def testSaveState(self):
fName = os.path.join(RDConfig.RDCodeDir, 'ML/Descriptors/test_data', 'molcalc.dsc')
with open(fName, 'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
inF = BytesIO(buf)
calc = cPickle.load(inF)
self.assertEqual(calc.GetDescriptorNames(), tuple(self.descs))
self.assertEqual(calc.GetDescriptorVersions(), tuple(self.vers))
self._testVals(calc, self.testD)
f = StringIO()
with redirect_stdout(f):
calc.ShowDescriptors()
s = f.getvalue()
for name in calc.GetDescriptorNames():
self.assertIn(name, s)
self.assertIn('Wildman-Crippen LogP value', calc.GetDescriptorSummaries())
self.assertIn('N/A', calc.GetDescriptorSummaries())
funcs = calc.GetDescriptorFuncs()
self.assertEqual(len(funcs), len(self.descs))
for f in funcs:
self.assertTrue(callable(f))
def test1(self):
# " testing pruning with known results "
oPts = [
[0, 0, 1, 0],
[0, 1, 1, 1],
[1, 0, 1, 1],
[1, 1, 0, 0],
[1, 1, 1, 1],
]
tPts = oPts + [[0, 1, 1, 0], [0, 1, 1, 0]]
tree = ID3.ID3Boot(oPts, attrs=range(3), nPossibleVals=[2] * 4)
err, badEx = CrossValidate.CrossValidate(tree, oPts)
assert err == 0.0, 'bad initial error'
assert len(badEx) == 0, 'bad initial error'
# prune with original data, shouldn't do anything
f = StringIO()
with redirect_stdout(f):
PruneTree._verbose = True
newTree, err = PruneTree.PruneTree(tree, [], oPts)
PruneTree._verbose = False
self.assertIn('Pruner', f.getvalue())
assert newTree == tree, 'improper pruning'
# prune with train data
newTree, err = PruneTree.PruneTree(tree, [], tPts)
assert newTree != tree, 'bad pruning'
assert feq(err, 0.14286), 'bad error result'
def test1(self):
# " testing pruning with known results "
oPts = [
[0, 0, 1, 0],
[0, 1, 1, 1],
[1, 0, 1, 1],
[1, 1, 0, 0],
[1, 1, 1, 1],
]
tPts = oPts + [[0, 1, 1, 0], [0, 1, 1, 0]]
tree = ID3.ID3Boot(oPts, attrs=range(3), nPossibleVals=[2] * 4)
err, badEx = CrossValidate.CrossValidate(tree, oPts)
assert err == 0.0, 'bad initial error'
assert len(badEx) == 0, 'bad initial error'
# prune with original data, shouldn't do anything
f = StringIO()
with redirect_stdout(f):
PruneTree._verbose = True
newTree, err = PruneTree.PruneTree(tree, [], oPts)
PruneTree._verbose = False
self.assertIn('Pruner', f.getvalue())
assert newTree == tree, 'improper pruning'
# prune with train data
newTree, err = PruneTree.PruneTree(tree, [], tPts)
assert newTree != tree, 'bad pruning'
assert feq(err, 0.14286), 'bad error result'
def test_all_numeric_with_no_numeric_columns(self):
sio = StringIO()
PandasTools.WriteSDF(self.df, sio, allNumeric=True)
s = sio.getvalue()
self.assertFalse(">" in s, s)
self.assertNotIn("7\n\n", s) # double-check that the numeric tests don't pass by accident
self.assertNotIn("8\n\n", s)
def test_exampleCode(self):
# We make sure that the example code runs
f = StringIO()
with redirect_stdout(f):
_exampleCode()
s = f.getvalue()
self.assertIn('[58, 75, 78, 84]', s)
def testSaveState(self):
fName = os.path.join(RDConfig.RDCodeDir, 'ML/Descriptors/test_data', 'molcalc.dsc')
with open(fName, 'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
inF = BytesIO(buf)
calc = cPickle.load(inF)
self.assertEqual(calc.GetDescriptorNames(), tuple(self.descs))
self.assertEqual(calc.GetDescriptorVersions(), tuple(self.vers))
self._testVals(calc, self.testD)
f = StringIO()
with redirect_stdout(f):
calc.ShowDescriptors()
s = f.getvalue()
for name in calc.GetDescriptorNames():
self.assertIn(name, s)
self.assertIn('Wildman-Crippen LogP value', calc.GetDescriptorSummaries())
self.assertIn('N/A', calc.GetDescriptorSummaries())
funcs = calc.GetDescriptorFuncs()
self.assertEqual(len(funcs), len(self.descs))
for f in funcs:
self.assertTrue(callable(f))
def _toSVG(mol):
if not ipython_useSVG:
return None
if hasattr(mol, '__sssAtoms'):
highlightAtoms = mol.__sssAtoms
else:
highlightAtoms = []
try:
mol.GetAtomWithIdx(0).GetExplicitValence()
except RuntimeError:
mol.UpdatePropertyCache(False)
mc = copy.deepcopy(mol)
sio = StringIO()
try:
Draw.MolToFile(mc, sio, size=molSize, imageType="svg",
kekulize=kekulizeStructures,
highlightAtoms=highlightAtoms)
except ValueError: # <- can happen on a kekulization failure
mc = copy.deepcopy(mol)
Draw.MolToFile(mc, sio, size=molSize, kekulize=False,
highlightAtoms=highlightAtoms, imageType="svg")
