def execute(self, args):
"""Run import method for every molecule in source."""
m = load_method('import', MessDB())
s = Source(MessDB())
s.setup(args.source)
p = Path(MessDB())
p.setup(m.method_id)
pybel.ob.obErrorLog.StopLogging()
for f in s.files():
if (f.split('.')[-1] == 'sql' or
f.split('.')[-1] == 'txt' or
f.split('.')[-1] == 'bak' or
f[-1] == '~'):
continue
for mol in pybel.readfile(f.split('.')[-1],
os.path.join(s.source_dir, f)):
decorate(mol, UnicodeDecorator)
pybel.ob.obErrorLog.ClearLog()
pybel.ob.obErrorLog.StartLogging()
inchikey = mol.write('inchikey').rstrip()
pybel.ob.obErrorLog.StopLogging()
cansmi = mol.write('can').split()[0]
frag_count = cansmi.count('.') + 1
for f in cansmi.split('.'):
method_args = {}
if (frag_count > 1):
frag = pybel.readstring('can', f)
decorate(frag, UnicodeDecorator)
# neutralize fragments
#if (frag.charge != 0):
# for atom in frag.atoms:
# atom.OBAtom.SetFormalCharge(0)
pybel.ob.obErrorLog.ClearLog()
pybel.ob.obErrorLog.StartLogging()
frag_inchikey = frag.write('inchikey').rstrip()
pybel.ob.obErrorLog.StopLogging()
if not is_inchikey(frag_inchikey):
print("'%s' is not an importable molecule.\n" % f,
file=sys.stderr)
continue
method_args['parent'] = ('from: %s' %
unicode(mol.title,
'utf-8', 'replace'))
method_args['inchikey'] = frag_inchikey
method_args['mol'] = frag
else:
if not is_inchikey(inchikey):
print("'%s' is not an importable molecule.\n" % f,
file=sys.stderr)
continue
method_args['inchikey'] = inchikey
method_args['mol'] = mol
method_args['source'] = s
method_args['path'] = p
method_args['skip_cir'] = args.skip_cir
status = m.execute(method_args)
print('%s: %s' % (method_args['inchikey'], 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
import imp
import os
import sys
from distutils.version import LooseVersion
import pybel
from _db import MessDB
from _decorators import decorate, UnicodeDecorator
from _paths import Path
from _sources import Source
from _tools import AbstractTool
from _utils import is_inchikey, load_method
decorate(pybel, UnicodeDecorator)
class Import(AbstractTool):
def __init__(self):
"""Set description of tool."""
self.description = ('Import molecule file, multi-molecule file, '
'or dir of molecules into MESS.DB')
self.epilog = ''
def subparse(self, subparser):
"""Set tool-specific argparse arguments."""
subparser.add_argument('source',
help='A molecule source file or directory')
subparser.add_argument('-s', '--skip-cir', action='store_true',
help=('Do not use CIR web service to import '
'IUPAC names and other synonyms'))