本文整理汇总了Python中rdkit.six.moves.cPickle.dumps函数的典型用法代码示例。如果您正苦于以下问题:Python dumps函数的具体用法?Python dumps怎么用?Python dumps使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了dumps函数的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: testPointPickles
def testPointPickles(self):
pt = geom.Point3D(2.0,-3.0,1.0)
pt2 = cPickle.loads(cPickle.dumps(pt))
self.assertTrue(feq(pt.x,pt2.x,1e-6))
self.assertTrue(feq(pt.y,pt2.y,1e-6))
self.assertTrue(feq(pt.z,pt2.z,1e-6))
pt = geom.Point2D(2.0,-4.0)
pt2 = cPickle.loads(cPickle.dumps(pt))
self.assertTrue(feq(pt.x,pt2.x,1e-6))
self.assertTrue(feq(pt.y,pt2.y,1e-6))
示例2: testPkl2
def testPkl2(self):
""" further pickle tests """
smis = self.bigSmiList
for smi in smis:
m = Chem.MolFromSmiles(smi)
newM1 = cPickle.loads(cPickle.dumps(m))
newM2 = cPickle.loads(cPickle.dumps(newM1))
oldSmi = Chem.MolToSmiles(newM1)
newSmi = Chem.MolToSmiles(newM2)
assert newM1.GetNumAtoms() == m.GetNumAtoms(), "num atoms comparison failed"
assert newM2.GetNumAtoms() == m.GetNumAtoms(), "num atoms comparison failed"
assert oldSmi == newSmi, "string compare failed: %s != %s" % (oldSmi, newSmi)
示例3: test2CatStringPickle
def test2CatStringPickle(self):
self._fillCat(self.smiList2)
# test non-binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat))
assert cat2.GetNumEntries()==21
assert cat2.GetFPLength()==21
self._testBits(cat2)
# test binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat,1))
assert cat2.GetNumEntries()==21
assert cat2.GetFPLength()==21
self._testBits(cat2)
示例4: test3Pickle2
def test3Pickle2(self):
"""
"""
l=1<<21
v1 = ds.IntSparseIntVect(l)
self.assertRaises(IndexError,lambda:v1[l+1])
v1[0]=1
v1[2]=2
v1[1<<12]=3
self.assertTrue(v1==v1)
v2= cPickle.loads(cPickle.dumps(v1))
self.assertTrue(v2==v1)
v3= ds.IntSparseIntVect(v2.ToBinary())
self.assertTrue(v2==v3)
self.assertTrue(v1==v3)
#cPickle.dump(v1,file('isiv.pkl','wb+'))
with open(
os.path.join(RDConfig.RDBaseDir,
'Code/DataStructs/Wrap/testData/isiv.pkl'),
'r'
) as tf:
buf = tf.read().replace('\r\n', '\n').encode('utf-8')
tf.close()
with io.BytesIO(buf) as f:
v3 = cPickle.load(f)
self.assertTrue(v3==v1)
示例5: test3Pickle2
def test3Pickle2(self):
"""
"""
l=1<<21
v1 = ds.IntSparseIntVect(l)
self.assertRaises(IndexError,lambda:v1[l+1])
v1[0]=1
v1[2]=2
v1[1<<12]=3
self.assertTrue(v1==v1)
v2= cPickle.loads(cPickle.dumps(v1))
self.assertTrue(v2==v1)
v3= ds.IntSparseIntVect(v2.ToBinary())
self.assertTrue(v2==v3)
self.assertTrue(v1==v3)
#cPickle.dump(v1,file('isiv.pkl','wb+'))
with open(
os.path.join(RDConfig.RDBaseDir,
'Code/DataStructs/Wrap/testData/isiv.pkl'),
'rb'
) as f:
v3 = cPickle.load(f)
self.assertTrue(v3==v1)
示例6: test4Serialize
def test4Serialize(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
pkl = cPickle.dumps(fcat)
fcat2 = cPickle.loads(pkl)
self.assertEqual(fcat2.GetNumEntries(), 21)
self.assertEqual(fcat2.GetFPLength(), 21)
fpgen = FragmentCatalog.FragFPGenerator()
