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 initStruchk(configDir=None, logFile=None):
global __initCalled
if configDir is None:
configDir = os.path.join(RDConfig.RDDataDir, 'struchk')
if configDir[-1] != os.path.sep:
configDir += os.path.sep
if logFile is None:
fd = tempfile.NamedTemporaryFile(suffix='.log', delete=False)
fd.close()
logFile = fd.name
struchk_init = '''-tm
-ta {0}checkfgs.trn
-tm
-or
-ca {0}checkfgs.chk
-cc
-cl 3
-cs
-cn 999
-l {1}\n'''.format(configDir, logFile)
initRes = pyAvalonTools.InitializeCheckMol(struchk_init)
if initRes:
raise ValueError('bad result from InitializeCheckMol: ' + str(initRes))
__initCalled = True
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()
