.argv[2]
start_idx = int(sys.argv[3])
n_smiles = int(sys.argv[4])
dbase_name = 'test'
target_name = 'pl_pro'
docker, receptor = interface_functions.get_receptr(target_filoe)
for pos in range(start_idx, start_idx + n_smiles):
smiles = smiles_files.iloc[pos, 0]
ligand_name = smiles_files.iloc[pos, 1]
score, res = interface_functions.RunDocking_(smiles,
None,
None,
dbase_name,
target_name,
pos=pos,
write=True,
receptor_file=None,
name=ligand_name,
docking_only=True,
dock_obj=docker,
recept=receptor)
print(pos, res, end='')
# ------------------------------------------------------------------------------