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp1 = fpgen.GetFPForMol(mol, fcat)
fp2 = fpgen.GetFPForMol(mol, fcat2)
self.assertEqual(fp1.GetNumOnBits(), fp2.GetNumOnBits())
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
self.assertEqual(tuple(obl1), tuple(obl2))
示例7: testPkl1
def testPkl1(self):
" testing single molecule pickle "
m = Chem.MolFromSmiles("CCOC")
outS = Chem.MolToSmiles(m)
m2 = cPickle.loads(cPickle.dumps(m))
outS2 = Chem.MolToSmiles(m2)
assert outS == outS2, "bad pickle: %s != %s" % (outS, outS2)
示例8: testPickle
def testPickle(self):
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0),123)
pkl = cPickle.dumps(ffeat)
ffeat2 = cPickle.loads(pkl, encoding='bytes')
self.assertTrue(ffeat2.GetId()==ffeat.GetId());
self.assertTrue(ffeat2.GetFamily()==ffeat.GetFamily())
self.assertTrue(ffeat2.GetType()==ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
# Check that the old pickled versions have not been broken
inF = open(os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/feat.pkl'),'rb')
ffeat2=cPickle.load(inF, encoding='bytes')
# this version (1.0) does not have an id in the byte stream
self.assertTrue(ffeat2.GetFamily()==ffeat.GetFamily())
self.assertTrue(ffeat2.GetType()==ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
# Test the new version also has the id and works as expected
# uncomment the following to generate (overrwrite) new version of pickled
# data file
#cPickle.dump(ffeat,file(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'wb+'))
inF = open(os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'rb')
ffeat2=cPickle.load(inF, encoding='bytes')
self.assertTrue(ffeat2.GetId()==ffeat.GetId());
self.assertTrue(ffeat2.GetFamily()==ffeat.GetFamily())
self.assertTrue(ffeat2.GetType()==ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
示例9: _testPkl10
def _testPkl10(self):
" testing 5k molecule pickles "
inLines = open('%s/NCI/first_5K.smi'%(RDConfig.RDDataDir),'r').readlines()
smis = []
for line in inLines:
smis.append(line.split('\t')[0])
for smi in smis:
m = Chem.MolFromSmiles(smi)
newM1 = cPickle.loads(cPickle.dumps(m))
newSmi1 = Chem.MolToSmiles(newM1)
newM2 = cPickle.loads(cPickle.dumps(newM1))
newSmi2 = Chem.MolToSmiles(newM2)
assert newM1.GetNumAtoms()==m.GetNumAtoms(),'num atoms comparison failed'
assert newM2.GetNumAtoms()==m.GetNumAtoms(),'num atoms comparison failed'
assert len(newSmi1)>0,'empty smi1'
assert len(newSmi2)>0,'empty smi2'
assert newSmi1==newSmi2,'string compare failed:\n%s\n\t!=\n%s\norig smiles:\n%s'%(newSmi1,newSmi2,smi)
示例10: test6PickleEquals
def test6PickleEquals(self):
" testing pickled tree equals "
self._readyTree()
pkl = cPickle.dumps(self.baseTree)
oTree = cPickle.loads(pkl)
assert oTree == self.baseTree, 'Pickle inequality test failed'
self.baseTree.PruneChild(self.baseTree.GetChildren()[0])
assert oTree != self.baseTree, 'Pickle inequality test failed (bad Tree.__cmp__)'
