本文整理汇总了Python中rdkit.six.moves.cPickle.load函数的典型用法代码示例。如果您正苦于以下问题:Python load函数的具体用法?Python load怎么用?Python load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load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: 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2: test1_Issue163
def test1_Issue163(self):
name1 = os.path.join(self.baseDir, 'humanoral.1.pkl')
try:
with open(name1, 'rb') as pklF:
c1 = pickle.load(pklF)
except Exception:
c1 = None
self.assertTrue(c1)
name2 = os.path.join(self.baseDir, 'humanoral.2.pkl')
try:
with open(name2, 'rb') as pklF:
c2 = pickle.load(pklF)
except Exception:
c2 = None
self.assertTrue(c2)
try:
res = sorted(AnalyzeComposite.ProcessIt([c1, c2], verbose=-1))
except Exception:
import traceback
traceback.print_exc()
ok = 0
else:
ok = 1
self.assertTrue(ok)
self.assertEqual(res[0][0],'BALABANJ')
self.assertEqual(res[1][0],'BERTZCT')
self.assertEqual(res[-1][0],'VSA_ESTATE9')
for entry in res:
self.assertEqual(len(entry),5)
示例3: testBuild
def testBuild(self):
""" tests building and screening a packager """
with open(os.path.join(self.dataDir,'Jan9_build3_calc.dsc'),'rb') as calcF:
calc = cPickle.load(calcF)
with open(os.path.join(self.dataDir,'Jan9_build3_model.pkl'),'rb') as modelF:
model = cPickle.load(modelF)
pkg = Packager.ModelPackage(descCalc=calc,model=model)
self._verify(pkg,self.testD)
示例4: test6Bug29_2
def test6Bug29_2(self):
""" a more extensive test of the cmp stuff using pickled trees"""
import os
with open(os.path.join(RDConfig.RDCodeDir,'ML','DecTree','test_data','CmpTree1.pkl'),'rb') as t1File:
t1 = cPickle.load(t1File)
with open(os.path.join(RDConfig.RDCodeDir,'ML','DecTree','test_data','CmpTree2.pkl'),'rb') as t2File:
t2 = cPickle.load(t2File)
assert cmp(t1,t2),'equality failed'
示例5: test6Bug29_2
def test6Bug29_2(self):
""" a more extensive test of the cmp stuff using pickled trees"""
import os
with open(os.path.join(RDConfig.RDCodeDir,'ML','DecTree','test_data','CmpTree1.pkl'),'r') as t1TFile:
buf = t1TFile.read().replace('\r\n', '\n').encode('utf-8')
t1TFile.close()
with io.BytesIO(buf) as t1File:
t1 = cPickle.load(t1File)
with open(os.path.join(RDConfig.RDCodeDir,'ML','DecTree','test_data','CmpTree2.pkl'),'r') as t2TFile:
buf = t2TFile.read().replace('\r\n', '\n').encode('utf-8')
t2TFile.close()
with io.BytesIO(buf) as t2File:
t2 = cPickle.load(t2File)
assert cmp(t1,t2),'equality failed'
示例6: 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7: testTreeGrow
def testTreeGrow(self):
" testing tree-based composite "
with open(RDConfig.RDCodeDir + "/ML/Composite/test_data/composite_base.pkl", "r") as pklTF:
buf = pklTF.read().replace("\r\n", "\n").encode("utf-8")
pklTF.close()
with io.BytesIO(buf) as pklF:
self.refCompos = cPickle.load(pklF)
composite = Composite.Composite()
composite._varNames = self.varNames
composite.SetQuantBounds(self.qBounds, self.nPoss)
from rdkit.ML.DecTree import CrossValidate
driver = CrossValidate.CrossValidationDriver
pruner = None
composite.Grow(self.examples, self.attrs, [], buildDriver=driver, pruner=pruner, nTries=100, silent=1)
composite.AverageErrors()
composite.SortModels()
# with open(RDConfig.RDCodeDir+'/ML/Composite/test_data/composite_base.pkl','wb') as pklF:
# cPickle.dump(composite,pklF)
self.treeComposite = composite
self.assertEqual(len(composite), len(self.refCompos))
for i in xrange(len(composite)):
t1, c1, e1 = composite[i]
t2, c2, e2 = self.refCompos[i]
self.assertEqual(e1, e2)
示例8: testSaveState
def testSaveState(self):
fName = os.path.join(RDConfig.RDCodeDir,'ML/Descriptors/test_data','molcalc.dsc')
with open(fName,'rb') as inF:
calc = cPickle.load(inF)
self.assertEqual(calc.GetDescriptorNames(),tuple(self.descs))
self.assertEqual(calc.GetDescriptorVersions(),tuple(self.vers))
self._testVals(calc,self.testD)
示例9: testPerm1
def testPerm1(self):
""" tests the descriptor remapping stuff in a packager """
from rdkit.Chem import Descriptors
with open(os.path.join(self.dataDir,'Jan9_build3_pkg.pkl'),'r') as pkgTF:
buf = pkgTF.read().replace('\r\n', '\n').encode('utf-8')
pkgTF.close()
with io.BytesIO(buf) as pkgF:
pkg = cPickle.load(pkgF)
calc = pkg.GetCalculator()
names = calc.GetDescriptorNames()
ref = {}
DataUtils.InitRandomNumbers((23,42))
