def check_dependencies():
"""Make sure pybel is availiable, as basically every tool uses it."""
emsg = "MESS.DB requires Open Babel (and its python module, pybel) " "version >=2.3.0."
try:
import pybel
decorate(pybel, UnicodeDecorator)
version = pybel.ob.OBReleaseVersion()
if LooseVersion(version) < LooseVersion("2.3.0"):
sys.exit("%s Current version is %s." % (emsg, version))
except (AttributeError, ImportError):
sys.exit(emsg)
def check(self):
inchikey_dir = get_inchikey_dir(self.inchikey)
try:
mol = pybel.readfile('xyz',
os.path.join(inchikey_dir,
self.method_dir,
'%s.xyz' % self.inchikey)).next()
except IOError:
return False
decorate(mol, UnicodeDecorator)
if not mol.write('inchikey').rstrip() == self.inchikey:
self.log_console.warning('inconsistent 3D geometry in %s (%s)',
self.inchikey, self.method_dir)
return False
return True
def execute(self, args):
"""Run import method for every molecule in source."""
source = Source()
source.setup(args.source)
self.log_console.info('reading molecules')
molecules = OrderedDict() # not required, but useful for debugging
# crashing imports
threedee = False
pybel.ob.obErrorLog.SetOutputLevel(-1)
for source_file in source.files():
for mol in pybel.readfile(source_file.split('.')[-1],
os.path.join(source.source_dir,
source_file)):
if not threedee and mol.dim == 3:
threedee = True
try:
decorate(mol, UnicodeDecorator)
except IndexError:
self.log_console.error('Unexpected error importing %s.',
mol.title)
continue
inchikey = mol.write('inchikey').rstrip()
if not is_inchikey(inchikey):
self.log_console.info(
("'%s' is not an importable molecule."), mol.title)
continue
molecules[inchikey] = (mol, source)
if not args.skip_fragments:
cansmi = mol.write('can').split()[0]
if cansmi.count('.') > 0:
for fragment in cansmi.split('.'):
fragmol = pybel.readstring('can', fragment)
decorate(fragmol, UnicodeDecorator)
inchikey = fragmol.write('inchikey').rstrip()
if not is_inchikey(inchikey):
self.log_console.info(
("'%s' fragment in %s "
"is not an importable molecule."),
fragment, mol.title)
else:
fragmol.title = mol.title
molecules[inchikey] = (fragmol, source)
import0d = Import0D()
import0d.setup()
if threedee:
import3d = Import3D()
import3d.shortdesc = source.dirname
import3d.setup()
self.log_console.info('setting up molecule dirs')
queries = {}
for inchikey, (mol, source) in molecules.iteritems():
for query, values in import0d.map(mol, source):
try:
queries[query].append(values)
except KeyError:
queries[query] = [values]
if mol.dim == 3:
import3d.map(mol, source)
self.log_console.info('loading simple properties')
for query, values in queries.iteritems():
import0d.reduce(query, values)