示例11: test2ExplicitPickle
def test2ExplicitPickle(self):
nbits = 10000
bv1 = DataStructs.ExplicitBitVect(nbits)
for i in range(1000):
x = random.randrange(0, nbits)
bv1.SetBit(x)
pkl = pickle.dumps(bv1, 1)
bv2 = pickle.loads(pkl)
for i in range(nbits):
assert bv1[i] == bv2[i]
示例12: test3Pickles
def test3Pickles(self):
#outF = file('../testData/rvvs.pkl','wb+')
with open(os.path.join(RDConfig.RDBaseDir,
'Code/DataStructs/Wrap/testData/rvvs.pkl'),
'rb') as inF:
v1 = ds.RealValueVect(30)
for i in range(15):
v1[2*i] = 1.3
v2 = cPickle.loads(cPickle.dumps(v1))
self.assertAlmostEqual(ds.ComputeL1Norm(v1, v2), 0)
#cPickle.dump(v1,outF)
v2=cPickle.load(inF, encoding='bytes')
self.assertAlmostEqual(ds.ComputeL1Norm(v1, v2), 0)
self.assertAlmostEqual(v1.GetTotalVal(), v2.GetTotalVal())
self.failUnless(v2.GetTotalVal()!=0)
示例13: test4GridPickles
def test4GridPickles(self):
grd = geom.UniformGrid3D(10.0, 9.0, 8.0, 0.5)
self.assertTrue(grd.GetNumX() == 20)
self.assertTrue(grd.GetNumY() == 18)
self.assertTrue(grd.GetNumZ() == 16)
grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)
self.assertTrue(geom.TanimotoDistance(grd,grd)==0.0)
grd2 = cPickle.loads(cPickle.dumps(grd))
self.assertTrue(grd2.GetNumX() == 20)
self.assertTrue(grd2.GetNumY() == 18)
self.assertTrue(grd2.GetNumZ() == 16)
self.assertTrue(geom.TanimotoDistance(grd,grd2)==0.0)
示例14: test12Pickles
def test12Pickles(self):
rxn = rdChemReactions.ReactionFromSmarts('[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1')
pkl = cPickle.dumps(rxn)
rxn = cPickle.loads(pkl)
mol = Chem.MolFromSmiles('C1ON1')
products = rxn.RunReactants([mol])
self.assertEqual(len(products),1)
for p in products:
self.assertEqual(len(p),1)
self.assertEqual(p[0].GetNumAtoms(),3)
self.assertEqual(p[0].GetNumBonds(),2)
rxn = rdChemReactions.ChemicalReaction(rxn.ToBinary())
products = rxn.RunReactants([mol])
self.assertEqual(len(products),1)
for p in products:
self.assertEqual(len(p),1)
self.assertEqual(p[0].GetNumAtoms(),3)
self.assertEqual(p[0].GetNumBonds(),2)
示例15: test1
def test1(self):
cat = MolCatalog.CreateMolCatalog()
es = []
for smi in ('C1CCC1OC', 'C1CCC1', 'C'):
m = Chem.MolFromSmiles(smi)
entry = MolCatalog.MolCatalogEntry()
entry.SetMol(m)
self.assertTrue(entry.GetMol())
eSmi = Chem.MolToSmiles(entry.GetMol())
self.assertTrue(eSmi == Chem.MolToSmiles(m))
entry.SetDescription(smi)
self.assertTrue(entry.GetDescription() == smi)
es.append(entry)
v = cat.AddEntry(es[0])
self.assertTrue(v == 0)
self.assertTrue(cat.GetNumEntries() == 1)
v = cat.AddEntry(es[1])
self.assertTrue(v == 1)
self.assertTrue(cat.GetNumEntries() == 2)
v = cat.AddEntry(es[2])
self.assertTrue(v == 2)
self.assertTrue(cat.GetNumEntries() == 3)
cat.AddEdge(0, 1)
cat.AddEdge(0, 2)
cat.AddEdge(1, 2)
d = cPickle.dumps(cat)
es = None
entry = None
cat = None
cat = cPickle.loads(d)
self.assertTrue(cat.GetNumEntries() == 3)
cat = None