def testThreadedRunner(self):
path = os.path.join(os.environ['RDBASE'], 'Code', 'GraphMol',
'test_data', 'pains.smi')
with open(path) as f:
smiles = [f.strip() for f in f.readlines()][1:]
self.assertEquals(len(smiles), 3)
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_B)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_C)
fc = FilterCatalog.FilterCatalog(params)
results = FilterCatalog.RunFilterCatalog(fc, smiles)
self.assertEquals(len(results), 3)
descriptions = [
"hzone_phenol_A(479)", "cyano_imine_B(17)", "keto_keto_gamma(5)"
]
for i, res in enumerate(results):
self.assertTrue(len(res) > 0)
self.assertEquals(res[0].GetDescription(), descriptions[i])
# Test with some bad input
smiles = ['mydoghasfleas']
results = FilterCatalog.RunFilterCatalog(fc, smiles, numThreads=3)
self.assertEquals(len(results[0]), 1)
self.assertEquals(results[0][0].GetDescription(),
"no valid RDKit molecule")
def testThreadedPythonFilter(self):
class MWFilter(FilterCatalog.FilterMatcher):
def __init__(self, minMw, maxMw):
FilterCatalog.FilterMatcher.__init__(self, "MW violation")
self.minMw = minMw
self.maxMw = maxMw
def IsValid(self):
return True
def HasMatch(self, mol):
mw = rdMolDescriptors.CalcExactMolWt(mol)
res = not self.minMw <= mw <= self.maxMw
Chem.MolFromSmiles("---")
Chem.LogErrorMsg("dasfsadf")
return res
path = os.path.join(os.environ['RDBASE'], 'Code', 'GraphMol',
'test_data', 'pains.smi')
with open(path) as f:
smiles = [f.strip() for f in f.readlines()][1:]
print("1")
self.assertEqual(len(smiles), 3)
print("2")
entry = FilterCatalog.FilterCatalogEntry("MW Violation",
MWFilter(100, 500))
fc = FilterCatalog.FilterCatalog()
fc.AddEntry(entry)
self.assertTrue(entry.GetDescription() == "MW Violation")
print("running")
results = FilterCatalog.RunFilterCatalog(fc, smiles * 10, numThreads=3)