# It seems that the svg renderer used doesn't quite hit the spec.
# Here are some fixes to make it work in the notebook, although I think
# the underlying issue needs to be resolved at the generation step
svg_split = sio.getvalue().replace("svg:", "").splitlines()
header = ('<svg version="1.1" xmlns="http://www.w3.org/2000/svg"'
'width="%dpx" height="%dpx">') % molSize
svg = "\n".join(svg_split[:1] + [header] + svg_split[5:])
return svg
def test_Cluster(self):
""" tests the Cluster class functionality """
root = Clusters.Cluster(index=1, position=1)
c1 = Clusters.Cluster(index=10, position=10)
c1.AddChild(Clusters.Cluster(index=30, position=30))
c1.AddChild(Clusters.Cluster(index=31, position=31))
t32 = Clusters.Cluster(index=32, position=32)
c1.AddChild(t32)
c2 = Clusters.Cluster(index=11)
# c2.AddChild(Clusters.Cluster(index=40))
# c2.AddChild(Clusters.Cluster(index=41))
c2.AddChildren(
[Clusters.Cluster(index=40),
Clusters.Cluster(index=41)])
root.AddChild(c1)
root.AddChild(c2)
nodes = ClusterUtils.GetNodeList(root)
indices = [x.GetIndex() for x in nodes]
assert indices == [30, 31, 32, 10, 40, 41, 11, 1], 'bad indices'
subtree = root.FindSubtree(11)
self.assertEqual(
[x.GetIndex() for x in ClusterUtils.GetNodeList(subtree)],
[40, 41, 11])
self.assertFalse(root.IsTerminal())
self.assertTrue(t32.IsTerminal())
self.assertEqual(root.GetData(), None)
root.SetData(3.14)
self.assertEqual(root.GetData(), 3.14)
self.assertEqual(root.GetMetric(), 0.0)
root.SetMetric(0.1)
self.assertEqual(root.GetMetric(), 0.1)
self.assertEqual(root.GetIndex(), 1)
root.SetIndex(100)
self.assertEqual(root.GetIndex(), 100)
self.assertEqual(root.GetPointsPositions(), [30, 31, 32, []])
root.RemoveChild(c1)
self.assertEqual(
[x.GetIndex() for x in ClusterUtils.GetNodeList(root)],
[40, 41, 11, 100])
self.assertEqual(root.GetName(), 'Cluster(100)')
root.SetName('abc')
self.assertEqual(root.GetName(), 'abc')
f = StringIO()
with redirect_stdout(f):
root.Print(showData=True)
self.assertIn('abc', f.getvalue())
self.assertIn('Cluster(41)', f.getvalue())
self.assertIn('Metric', f.getvalue())
def test_exampleCode(self):
# We make sure that the example code runs
from rdkit.TestRunner import redirect_stdout
f = StringIO()
with redirect_stdout(f):
Fingerprinter._exampleCode()
s = f.getvalue()
self.assertIn('NCCc1ccc(O)c(O)c1', s)
def getStreamIO(sdfString):
""" Return a StringIO/BytesIO for the string """
if PY3:
sio = BytesIO() if sdfString is None else BytesIO(
sdfString.encode('utf-8'))
else: # pragma: nocover
sio = StringIO() if sdfString is None else StringIO(sdfString)
return sio
def test_exampleCode(self):
# We make sure that the example code runs
from rdkit.TestRunner import redirect_stdout
f = StringIO()
with redirect_stdout(f):
EState.EState._exampleCode()
s = f.getvalue()
self.assertIn('CC(N)C(=O)O', s)
def test_exampleCode(self):
# We make sure that the example code runs
from rdkit.TestRunner import redirect_stdout
f = StringIO()
with redirect_stdout(f):
Fingerprinter._exampleCode()
s = f.getvalue()
self.assertIn('NCCc1ccc(O)c(O)c1', s)
def test_all_numeric_with_numeric_columns(self):
sio = StringIO()
df = self.df
df["len"] = df["ID"].map(len)
PandasTools.WriteSDF(df, sio, allNumeric=True)
s = sio.getvalue()
self.assertEqual(s.count("<len>"), 2)
self.assertIn("7\n\n", s)