for smi,pred,conf in self.testD:
for desc in names:
fn = getattr(Descriptors,desc,lambda x:777)
m = Chem.MolFromSmiles(smi)
ref[desc] = fn(m)
for i in range(5):
perm = list(names)
random.shuffle(perm,random=random.random)
m = Chem.MolFromSmiles(smi)
for desc in perm:
fn = getattr(Descriptors,desc,lambda x:777)
val = fn(m)
assert feq(val,ref[desc],1e-4),'%s: %s(%s): %f!=%f'%(str(perm),
smi,
desc,
val,
ref[desc])
示例10: test1PPDataset
def test1PPDataset(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap',
'test_data', 'PP_descrs_regress.2.csv')
infil = open(fileN, 'r')
lines = infil.readlines()
infil.close()
infile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap',
'test_data', 'PP_combi_charges.pkl')
with open(infile, 'r') as cchtFile:
buf = cchtFile.read().replace('\r\n', '\n').encode('utf-8')
cchtFile.close()
with io.BytesIO(buf) as cchFile:
combiCharges = pickle.load(cchFile)
for lin in lines:
if (lin[0] == '#'):
continue
tlst = lin.strip().split(',')
smi = tlst[0]
rdmol = Chem.MolFromSmiles(smi)
rdPartialCharges.ComputeGasteigerCharges(rdmol)
nat = rdmol.GetNumAtoms()
failed = False
for ai in range(nat):
rdch = float(rdmol.GetAtomWithIdx(ai).GetProp('_GasteigerCharge'))
if not feq(rdch, combiCharges[smi][ai], 1.e-2):
failed = True
print(smi, ai, rdch, combiCharges[smi][ai])
if failed:
rdmol.Debug()
self.assertFalse(failed)
示例11: test6
def test6(self):
""" multiple models """
self.details.tableName = 'ferro_noquant'
with open(os.path.join(self.baseDir,'ferromag_auto_10_3.pkl'),'r') as pklTF:
buf = pklTF.read().replace('\r\n', '\n').encode('utf-8')
pklTF.close()
with io.BytesIO(buf) as pklF:
compos = pickle.load(pklF)
tgt = 10
self.assertEqual(len(compos),tgt)
composites = [compos,compos]
tpl = ScreenComposite.ScreenFromDetails(composites,self.details)
nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = tpl
self.assertEqual(nGood[0],95)
self.assertEqual(misCount[0],8)
self.assertEqual(nSkipped[0],0)
self.assertAlmostEqual(avgGood[0],.9684,4)
self.assertAlmostEqual(avgBad[0],.8375,4)
self.assertEqual(nGood[1],0)
self.assertEqual(misCount[1],0)
self.assertEqual(nSkipped[1],0)
self.assertEqual(avgGood[1],0)
self.assertEqual(avgBad[1],0)
self.assertEqual(tbl[0,0],50)
self.assertEqual(tbl[1,1],45)
self.assertEqual(tbl[0,1],5)
self.assertEqual(tbl[1,0],3)
示例12: test11
def test11(self):
""" filtering with segmentation """
self.details.tableName = 'ferro_noquant'
with open(os.path.join(self.baseDir,'ferromag_filt_10_3.pkl'),
'r') as pklTF:
buf = pklTF.read().replace('\r\n', '\n').encode('utf-8')
pklTF.close()
with io.BytesIO(buf) as pklF:
compos = pickle.load(pklF)
tgt = 10
self.assertEqual(len(compos),tgt)
self.details.doHoldout=1
self.details.filterVal=1
self.details.filterFrac=.33
nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
self.assertEqual(nGood,37)
self.assertEqual(misCount,6)
self.assertEqual(nSkipped,0)
self.assertAlmostEqual(avgGood,.95946,4)
self.assertAlmostEqual(avgBad,.85,4)
self.assertEqual(tbl[0,0] , 14)
self.assertEqual(tbl[1,1] , 23)
self.assertEqual(tbl[0,1] , 1)
self.assertEqual(tbl[1,0] , 5)
示例13: 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14: test4
def test4(self):
""" include thresholding """
self.details.tableName = 'ferro_quant'
self.details.threshold = 0.80
self.details.doHoldout=0
self.details.doTraining=0
with open(os.path.join(self.baseDir,'ferromag_quant_10.pkl'),'r') as pklTF:
buf = pklTF.read().replace('\r\n', '\n').encode('utf-8')
pklTF.close()
with io.BytesIO(buf) as pklF:
compos = pickle.load(pklF)
tgt = 5
self.assertEqual(len(compos),tgt)
nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
self.assertEqual(nGood,91)
self.assertEqual(misCount,1)
self.assertEqual(nSkipped,3)
self.assertAlmostEqual(avgGood,0.9956,4)
self.assertAlmostEqual(avgBad,1.000,4)
self.assertAlmostEqual(avgSkip,0.6000,4)
self.assertEqual(tbl[0,0] , 54)
self.assertEqual(tbl[1,1] , 37)
self.assertEqual(tbl[0,1] , 1)
self.assertEqual(tbl[1,0] , 0)
示例15: test3CatFilePickle
def test3CatFilePickle(self):
with open(os.path.join(RDConfig.RDCodeDir,'Chem',
'test_data','simple_catalog.pkl'),
'rb') as pklFile:
cat = cPickle.load(pklFile, encoding='bytes')
assert cat.GetNumEntries()==21
assert cat.GetFPLength()==21
self._testBits(cat)