def map(self, mol, source):
"""Import molecule into MESS.DB."""
# setup local variables
self.inchikey = mol.write('inchikey').rstrip()
inchikey_dir = get_inchikey_dir(self.inchikey)
inchikey_basename = os.path.join(inchikey_dir, self.inchikey)
identifier = unicode(mol.title, 'utf-8', 'replace')
# setup directory
setup_dir(inchikey_dir)
if not self.check():
mol.title = b''
mol.write('inchi',
(inchikey_basename + '.inchi'),
overwrite=True)
if not os.path.exists(inchikey_basename + '.png'):
mol.write('_png2',
(inchikey_basename + '.png'))
touch(inchikey_basename + '.log')
touch(inchikey_basename + '.notes')
touch(os.path.join(inchikey_dir,
'%s.sources.tsv' % inchikey_basename))
self.log_all.info('%s molecule directory initialized',
self.inchikey)
source.update_source_tsv(self.inchikey, identifier)
yield source.update_molecule_source_query(self.inchikey, identifier)
yield self.insert_molecule_query(self.inchikey, mol)
for query, values in self.get_insert_moldata_queries(
self.inchikey,
mol,
description='molecule data from %s input' % source.dirname):
yield query, values
for query, values in self.get_openbabel_property_queries(self.inchikey,
mol):
yield query, values
def map(self, mol, source):
"""Import molecule into MESS.DB."""
self.inchikey = mol.write('inchikey').rstrip()
if not self.check():
inchikey_dir = get_inchikey_dir(self.inchikey)
setup_dir(os.path.join(inchikey_dir, self.method_dir))
mol.write('xyz',
os.path.join(inchikey_dir,
self.method_dir,
'%s.xyz' % self.inchikey),
overwrite=True)
self.log_all.info('%s 3D structure from %s added',
self.inchikey, source.dirname)
def map(self, inchikey, inchikey_dir):
start = time.time()
self.inchikey = inchikey
if self.parent_method_dir is None:
sys.exit(('This method requires a parent path with a valid '
'xyz file (i.e., it cannot accept an InChI).'))
if not self.has_parent_path(self.inchikey):
self.log_console.info(('parent path %i has not been calculated '
'for %s, skipping current calculation'),
self._parent_path_id, self.inchikey)
return
out_dir = os.path.realpath(os.path.join(inchikey_dir, self.method_dir))
setup_dir(out_dir)
mop_file = os.path.join(out_dir, '%s.mop' % self.inchikey)
out_file = os.path.join(out_dir, '%s.out' % self.inchikey)
xyz_in = os.path.abspath(os.path.join(inchikey_dir,
self.parent_method_dir,
'%s.xyz' % self.inchikey))
if not os.path.isfile(xyz_in):
self.log_console.warning('xyz file expected but not found: %s.',
xyz_in)
return
xyz_out = os.path.abspath(os.path.join(out_dir,
'%s.xyz' % self.inchikey))
if not self.check(out_file, xyz_out):
keywords = ''
for k, v in self.parameters.items():
if v:
keywords += '%s=%s ' % (k, v)
else:
keywords += '%s ' % k
for k, v in self.secondary_parameters.items():
if v:
keywords += '%s=%s ' % (k, v)
else:
keywords += '%s ' % k
query = ('SELECT result AS charge '
'FROM molecule_method_property mpp '
'JOIN property p ON mpp.property_id = p.property_id '
"WHERE p.name='charge' AND mpp.inchikey=?")