self.assertIn("8\n\n", s)
def test_all_numeric_with_numeric_columns(self):
sio = StringIO()
df = self.df
df["len"] = df["ID"].map(len)
PandasTools.WriteSDF(df, sio, allNumeric=True)
s = sio.getvalue()
self.assertEqual(s.count("<len>"), 2)
self.assertIn("7\n\n", s)
self.assertIn("8\n\n", s)
def test_specify_numeric_column(self):
sio = StringIO()
df = self.df
df["len2"] = df["ID"].map(len)
PandasTools.WriteSDF(df, sio, properties=["len2"])
s = sio.getvalue()
self.assertEqual(s.count("<len2>"), 2)
self.assertIn("7\n\n", s)
self.assertIn("8\n\n", s)
def test_specify_numeric_column(self):
sio = StringIO()
df = self.df
df["len2"] = df["ID"].map(len)
PandasTools.WriteSDF(df, sio, properties=["len2"])
s = sio.getvalue()
self.assertEqual(s.count("<len2>"), 2)
self.assertIn("7\n\n", s)
self.assertIn("8\n\n", s)
def test_all_numeric_with_no_numeric_columns(self):
sio = StringIO()
PandasTools.WriteSDF(self.df, sio, allNumeric=True)
s = sio.getvalue()
self.assertFalse(">" in s, s)
self.assertNotIn(
"7\n\n",
s) # double-check that the numeric tests don't pass by accident
self.assertNotIn("8\n\n", s)
def test_exampleCode(self):
try:
f = StringIO()
with redirect_stdout(f):
Tree._exampleCode()
self.assertTrue(os.path.isfile('save.pkl'))
self.assertIn('tree==tree2 False', f.getvalue(), 'Example didn' 't run to end')
finally:
if os.path.isfile('save.pkl'):
os.remove('save.pkl')
def test_exceptions(self):
self.assertRaises(ValueError, SplitData.SplitIndices, 10, -0.1)
self.assertRaises(ValueError, SplitData.SplitIndices, 10, 1.1)
f = StringIO()
with redirect_stdout(f):
SplitData.SplitIndices(10, 0.5, replacement=True, silent=False)
s = f.getvalue()
self.assertIn('Training', s)
self.assertIn('hold-out', s)
def test_TestRun(self):
try:
f = StringIO()
with redirect_stdout(f):
CrossValidate.TestRun()
self.assertTrue(os.path.isfile('save.pkl'))
s = f.getvalue()
self.assertIn('t1 == t2 True', s)
finally:
if os.path.isfile('save.pkl'):
os.remove('save.pkl')
def test_exampleCode(self):
try:
f = StringIO()
with redirect_stdout(f):
Tree._exampleCode()
self.assertTrue(os.path.isfile('save.pkl'))
self.assertIn('tree==tree2 False', f.getvalue(), 'Example didn'
't run to end')
finally:
if os.path.isfile('save.pkl'):
os.remove('save.pkl')
def test_TestRun(self):
try:
f = StringIO()
with redirect_stdout(f):
CrossValidate.TestRun()
self.assertTrue(os.path.isfile('save.pkl'))
s = f.getvalue()
self.assertIn('t1 == t2 True', s)
finally:
if os.path.isfile('save.pkl'):
os.remove('save.pkl')
def test_SaveSMILESFromFrame(self):
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df, sio)
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['ID'][10], result)
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df, sio, NamesCol='PUBCHEM_IUPAC_INCHIKEY')
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['PUBCHEM_IUPAC_INCHIKEY'][10], result)
def testRun(self):
# " test that the CrossValidationDriver runs "
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(nExamples=200)
f = StringIO()
with redirect_stdout(f):
tree, frac = CrossValidate.CrossValidationDriver(examples, attrs, nPossibleVals, silent=False)
self.assertGreater(frac, 0)
self.assertEqual('Var: 1', tree.GetName())
self.assertIn('Validation error', f.getvalue())
CrossValidate.CrossValidationDriver(examples, attrs, nPossibleVals, lessGreedy=True,
