def mol_to_standardised_mol(mol, name=None):
"""Standardise mol(s)."""
if name is None:
try:
name = mol.GetProp("_Name")
except:
name = repr(mol)
if isinstance(mol, PropertyMol):
mol_type = PropertyMol
mol = rdkit.Chem.Mol(mol)
else:
mol_type = rdkit.Chem.Mol
try:
from standardiser import standardise
from standardiser.utils import StandardiseException
except ImportError:
logging.warning(
"standardiser module unavailable. Using unstandardised mol.")
return mol
logging.debug("Standardising {}".format(name))
try:
std_mol = standardise.apply(mol)
try:
std_mol.SetProp("_Name", mol.GetProp("_Name"))
except:
pass
return std_mol
except StandardiseException:
logging.error(("Standardisation of {} failed. Using unstandardised "
"mol.".format(name)),
exc_info=True)
return mol_type(mol)
def main():
########################################################################
#
# Program Parameters...
#
script_name = os.path.splitext(os.path.basename(sys.argv[0]))[0]
######
# Options and arguments...
argparser = argparse.ArgumentParser(description="Standardise compounds")
argparser.add_argument("-V", "--verbose", action="store_true", help="enable verbose logging")
argparser.add_argument("-r", "--output_rules_applied", action="store_true", help="enable output of rules applied")
argparser.add_argument("infile", help="Input file (SDF or SMILES)")
config = argparser.parse_args()
######
# Initialisation...
logging.basicConfig(level=logging.DEBUG if config.verbose else logging.INFO, format="[%(asctime)s %(levelname)-8s] %(message)s", datefmt="%Y/%b/%d %H:%M:%S")
########################################################################
# Initialise...
error_names = errors.keys()
counts = dict((name, 0) for name in error_names + ["read", "standardised"]) # python2.6-compatible
# Input type...
input_type = os.path.splitext(config.infile)[1] # sdf or smi
logging.info("Input type = '{in_type}'".format(in_type=input_type))
if input_type == ".sdf": # Read/write SDF...
infile = SDF.readFile(open(config.infile))
outfile = open("standardised.sdf", "w")
errfile = open("errors.sdf", "w")
for original in infile:
counts["read"] += 1
logging.info(">>> Starting mol '{name}'...".format(name=original.name))
ok = True
try:
if config.output_rules_applied:
rules_applied = []
parent = standardise.apply(original.molblock, output_rules_applied=rules_applied)
else:
parent = standardise.apply(original.molblock)
except standardise.StandardiseException as err:
logging.warn(">>> {error} for '{name}'".format(error=errors[err.name], name=original.name))
counts[err.name] += 1
errfile.write("{mol}> <n>\n{nread}\n\n<error>\n{error}\n\n$$$$\n".format(mol=original.molblock, nread=counts["read"], error=errors[err.name]))
ok = False
if ok:
logging.info("Mol '{name}' OK".format(name=original.name))
counts["standardised"] += 1
if config.output_rules_applied:
outfile.write("{mol}> <n>\n{nread}\n\n<rules_applied>\n{rules}\n\n$$$$\n".format(mol=parent, nread=counts["read"], rules=','.join(str(x) for x in rules_applied)))
else:
outfile.write("{mol}> <n>\n{nread}\n\n$$$$\n".format(mol=parent, nread=counts["read"]))
if counts["read"] % 100 == 0: logging.info("...done: {read} read, {standardised} OK...".format(**counts))
else: # Read/write (tab-seperated) SMILES + name...
infile = csv.reader(open(config.infile), delimiter="\t")
outfile = csv.writer(open("standardised.smi", "w"), delimiter="\t")
errfile = csv.writer(open("errors.smi", "w"), delimiter="\t")
for original in infile:
counts["read"] += 1
smiles, name = original
logging.info(">>> Starting mol '{name}'...".format(name=name))
ok = True
try:
if config.output_rules_applied:
rules_applied = []
parent = standardise.apply(smiles, output_rules_applied=rules_applied)
else:
parent = standardise.apply(smiles)
except standardise.StandardiseException as err:
logging.warn(">>> {error} for mol '{name}'".format(error=errors[err.name], name=name))
counts[err.name] += 1
errfile.writerow(original + [err.name])
ok = False
if ok:
logging.info("Mol '{name}' OK".format(name=name))
counts["standardised"] += 1
if config.output_rules_applied:
outfile.writerow([parent, name, smiles, ','.join(str(x) for x in rules_applied)])
else:
outfile.writerow([parent, name])
if counts["read"] % 100 == 0: logging.info("...done: {read} read, {standardised} OK...".format(**counts))
logging.info("Finished: {read} read, {standardised} OK in total.".format(**counts))
logging.info("Counts: " + json.dumps(counts, indent=4))