def execute(self, args):
"""Match molecules to SMARTS patterns."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
sys.exit('No input specified.')
if not (args.cir or args.fingerprint or args.spectrophore):
sys.exit('You did not request any annotations.')
if args.spectrophore:
if args.path is None:
sys.exit(('Spectrophore calculation requires 3D geometry. '
'You must specify a 3D geometry with --path.'))
else:
path = MethodPath()
path.set_path(args.path)
method_dir = path.get_path_directory()
sp_args = {'normalization': args.spectrophore_normalization,
'accuracy': args.spectrophore_accuracy,
'stereo': args.spectrophore_stereospecificity,
'resolution': args.spectrophore_resolution}
self.db = MessDB()
inchi_select_query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
fp_select_query = ('SELECT fingerprint FROM molecule_fingerprint '
'WHERE inchikey = ? '
'AND name = ? '
'AND settings = ? '
'AND method_path_id = ?')
fp_insert_query = ('INSERT INTO molecule_fingerprint '
'(inchikey, name, settings, '
'fingerprint, method_path_id) '
'VALUES (?, ?, ?, ?, ?)')
for row in args.inchikeys:
self.inchikey = row.split()[0].strip()
if args.cir:
self.update_iupac(self.inchikey)
self.update_synonyms(self.inchikey)
if args.fingerprint:
inchi = self.db.execute(inchi_select_query,
(self.inchikey,)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
canonical = pybel.ob.OBOp.FindType(b'canonical')
canonical.Do(mol.OBMol)
fp = Match.calculate_fingerprint(mol, args.fingerprint)
try:
db_fp = self.db.execute(fp_select_query,
(self.inchikey,
args.fingerprint,
'',
'')).fetchone()[0]
if not str(fp) == db_fp:
self.log_console.warning(('new %s fingerprint '
'for %s did not match '
'fingerprint in db, '
'db not updated'),
args.fingerprint,
self.inchikey)
except TypeError:
self.db.execute(fp_insert_query, (self.inchikey,
args.fingerprint,
'',
str(fp),
''))
self.log_all.info('%s fingerprint for %s added to db',
args.fingerprint, self.inchikey)
if args.spectrophore:
xyz_file = os.path.join(get_inchikey_dir(self.inchikey),
method_dir,
'%s.xyz' % self.inchikey)
mol = pybel.readfile('xyz', xyz_file).next()
sp = Match.calculate_spectrophore(mol, sp_args)
try:
db_sp = self.db.execute(fp_select_query,
(self.inchikey,
'Spectrophore',
json.dumps(sp_args,
sort_keys=True),
args.path)).fetchone()[0]
if not str(sp) == db_sp:
self.log_console.warning(('new Spectrophore '
'fingerprint for '
'%s did not match '
'fingerprint in db, '
'db not updated'),
self.inchikey)
except TypeError:
json_sp_args = json.dumps(sp_args, sort_keys=True)
self.db.execute(fp_insert_query, (self.inchikey,
'Spectrophore',
json_sp_args,
str(sp),
args.path))
self.log_all.info(('Spectrophore fingerprint for %s '
'with parameters %s and '
'geometry from path %i '
'added to db'),
self.inchikey, json_sp_args, args.path)