calcTotalError=True, silent=True)
def test_Cluster(self):
""" tests the Cluster class functionality """
root = Clusters.Cluster(index=1, position=1)
c1 = Clusters.Cluster(index=10, position=10)
c1.AddChild(Clusters.Cluster(index=30, position=30))
c1.AddChild(Clusters.Cluster(index=31, position=31))
t32 = Clusters.Cluster(index=32, position=32)
c1.AddChild(t32)
c2 = Clusters.Cluster(index=11)
# c2.AddChild(Clusters.Cluster(index=40))
# c2.AddChild(Clusters.Cluster(index=41))
c2.AddChildren([Clusters.Cluster(index=40), Clusters.Cluster(index=41)])
root.AddChild(c1)
root.AddChild(c2)
nodes = ClusterUtils.GetNodeList(root)
indices = [x.GetIndex() for x in nodes]
assert indices == [30, 31, 32, 10, 40, 41, 11, 1], 'bad indices'
subtree = root.FindSubtree(11)
self.assertEqual([x.GetIndex() for x in ClusterUtils.GetNodeList(subtree)], [40, 41, 11])
self.assertFalse(root.IsTerminal())
self.assertTrue(t32.IsTerminal())
self.assertEqual(root.GetData(), None)
root.SetData(3.14)
self.assertEqual(root.GetData(), 3.14)
self.assertEqual(root.GetMetric(), 0.0)
root.SetMetric(0.1)
self.assertEqual(root.GetMetric(), 0.1)
self.assertEqual(root.GetIndex(), 1)
root.SetIndex(100)
self.assertEqual(root.GetIndex(), 100)
self.assertEqual(root.GetPointsPositions(), [30, 31, 32, []])
root.RemoveChild(c1)
self.assertEqual([x.GetIndex() for x in ClusterUtils.GetNodeList(root)], [40, 41, 11, 100])
self.assertEqual(root.GetName(), 'Cluster(100)')
root.SetName('abc')
self.assertEqual(root.GetName(), 'abc')
f = StringIO()
with redirect_stdout(f):
root.Print(showData=True)
self.assertIn('abc', f.getvalue())
self.assertIn('Cluster(41)', f.getvalue())
self.assertIn('Metric', f.getvalue())
def DatabaseToDatabase(fromDb, fromTbl, toDb, toTbl, fields='*', join='', where='', user='******',
password='******', keyCol=None, nullMarker='None'):
"""
FIX: at the moment this is a hack
"""
sio = StringIO()
sio.write(
DatabaseToText(fromDb, fromTbl, fields=fields, join=join, where=where, user=user,
password=password))
sio.seek(0)
TextFileToDatabase(toDb, toTbl, sio, user=user, password=password, keyCol=keyCol,
nullMarker=nullMarker)
def test_SplitData(self):
self.assertRaises(ValueError, SplitData.SplitDataSet, None, -1.1)
self.assertRaises(ValueError, SplitData.SplitDataSet, None, 1.1)
data = list(range(10))
DataUtils.InitRandomNumbers((23, 42))
f = StringIO()
with redirect_stdout(f):
result = SplitData.SplitDataSet(data, 0.5)
self.assertEqual(set(result[0]).intersection(result[1]), set())
self.assertEqual(len(result[0]), 5)
s = f.getvalue()
self.assertIn('Training', s)
self.assertIn('hold-out', s)
def test_Tree(self):
tree = Tree.TreeNode(None, 'root', label=0)
self.assertEqual(tree.GetLevel(), 0)
self.assertEqual(tree.GetName(), 'root')
self.assertEqual(tree.GetData(), None)
self.assertEqual(tree.GetTerminal(), False)
self.assertEqual(tree.GetLabel(), 0)
self.assertEqual(tree.GetParent(), None)
self.assertEqual(tree.GetChildren(), [])
for i in range(3):
child = tree.AddChild('child {0}'.format(i), i + 1, data={'key': 'value'})
self.assertEqual(child.GetLevel(), 1)
self.assertEqual(child.GetName(), 'child {0}'.format(i))
self.assertEqual(child.GetData(), {'key': 'value'})
self.assertEqual(child.GetLabel(), i + 1)
self.assertEqual(child.GetParent(), tree)
self.assertEqual(child.GetChildren(), [])
