def execute(self, args):
"""Run select query, output table."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
filter_from = None
else:
try:
filter_from = set(row.split()[0].strip()
for row in args.inchikeys)
except IndexError:
filter_from = set([])
return
if args.query and (args.property_name
or args.property_operator
or args.property_value):
sys.exit(('Custom SQL queries are mutually exclusive with '
'property filtering.'))
if (args.part or args.of) and not (args.part and args.of):
sys.exit(('If you specify a --part n, you must also specify --of '
'N (e.g. something like --part 1 --of 5).'))
if args.part and args.of:
if args.part > args.of:
sys.exit('--part must be smaller than --of.')
if args.part < 1:
sys.exit('--part must be >=1.')
alpha = string.ascii_uppercase
alpha3 = [''.join([a, b, c]) for a in alpha
for b in alpha
for c in alpha] # AAA to ZZZ
if args.of > len(alpha3):
sys.exit(('MESS.DB does not support subsetting into more than '
'%i parts.' % len(alpha3)))
subsets = [alpha3[i::args.of] for i in xrange(args.of)]
subset = subsets[args.part - 1]
db = MessDB()
cur = db.cursor()
if args.query:
try:
cur.execute(codecs.open(args.query, encoding='utf-8').read())
except sqlite3.OperationalError:
sys.exit("'%s' does not contain valid sql." % args.query)
except IOError:
try:
cur.execute(args.query)
except sqlite3.OperationalError:
sys.exit(("'%s' is neither valid sql nor a path "
'to a file containing valid sql.') % args.query)
elif (args.property_name and args.property_operator and
args.property_value is not None):
query, values = self.property_query(args.property_name,
args.property_operator,
args.property_value,
args.path)
cur.execute(query, values)
else:
cur.execute('SELECT inchikey FROM molecule')
# check that sql returns inchikey in first column
if not cur.description[0][0].lower() == 'inchikey':
sys.exit('Query must return inchikey in first column.')
# print table
writer = csv.writer(sys.stdout, delimiter=args.delimiter)
if args.headers:
writer.writerow(list(h[0] for h in cur.description))
for result in cur:
if filter_from is not None and result[0] not in filter_from:
continue
if args.regex_subset and not re.match(args.regex_subset, result[0],
re.IGNORECASE):
continue
if args.part and args.of:
if not any(result[0].startswith(a) for a in subset):
continue
if args.smarts:
matches = 0
query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
inchi = db.execute(query, (result[0],)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
for (smarts_obj,
smarts_str) in Match.smarts_generator(args.smarts):
matches += len(smarts_obj.findall(mol))
if not matches:
continue
writer.writerow(list(xstr(v).decode('utf-8') for v in result))
db.close() # must be closed manually to prevent db locking during pipe
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)
