def test_SmartsMolFilter(self):
smis = ['C1CCC1', 'C1CCC1C=O', 'CCCC', 'CCC=O', 'CC(=O)C', 'CCN', 'NCCN', 'NCC=O']
mols = [Chem.MolFromSmiles(x) for x in smis]
suppl = SupplyNode(contents=mols)
self.assertEqual(len(list(suppl)), 8)
smas = ['C=O', 'CN']
counts = [1, 2]
filt = SmartsMolFilter.SmartsFilter(patterns=smas, counts=counts)
filt.AddParent(suppl)
self.assertEqual(len(list(filt)), 5)
suppl.reset()
filt.SetNegate(True)
self.assertEqual(len(list(filt)), 3)
smas = ['C=O', 'CN']
filt = SmartsMolFilter.SmartsFilter(patterns=smas)
filt.AddParent(suppl)
self.assertEqual(len(list(filt)), 6)
self.assertRaises(ValueError, SmartsMolFilter.SmartsFilter, patterns=smas,
counts=['notEnough', ])
RDLogger.DisableLog('rdApp.error')
self.assertRaises(ValueError, SmartsMolFilter.SmartsFilter, patterns=['BadSmarts'])
RDLogger.EnableLog('rdApp.error')
def test_SmartsMolFilter(self):
smis = ['C1CCC1', 'C1CCC1C=O', 'CCCC', 'CCC=O', 'CC(=O)C', 'CCN', 'NCCN', 'NCC=O']
mols = [Chem.MolFromSmiles(x) for x in smis]
suppl = SupplyNode(contents=mols)
self.assertEqual(len(list(suppl)), 8)
smas = ['C=O', 'CN']
counts = [1, 2]
filt = SmartsMolFilter.SmartsFilter(patterns=smas, counts=counts)
filt.AddParent(suppl)
self.assertEqual(len(list(filt)), 5)
suppl.reset()
filt.SetNegate(True)
self.assertEqual(len(list(filt)), 3)
smas = ['C=O', 'CN']
filt = SmartsMolFilter.SmartsFilter(patterns=smas)
filt.AddParent(suppl)
self.assertEqual(len(list(filt)), 6)
self.assertRaises(ValueError, SmartsMolFilter.SmartsFilter, patterns=smas,
counts=['notEnough', ])
RDLogger.DisableLog('rdApp.error')
self.assertRaises(ValueError, SmartsMolFilter.SmartsFilter, patterns=['BadSmarts'])
RDLogger.EnableLog('rdApp.error')
def __init__(self,fileName,delim="\t",nameColumn=1,smilesColumn=0,titleLine=0,
**kwargs):
SupplyNode.__init__(self,**kwargs)
self._fileName = fileName
self._supplier = Chem.SmilesMolSupplier(self._fileName,delimiter=delim,
smilesColumn=smilesColumn,
nameColumn=nameColumn,
titleLine=titleLine)
def __init__(self,
fileName,
delim="\t",
nameColumn=1,
smilesColumn=0,
titleLine=0,
**kwargs):
SupplyNode.__init__(self, **kwargs)
self._fileName = fileName
self._supplier = Chem.SmilesMolSupplier(self._fileName,
delimiter=delim,
smilesColumn=smilesColumn,
nameColumn=nameColumn,
titleLine=titleLine)
def test_SmilesOutput(self):
smis = ['C1CCC1', 'C1CC1', 'C=O', 'CCN']
mols = [Chem.MolFromSmiles(x) for x in smis]
for i, mol in enumerate(mols, 100):
mol.SetProp('ID', str(i))
suppl1 = SupplyNode(contents=mols)
suppl2 = SupplyNode(contents='abcd')
sio = StringIO()
node = SmilesOutput.OutputNode(idField='ID', dest=sio, delim=', ')
node.AddParent(suppl1)
node.AddParent(suppl2)
list(node)
self.assertEqual(
sio.getvalue(), '100, C1CCC1, a\n101, C1CC1, b\n102, C=O, c\n103, CCN, d\n')
def test_SmilesDupeFilter(self):
smis = ['C1CCC1', 'CCCC', 'CCCC', 'C1CCC1']
mols = [Chem.MolFromSmiles(x) for x in smis]
suppl = SupplyNode(contents=mols)
self.assertEqual(len(list(suppl)), 4)
dupFilter = SmilesDupeFilter.DupeFilter()
dupFilter.AddParent(suppl)
self.assertEqual(len(list(dupFilter)), 2)
def reset(self):
SupplyNode.reset(self)
self._supplier.reset()
def reset(self):
SupplyNode.reset(self)
self._supplier.reset()
def __init__(self, dbResults, **kwargs): SupplyNode.__init__(self, **kwargs) self._dbResults = dbResults self._supplier = DbMolSupplier.RandomAccessDbMolSupplier(self._dbResults, **kwargs)
def __init__(self, cursor, cmd, binaryCol, **kwargs):
SupplyNode.__init__(self, **kwargs)
self._dbResults = dbResults
self._supplier = DbMolSupplier.RandomAccessDbMolSupplier(
self._dbResults, **kwargs)
def __init__(self, cursor, cmd, binaryCol, **kwargs): SupplyNode.__init__(self, **kwargs) self._dbResults = dbResults self._supplier = DbMolSupplier.RandomAccessDbMolSupplier(self._dbResults, **kwargs)
def __init__(self, fileName, **kwargs):
SupplyNode.__init__(self, **kwargs)
self._fileName = fileName
self._supplier = Chem.SDMolSupplier(self._fileName)
def __init__(self, fileName, **kwargs): SupplyNode.__init__(self, **kwargs) self._fileName = fileName self._supplier = Chem.SDMolSupplier(self._fileName)
def __init__(self, dbResults, **kwargs):
SupplyNode.__init__(self, **kwargs)
self._dbResults = dbResults
self._supplier = DbMolSupplier.RandomAccessDbMolSupplier(
self._dbResults, **kwargs)