children = tree.GetChildren()
self.assertEqual(len(children), 3)
children[0].AddChild('terminal', 4, isTerminal=True)
s = str(tree)
self.assertIn('root', s)
self.assertIn(' terminal', s)
self.assertIn(' child 2', s)
tree.NameTree(['a', 'b', 'c', 'd', 'e'])
self.assertEqual(str(tree), 'a\n b\n terminal\n c\n d\n')
tree.PruneChild(children[1])
self.assertEqual(str(tree), 'a\n b\n terminal\n d\n')
f = StringIO()
with redirect_stdout(f):
tree.Print(showData=True)
s = f.getvalue()
self.assertIn('value', s)
self.assertIn('None', s)
f = StringIO()
with redirect_stdout(f):
tree.Print()
s = f.getvalue()
self.assertNotIn('value', s)
self.assertNotIn('None', s)
tree.Destroy()
self.assertEqual(str(tree), 'a\n')
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_DescriptorCalculator(self):
calc = Descriptors.DescriptorCalculator()
self.assertRaises(NotImplementedError, calc.ShowDescriptors)
self.assertRaises(NotImplementedError, calc.GetDescriptorNames)
self.assertRaises(NotImplementedError, calc.CalcDescriptors, None)
calc.simpleList = ['simple1', 'simple2']
calc.compoundList = ['cmpd1', 'cmpd2']
f = StringIO()
with redirect_stdout(f):
calc.ShowDescriptors()
s = f.getvalue()
for name in calc.simpleList:
self.assertIn(name, s)
for name in calc.compoundList:
self.assertIn(name, s)
def test_DescriptorCalculator(self):
calc = Descriptors.DescriptorCalculator()
self.assertRaises(NotImplementedError, calc.ShowDescriptors)
self.assertRaises(NotImplementedError, calc.GetDescriptorNames)
self.assertRaises(NotImplementedError, calc.CalcDescriptors, None)
calc.simpleList = ['simple1', 'simple2']
calc.compoundList = ['cmpd1', 'cmpd2']
f = StringIO()
with redirect_stdout(f):
calc.ShowDescriptors()
s = f.getvalue()
for name in calc.simpleList:
self.assertIn(name, s)
for name in calc.compoundList:
self.assertIn(name, s)
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_WriteData(self):
self.setUpQuantLoad()
with contextlib.closing(StringIO()) as f:
DataUtils.WriteData(f, self.d.GetVarNames(), self.d.GetQuantBounds(), self.d.data)
s = f.getvalue()
self.assertIn('DataUtils', s)
self.assertIn('foo1', s)
self.assertIn('2 2 1 0 1', s)
def test_OutputNode(self):
supplier1 = Supply.SupplyNode(contents=[1, 2, 3])
supplier2 = Supply.SupplyNode(contents=["a", "b", "c"])
sio = StringIO()
node = Output.OutputNode(dest=sio, strFunc=lambda x: "{0[0]}-{0[1]} ".format(x))
node.AddParent(supplier1)
node.AddParent(supplier2)
result = list(s for s in node)
self.assertEqual(result, [(1, "a"), (2, "b"), (3, "c")])
self.assertEqual(sio.getvalue(), "1-a 2-b 3-c ")
sio = StringIO()
node = Output.OutputNode(dest=sio)
node.AddParent(supplier1)
result = list(s for s in node)
self.assertEqual(result, [1, 2, 3])
self.assertEqual(sio.getvalue(), "123")
def testRun(self):
# " test that the CrossValidationDriver runs "
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200)
f = StringIO()
with redirect_stdout(f):
tree, frac = CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
silent=False)
self.assertGreater(frac, 0)
self.assertEqual('Var: 1', tree.GetName())
self.assertIn('Validation error', f.getvalue())
CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
lessGreedy=True,
calcTotalError=True,
silent=True)
def DatabaseToDatabase(fromDb,
fromTbl,
toDb,
toTbl,
fields='*',
join='',
