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 check_dir_structure(self):
"""Check that the structure of the molecules dir is consistent."""
moldir = os.path.join(os.path.dirname(__file__), '../molecules')
for l in os.listdir(moldir):
lp = os.path.join(moldir, l)
if not os.path.isdir(lp):
print('Unexpected file in molecules dir: %s' % l)
continue
if not len(l) == 1:
print('Unexpected dir in molecules dir: %s' % l)
continue
for ll in os.listdir(lp):
llp = os.path.join(moldir, l, ll)
if not os.path.isdir(llp):
print('Unexpected file in molecules dir: %s/%s' % (l, ll))
continue
if not (len(ll) == 2 and ll.isalpha()):
print('Unexpected dir in molecules dir: %s/%s' % (l, ll))
continue
for lll in os.listdir(llp):
lllp = os.path.join(moldir, l, ll, lll)
if not os.path.isdir(lllp):
print('Unexpected file in molecules dir: %s/%s/%s' %
(l, ll, lll))
continue
if not is_inchikey(l + ll + lll, enforce_standard=True):
print('Unexpected dir in molecules dir: %s/%s/%s' %
(l, ll, lll))
continue
self.check_molecule_dir(l + ll + lll, lllp)
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))
def execute(self, args):
"""Run self checks."""
db = MessDB()
self.c = db.cursor()
self.c.execute('SELECT inchikey FROM molecule')
self.db_inchikeys = set()
# check that inchikeys are all valid
for r in self.c:
if is_inchikey(r.inchikey, enforce_standard=True):
self.db_inchikeys.add(r.inchikey)
else:
print('%s is not a valid standard InChiKey!' % r.inchikey)
self.check_dir_structure()
self.check_db_structure()
self.check_db_dir_inchikey_concordance()
self.summary()