def CheckCTAB(ctab, isSmiles=True):
if not __initCalled:
initStruchk()
mol_str = ctab
if not mol_str:
raise BadMoleculeException('Unexpected blank or NULL molecule')
else:
mol_str = _fix_line_ends(mol_str)
mol_str = _fix_chemdraw_header(mol_str)
if isSmiles: # branch for NULL_MOL checks
if mol_str and NULL_SMILES_RE.match(mol_str):
rval = T_NULL_MOL
else:
rval = pyAvalonTools.CheckMoleculeString(mol_str, isSmiles)
else:
# decompose the ctab into lines
# the line terminator may be \n or \r\n, or even r'\n'
ctab_lines = mol_str.split('\n')
if len(ctab_lines) <= 3:
raise BadMoleculeException('Not enough lines in CTAB')
_ctab_remove_chiral_flag(ctab_lines)
if not _ctab_has_atoms(ctab_lines):
rval = T_NULL_MOL
else: # reassemble the ctab lines into one string.
mol_str = '\n'.join(ctab_lines)
rval = pyAvalonTools.CheckMoleculeString(mol_str, isSmiles)
return rval
def testStruChkInMemoryLog(self):
r = pyAvalonTools.InitializeCheckMol(STRUCHK_INIT_IN_MEMORY_LOGGING)
try:
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(atom_clash, False)
log = pyAvalonTools.GetCheckMolLog()
self.assertTrue("of average bond length from bond" in log)
# make sure that the log is cleared for the next molecule
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString("c1ccccc1", True)
log = pyAvalonTools.GetCheckMolLog()
self.assertFalse(log)
finally:
pyAvalonTools.CloseCheckMolFiles()
def testStruChk(self):
smi_good = 'c1ccccc1C1(CC-C(C)C1)C'
smi_bad = 'c1c(R)cccc1C1(CC-C(C)C1)C'
r = pyAvalonTools.InitializeCheckMol(STRUCHK_INIT)
self.assertEqual(r, 0)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(smi_good, True)
self.assertEqual(err, 0)
mol = Chem.MolFromSmiles(smi_good)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(mol)
self.assertEqual(err, 0)
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(smi_good, True)
self.assertEqual(err, 0)
self.assertNotEqual(fixed_mol, "")
self.assertTrue(fixed_mol.find('M END') > 0)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(smi_bad, False)
self.assertNotEqual(err, 0)
self.assertFalse(fixed_mol)
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(smi_bad, False)
self.assertNotEqual(err, 0)
self.assertFalse(fixed_mol)
pyAvalonTools.CloseCheckMolFiles()