where='',
user='******',
password='******',
keyCol=None,
nullMarker='None'):
"""
FIX: at the moment this is a hack
"""
sio = StringIO()
sio.write(
DatabaseToText(fromDb,
fromTbl,
fields=fields,
join=join,
where=where,
user=user,
password=password))
sio.seek(0)
TextFileToDatabase(toDb,
toTbl,
sio,
user=user,
password=password,
keyCol=keyCol,
nullMarker=nullMarker)
def test_exampleCode(self):
f = StringIO()
with redirect_stdout(f):
try:
PruneTree._testRandom()
self.assertTrue(os.path.isfile('prune.pkl'))
finally:
if os.path.isfile('orig.pkl'):
os.remove('orig.pkl')
if os.path.isfile('prune.pkl'):
os.remove('prune.pkl')
self.assertIn('pruned error', f.getvalue())
f = StringIO()
with redirect_stdout(f):
PruneTree._testSpecific()
self.assertIn('pruned holdout error', f.getvalue())
f = StringIO()
with redirect_stdout(f):
PruneTree._testChain()
self.assertIn('pruned holdout error', f.getvalue())
def test_Tree(self):
tree = Tree.TreeNode(None, 'root', label=0)
self.assertEqual(tree.GetLevel(), 0)
self.assertEqual(tree.GetName(), 'root')
self.assertEqual(tree.GetData(), None)
self.assertEqual(tree.GetTerminal(), False)
self.assertEqual(tree.GetLabel(), 0)
self.assertEqual(tree.GetParent(), None)
self.assertEqual(tree.GetChildren(), [])
for i in range(3):
child = tree.AddChild('child {0}'.format(i),
i + 1,
data={'key': 'value'})
self.assertEqual(child.GetLevel(), 1)
self.assertEqual(child.GetName(), 'child {0}'.format(i))
self.assertEqual(child.GetData(), {'key': 'value'})
self.assertEqual(child.GetLabel(), i + 1)
self.assertEqual(child.GetParent(), tree)
self.assertEqual(child.GetChildren(), [])
children = tree.GetChildren()
self.assertEqual(len(children), 3)
children[0].AddChild('terminal', 4, isTerminal=True)
s = str(tree)
self.assertIn('root', s)
self.assertIn(' terminal', s)
self.assertIn(' child 2', s)
tree.NameTree(['a', 'b', 'c', 'd', 'e'])
self.assertEqual(str(tree), 'a\n b\n terminal\n c\n d\n')
tree.PruneChild(children[1])
self.assertEqual(str(tree), 'a\n b\n terminal\n d\n')
f = StringIO()
with redirect_stdout(f):
tree.Print(showData=True)
s = f.getvalue()
self.assertIn('value', s)
self.assertIn('None', s)
f = StringIO()
with redirect_stdout(f):
tree.Print()
s = f.getvalue()
self.assertNotIn('value', s)
self.assertNotIn('None', s)
tree.Destroy()
self.assertEqual(str(tree), 'a\n')
def test_SaveSMILESFromFrame(self):
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df, sio)
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['ID'][10], result)
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df,
sio,
NamesCol='PUBCHEM_IUPAC_INCHIKEY')
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['PUBCHEM_IUPAC_INCHIKEY'][10], result)
def test_FeatMapParser(self):
# We can use a string
p = FeatMapParser.FeatMapParser(data=self.data)
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
# We can use a list of strings
p = FeatMapParser.FeatMapParser(data=self.data.split('\n'))
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
# and a stream
with closing(StringIO(self.data)) as file:
p = FeatMapParser.FeatMapParser(file=file)
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
def test_OutputNode(self):
supplier1 = Supply.SupplyNode(contents=[1, 2, 3])
supplier2 = Supply.SupplyNode(contents=['a', 'b', 'c'])
sio = StringIO()
