def execute(self, args):
"""Run mopac and import calculated properties for molecule."""
p = args['path']
parent_method_dir = p.parent_method_dir
if parent_method_dir is '':
sys.exit(('This method requires a parent path with a valid '
'xyz file (i.e., it cannot accept an InChI).'))
method_dir = p.method_dir
inchikey = args['inchikey']
inchikey_dir = get_inchikey_dir(inchikey)
out_dir = os.path.realpath(os.path.join(inchikey_dir, method_dir))
setup_dir(out_dir)
mop_file = os.path.join(out_dir, '%s.mop' % inchikey)
out_file = os.path.join(out_dir, '%s.out' % inchikey)
xyz_in = os.path.abspath(os.path.join(inchikey_dir, parent_method_dir,
'%s.xyz' % inchikey))
xyz_out = os.path.abspath(os.path.join(out_dir,
'%s.xyz' % 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
keywords += 'THREADS=%s ' % self.threads
q = ('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=?")
r = self.c.execute(q, (inchikey,)).fetchone()
keywords += 'CHARGE=%i' % r.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' % inchikey]).wait()
os.chdir(pwd)
self.moo_to_xyz(os.path.abspath(out_file), xyz_out)
if self.check(out_file, xyz_out):
self.import_properties(inchikey, p.path_id, out_file)
else:
print(babel_stderr, file=sys.stderr)
else:
self.status = 'calculation skipped'
self.import_properties(inchikey, p.path_id, out_file)
self.log(args, inchikey_dir)
return self.status
def execute(self, args):
"""Match molecules to SMARTS patterns."""
inchikey = args['inchikey']
method_dir = args['path'].method_dir
inchikey_dir = get_inchikey_dir(inchikey)
out_dir = os.path.realpath(os.path.join(inchikey_dir, method_dir))
setup_dir(out_dir)
import_smarts(args['smarts'])
#messages = []
mol = pybel.readfile('inchi', os.path.join(inchikey_dir, '%s.inch' % inchikey))
#self.log(args, inchikey_dir, messages)
return self.status
def execute(self, args):
"""Generate 3D structures with Balloon."""
inchikey = args['inchikey']
method_dir = args['path'].method_dir
inchikey_dir = get_inchikey_dir(inchikey)
out_dir = os.path.realpath(os.path.join(inchikey_dir, method_dir))
setup_dir(out_dir)
sdf_out = os.path.realpath(os.path.join(out_dir, '%s.sdf' % inchikey))
xyz_out = os.path.join(out_dir, inchikey + '.xyz')
messages = []
if not self.check(xyz_out):
q = 'SELECT smiles FROM molecule WHERE inchikey=?'
r = self.c.execute(q, (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())
try:
mol = pybel.readfile('sdf', sdf_out).next()
except IOError:
sdf_bad = os.path.join(out_dir, '%s_bad.sdf' % inchikey)
mol = pybel.readfile('sdf', sdf_bad).next()
decorate(mol, UnicodeDecorator)
mol.localopt(forcefield='mmff94s', steps=128)
mol.write('xyz', xyz_out)
self.check(xyz_out)
else:
self.status = 'skipped'
self.log(args, inchikey_dir, messages)
return self.status
def execute(self, args):
"""Import molecule into MESS.DB."""
inchikey = args['inchikey']
mol = args['mol']
s = args['source']
p = args['path']
skip_cir = args['skip_cir']
inchikey_dir = get_inchikey_dir(inchikey)
inchikey_basename = os.path.join(inchikey_dir, inchikey)
setup_dir(inchikey_dir)
try:
identifier = args['parent']
except KeyError:
identifier = unicode(mol.title, 'utf-8', 'replace')
# import basic properties
if not self.check(inchikey, inchikey_dir):
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, 'sources.tsv'))
with codecs.open(os.path.join(inchikey_dir, 'charge.txt'),
'w', 'utf-8') as c:
c.write('%i' % mol.charge)
self.update_molecule(inchikey, mol, skip_cir)
self.import_properties(inchikey, p.path_id, mol)
self.check(inchikey, inchikey_dir)
else:
self.update_molecule(inchikey, mol, skip_cir)
s.update_molecule_source(inchikey, identifier)
s.update_source_tsv(inchikey_dir, identifier)
if not skip_cir:
self.update_synonyms(inchikey)
self.update_iupac(inchikey)
self.log(args, inchikey_dir)
return self.status