charge = self.db.execute(query, (self.inchikey,)).fetchone()[0]
keywords += 'CHARGE=%i ' % charge
babel = subprocess.Popen(['obabel', '-ixyz', xyz_in, '-omop',
'-xk' + keywords],
stdout=codecs.open(mop_file, 'w',
'utf-8'),
stderr=subprocess.PIPE)
babel_stderr = babel.stderr.read()
pwd = os.getcwd()
os.chdir(out_dir) # mopac unhappy if not run in same dir as input
subprocess.Popen(['MOPAC2012.exe',
'%s.mop' % self.inchikey]).wait()
os.chdir(pwd)
self.moo_to_xyz(os.path.abspath(out_file), xyz_out)
if self.check(out_file, xyz_out):
self.log_all.info('%s calculation successful', self.inchikey)
yield self.get_timing_query(self.inchikey, start)
for query, values in self.import_properties(out_file):
yield query, values
else:
print(babel_stderr, file=sys.stderr)
else:
self.log_console.info('%s calculation skipped', self.inchikey)
for query, values in self.import_properties(out_file):
yield query, values
def test_setup_dir(self):
test_dir = os.path.join(self.tmp_dir, 'test_dir/test_subdir')
utils.setup_dir(test_dir)
self.assertTrue(os.path.exists(test_dir))
def map(self, inchikey, inchikey_dir):
"""Generate 3D structures with Balloon."""
self.inchikey = inchikey
start = time.time()
out_dir = os.path.realpath(os.path.join(inchikey_dir, self.method_dir))
setup_dir(out_dir)
sdf_out = os.path.realpath(os.path.join(out_dir,
'%s.sdf' % self.inchikey))
xyz_out = os.path.join(out_dir, '%s.xyz' % self.inchikey)
messages = []
if not self.check(xyz_out):
query = 'SELECT smiles FROM molecule WHERE inchikey=?'
r = self.db.execute(query, (self.inchikey,)).next()
# get positive 32-bit integer
seed = binascii.crc32(inchikey) & 0xffffffff
try:
os.remove(sdf_out)
except OSError:
pass
balloon_cmd = ['balloon']
for k, v in self.parameters.items():
if k.startswith('#') or v.startswith('#'):
continue
balloon_cmd.append(k)
if v:
balloon_cmd.append(v)
balloon_cmd.extend(['--randomSeed', str(seed), r.smiles, sdf_out])
balloon = subprocess.Popen(balloon_cmd, cwd=out_dir,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
balloon.stdin.write('Y') # in case balloon asks about overwrite
messages.append(balloon.stdout.read())
messages.append(balloon.stderr.read())
forcefield = b'mmff94s'
steps = 512
moldata = {}
try:
mol = pybel.readfile('sdf', sdf_out).next()
mol.write(b'xyz', str(xyz_out))
for query, values in self.get_insert_moldata_queries(
self.inchikey,
mol,
description='balloon molecule data'):
try:
moldata[query].append(values)
except KeyError:
moldata[query] = [values]
except IOError:
sdf_bad = os.path.join(out_dir, '%s_bad.sdf' % inchikey)
try:
mol = pybel.readfile('sdf', sdf_bad).next()
mol.localopt(forcefield=forcefield, steps=steps)
self.log_all.info(('"bad" %s sdf cleaned up '
'with %s forcefield '
'and %i steps'),
self.inchikey,
forcefield,
steps)
mol.write(b'xyz', str(xyz_out))
except IOError:
pass
if self.check(xyz_out):
if abs(mol.molwt - pybel.readstring('smi',
r.smiles).molwt) > 0.001:
moldata = {}
mol = pybel.readstring(b'smi', str(r.smiles))
mol.make3D(forcefield, steps)
mol.write(b'xyz', str(xyz_out), overwrite=True)
self.log_all.info(('%s 3D coordinates generation '
'attempted by '
'Open Babel rule-based algorithm '
'(forcefields=%s steps=%i) instead of '
'balloon due to hydrogen atom '
'mismatch'),
self.inchikey, forcefield, steps)
else:
moldata = {}
mol = pybel.readstring(b'smi', str(r.smiles))
mol.make3D(forcefield, steps)
mol.write(b'xyz', str(xyz_out), overwrite=True)
self.log_all.info(('%s 3D coordinates generation attempted by '
'Open Babel rule-based algorithm '
'(forcefields=%s steps=%i) instead of '
'balloon due to unexpected failure'),
self.inchikey, forcefield, steps)
if self.check(xyz_out):
self.log_all.info('%s 3D coordinates generated successfully',
self.inchikey)
else:
self.log_all.warning('%s coordinate generation failed',
self.inchikey)
for query, values in moldata.iteritems():
for v in values:
yield query, v
yield self.get_timing_query(self.inchikey, start)
else:
self.log_console.info('%s skipped', self.inchikey)