node = Output.OutputNode(dest=sio, strFunc=lambda x: '{0[0]}-{0[1]} '.format(x))
node.AddParent(supplier1)
node.AddParent(supplier2)
result = list(s for s in node)
self.assertEqual(result, [(1, 'a'), (2, 'b'), (3, 'c')])
self.assertEqual(sio.getvalue(), '1-a 2-b 3-c ')
sio = StringIO()
node = Output.OutputNode(dest=sio)
node.AddParent(supplier1)
result = list(s for s in node)
self.assertEqual(result, [1, 2, 3])
self.assertEqual(sio.getvalue(), '123')
def test_exampleCode(self):
f = StringIO()
with redirect_stdout(f):
try:
PruneTree._testRandom()
self.assertTrue(os.path.isfile('prune.pkl'))
finally:
if os.path.isfile('orig.pkl'):
os.remove('orig.pkl')
if os.path.isfile('prune.pkl'):
os.remove('prune.pkl')
self.assertIn('pruned error', f.getvalue())
f = StringIO()
with redirect_stdout(f):
PruneTree._testSpecific()
self.assertIn('pruned holdout error', f.getvalue())
f = StringIO()
with redirect_stdout(f):
PruneTree._testChain()
self.assertIn('pruned holdout error', f.getvalue())
hist = SubElement(head, "ModelHistory")
revision = SubElement(hist, "Revision")
tm = time.localtime()
date = SubElement(revision, "RevisionDate")
elem = SubElement(date, "Year")
elem.text = str(tm[0])
elem = SubElement(date, "Month")
elem.text = str(tm[1])
elem = SubElement(date, "Day")
elem.text = str(tm[2])
note = SubElement(revision, "RevisionNote")
note.text = "Created"
return ElementTree(head)
if __name__ == '__main__': # pragma: nocover
import sys
from rdkit.six.moves import cPickle # @UnresolvedImport
from rdkit.six import StringIO
pkg = cPickle.load(open(sys.argv[1], 'rb'))
perf = (.80, .95, .70, [[4, 1], [1, 4]])
tree = PackageToXml(pkg, dataPerformance=[('training data performance', perf)])
io = StringIO()
tree.write(io)
txt = io.getvalue()
header = """<?xml version="1.0"?>
<!DOCTYPE RDModelInfo PUBLIC "-//RD//DTD RDModelInfo //EN" "RD_Model.dtd">
"""
print(header)
print(txt.replace('><', '>\n<'))
def test_exampleCode(self):
# We make sure that the example code runs
f = StringIO()
with redirect_stdout(f):
Matcher._exampleCode()
self.assertIn('finished', f.getvalue())
def test_exampleCode(self):
f = StringIO()
with redirect_stdout(f):
CompoundDescriptors._exampleCode()
def test_default_write_does_not_include_tags(self): sio = StringIO() PandasTools.WriteSDF(self.df, sio) s = sio.getvalue() self.assertNotIn(s, "prop2")
def test_identifier_from_a_column(self):
sio = StringIO()
PandasTools.WriteSDF(self.df, sio, idName="prop2")
s = sio.getvalue()
first_line = s.split("\n", 1)[0]
self.assertEqual(first_line, "qwe")
def test_identifier_from_a_column(self):
sio = StringIO()
PandasTools.WriteSDF(self.df, sio, idName="prop2")
s = sio.getvalue()
first_line = s.split("\n", 1)[0]
self.assertEqual(first_line, "qwe")
def test_exampleCode(self):
f = StringIO()
with redirect_stdout(f):
BuildQuantTree.TestTree()
self.assertIn('Var: 2', f.getvalue())
def test3(self):
examples = []
bv = ExplicitBitVect(2)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['a', vc, 1])
bv = ExplicitBitVect(2)
bv.SetBit(1)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['c', vc, 0])
bv = ExplicitBitVect(2)
bv.SetBit(1)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['c2', vc, 0])
bv = ExplicitBitVect(2)
bv.SetBit(0)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['d', vc, 0])
bv = ExplicitBitVect(2)
