def execute(self, args):
"""Run import method for every molecule in source."""
m = load_method('import', MessDB())
s = Source(MessDB())
s.setup(args.source)
p = Path(MessDB())
p.setup(m.method_id)
pybel.ob.obErrorLog.StopLogging()
for f in s.files():
if (f.split('.')[-1] == 'sql' or
f.split('.')[-1] == 'txt' or
f.split('.')[-1] == 'bak' or
f[-1] == '~'):
continue
for mol in pybel.readfile(f.split('.')[-1],
os.path.join(s.source_dir, f)):
decorate(mol, UnicodeDecorator)
pybel.ob.obErrorLog.ClearLog()
pybel.ob.obErrorLog.StartLogging()
inchikey = mol.write('inchikey').rstrip()
pybel.ob.obErrorLog.StopLogging()
cansmi = mol.write('can').split()[0]
frag_count = cansmi.count('.') + 1
for f in cansmi.split('.'):
method_args = {}
if (frag_count > 1):
frag = pybel.readstring('can', f)
decorate(frag, UnicodeDecorator)
# neutralize fragments
#if (frag.charge != 0):
# for atom in frag.atoms:
# atom.OBAtom.SetFormalCharge(0)
pybel.ob.obErrorLog.ClearLog()
pybel.ob.obErrorLog.StartLogging()
frag_inchikey = frag.write('inchikey').rstrip()
pybel.ob.obErrorLog.StopLogging()
if not is_inchikey(frag_inchikey):
print("'%s' is not an importable molecule.\n" % f,
file=sys.stderr)
continue
method_args['parent'] = ('from: %s' %
unicode(mol.title,
'utf-8', 'replace'))
method_args['inchikey'] = frag_inchikey
method_args['mol'] = frag
else:
if not is_inchikey(inchikey):
print("'%s' is not an importable molecule.\n" % f,
file=sys.stderr)
continue
method_args['inchikey'] = inchikey
method_args['mol'] = mol
method_args['source'] = s
method_args['path'] = p
method_args['skip_cir'] = args.skip_cir
status = m.execute(method_args)
print('%s: %s' % (method_args['inchikey'], status))
def execute(self, args):
"""Run calculations."""
m = load_method(args.method, MessDB())
p = Path(MessDB())
p.setup(m.method_id, args.parent_path)
pybel.ob.obErrorLog.StopLogging()
method_args = {}
method_args['path'] = p
for row in args.inchikeys:
method_args['inchikey'] = row.split()[0].strip()
if not is_inchikey(method_args['inchikey'], enforce_standard=True):
sys.exit('%s is not a valid InChIKey.' %
method_args['inchikey'])
status = m.execute(method_args)
print('%s: %s' % (method_args['inchikey'], status))