bv.SetBit(0)
vc = VectCollection()
vc.AddVect(1, bv)
bv = ExplicitBitVect(2)
bv.SetBit(1)
vc.AddVect(2, bv)
examples.append(['d2', vc, 0])
bv = ExplicitBitVect(2)
bv.SetBit(0)
bv.SetBit(1)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['d', vc, 1])
bv = ExplicitBitVect(2)
bv.SetBit(0)
bv.SetBit(1)
vc = VectCollection()
vc.AddVect(1, bv)
examples.append(['e', vc, 1])
f = StringIO()
with redirect_stdout(f):
t = BuildSigTree(examples, 2, metric=InfoTheory.InfoType.ENTROPY, maxDepth=2, verbose=True)
self.assertIn('Build', f.getvalue())
self.assertEqual(t.GetName(), 'Bit-0')
self.assertEqual(t.GetLabel(), 0)
c0 = t.GetChildren()[0]
self.assertEqual(c0.GetName(), 'Bit-1')
self.assertEqual(c0.GetLabel(), 1)
c1 = t.GetChildren()[1]
self.assertEqual(c1.GetName(), 'Bit-1')
self.assertEqual(c1.GetLabel(), 1)
bv = ExplicitBitVect(2)
bv.SetBit(0)
vc = VectCollection()
vc.AddVect(1, bv)
bv = ExplicitBitVect(2)
bv.SetBit(1)
vc.AddVect(2, bv)
r = t.ClassifyExample(['t', vc, 0])
self.assertEqual(r, 0)
supp3 = Chem.SDMolSupplier('E:/jupyter/cc/20181204-products/a-br.sdf')
mol2 = []
mol3 = []
for mol_2 in supp2:
mol2.append(mol_2)
for mol_3 in supp3:
mol3.append(mol_3)
print(len(mol2))
print(len(mol3))
print(Chem.MolToSmiles(mol2[2]))
print(Chem.MolToSmiles(mol3[0]))
# rdkit.Chem.MolStandardize.rdMolStandardize.Uncharger.uncharge 去电荷
from rdkit.Chem.MolStandardize import rdMolStandardize
from rdkit.six import StringIO
sio = StringIO()
w = Chem.SDWriter(sio)
rxn = AllChem.ReactionFromSmarts(
'[N:2]1(:[C]:[C]([C]):[N:4]:[N:3]:1)[C].[*:8][C:5]#[C:6].[*:7][Br]>>[N:2]1([C:6]=[C:5]([*:8])[N:4]=[N:3]1)[*:7]'
)
rxn.GetNumReactantTemplates()
x1 = Chem.MolFromSmarts('[N]1(:[C]:[C]([C]):[N]:[N]:1)[C]')
#print (len(x))
name = []
product_smiles = []
for i in range(len(mol2)):
x2 = mol2[i]
for j in range(len(mol3)):
x3 = mol3[j]
x = rxn.RunReactants((x1, x2, x3))
sio.write(
DatabaseToText(fromDb,
fromTbl,
fields=fields,
join=join,
where=where,
user=user,
password=password))
sio.seek(0)
TextFileToDatabase(toDb,
toTbl,
sio,
user=user,
password=password,
keyCol=keyCol,
nullMarker=nullMarker)
if __name__ == '__main__': # pragma: nocover
sio = StringIO()
sio.write('foo,bar,baz\n')
sio.write('1,2,3\n')
sio.write('1.1,4,5\n')
sio.write('4,foo,6\n')
sio.seek(0)
from rdkit import RDConfig
import os
dirLoc = os.path.join(RDConfig.RDCodeDir, 'Dbase', 'TEST.GDB')
TextFileToDatabase(dirLoc, 'fromtext', sio)
def DatabaseToDatabase(fromDb, fromTbl, toDb, toTbl, fields='*', join='', where='', user='******',
password='******', keyCol=None, nullMarker='None'):
"""
FIX: at the moment this is a hack
"""
sio = StringIO()
sio.write(
DatabaseToText(fromDb, fromTbl, fields=fields, join=join, where=where, user=user,
password=password))
sio.seek(0)
TextFileToDatabase(toDb, toTbl, sio, user=user, password=password, keyCol=keyCol,
nullMarker=nullMarker)
if __name__ == '__main__': # pragma: nocover
sio = StringIO()
sio.write('foo,bar,baz\n')
sio.write('1,2,3\n')
sio.write('1.1,4,5\n')
sio.write('4,foo,6\n')
sio.seek(0)
from rdkit import RDConfig
import os
dirLoc = os.path.join(RDConfig.RDCodeDir, 'Dbase', 'TEST.GDB')
TextFileToDatabase(dirLoc, 'fromtext', sio)
def test_default_write_does_not_include_tags(self):
sio = StringIO()
PandasTools.WriteSDF(self.df, sio)
s = sio.getvalue()
self.assertNotIn(s, "prop2")
