本文整理汇总了Python中rdkit.six.moves.cPickle.dump函数的典型用法代码示例。如果您正苦于以下问题:Python dump函数的具体用法?Python dump怎么用?Python dump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dump函数的20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,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: Pickle
def Pickle(self,fileName='foo.pkl'):
""" Writes this forest off to a file so that it can be easily loaded later
**Arguments**
fileName is the name of the file to be written
"""
pFile = open(fileName,'wb+')
cPickle.dump(self,pFile,1)
pFile.close()
开发者ID:ASKCOS,项目名称:rdkit,代码行数:11,代码来源:Forest.py
示例2: testPkl
def testPkl(self):
# Test pickling
v1 = self.klass(10)
v1[1] = 1
v1[2] = 1
v1[3] = 1
pklName = 'foo.pkl'
outF = open(pklName, 'wb+')
cPickle.dump(v1, outF)
outF.close()
inF = open(pklName, 'rb')
v2 = cPickle.load(inF)
inF.close()
os.unlink(pklName)
assert tuple(v1.GetOnBits()) == tuple(v2.GetOnBits()), 'pkl failed'
开发者ID:connorcoley,项目名称:rdkit,代码行数:15,代码来源:UnitTestcBitVect.py
示例3: SaveState
def SaveState(self, fileName):
""" Writes this calculator off to a file so that it can be easily loaded later
**Arguments**
- fileName: the name of the file to be written
"""
try:
f = open(fileName, 'wb+')
except Exception:
logger.error('cannot open output file %s for writing' % (fileName))
return
cPickle.dump(self, f)
f.close()
开发者ID:connorcoley,项目名称:rdkit,代码行数:15,代码来源:MoleculeDescriptors.py
示例4: _writeDetailFile
def _writeDetailFile(self,inF,outF):
while 1:
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
break
else:
mol = Chem.MolFromSmiles(smi)
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
cPickle.dump((smi,contribs),outF)
else:
print('Problems with SMILES:',smi)
开发者ID:ASKCOS,项目名称:rdkit,代码行数:15,代码来源:UnitTestCrippen.py
示例5: testPkl
def testPkl(self):
""" test pickling
"""
v1 = klass(10)
v1[1] = 1
v1[2] = 1
v1[3] = 1
pklName = "foo.pkl"
outF = open(pklName, "wb+")
cPickle.dump(v1, outF)
outF.close()
inF = open(pklName, "rb")
v2 = cPickle.load(inF)
inF.close()
os.unlink(pklName)
assert tuple(v1.GetOnBits()) == tuple(v2.GetOnBits()), "pkl failed"
开发者ID:steve-federowicz,项目名称:rdkit,代码行数:16,代码来源:UnitTestcBitVect2.py
示例6: SaveState
def SaveState(self,fileName):
""" Writes this calculator off to a file so that it can be easily loaded later
**Arguments**
- fileName: the name of the file to be written
"""
from rdkit.six.moves import cPickle
try:
f = open(fileName,'wb+')
except:
print('cannot open output file %s for writing'%(fileName))
return
cPickle.dump(self,f)
f.close()
开发者ID:Acpharis,项目名称:rdkit,代码行数:16,代码来源:Descriptors.py
示例7: Pickle
def Pickle(self, fileName='foo.pkl', saveExamples=0):
""" Writes this composite off to a file so that it can be easily loaded later
**Arguments**
- fileName: the name of the file to be written
- saveExamples: if this is zero, the individual models will have
their stored examples cleared.
"""
if not saveExamples:
self.ClearModelExamples()
pFile = open(fileName, 'wb+')
cPickle.dump(self, pFile, 1)
pFile.close()
开发者ID:connorcoley,项目名称:rdkit,代码行数:17,代码来源:Composite.py
示例8: runIt
def runIt(inFileName, outFileName, smiCol=0, maxMols=-1, delim=','):
inF = gzip.open(inFileName, 'r')
outF = open(outFileName, 'wb+')
mols = []
nDone = 0
for line in inF.readlines():
if line[0] != '#':
splitL = line.strip().split(delim)
smi = splitL[smiCol].strip()
print(smi)
mol = Chem.MolFromSmiles(smi)
if mol:
contribs = Crippen._GetAtomContribs(mol)
cPickle.dump((smi, contribs), outF)
nDone += 1
if maxMols > 0 and nDone >= maxMols:
break
outF.close()
开发者ID:abradle,项目名称:rdkit,代码行数:18,代码来源:BuildCrippenTestSet.py
示例9: testPkl
def testPkl(self):
" testing molecule pickle "
import tempfile
f, self.fName = tempfile.mkstemp('.pkl')
f = None
self.m = Chem.MolFromSmiles('CC(=O)CC')
outF = open(self.fName, 'wb+')
cPickle.dump(self.m, outF)
outF.close()
inF = open(self.fName, 'rb')
m2 = cPickle.load(inF)
inF.close()
try:
os.unlink(self.fName)
except Exception:
pass
oldSmi = Chem.MolToSmiles(self.m)
newSmi = Chem.MolToSmiles(m2)
assert oldSmi == newSmi, 'string compare failed'
开发者ID:abradle,项目名称:rdkit,代码行数:19,代码来源:UnitTestChem.py
示例10: testPkl
def testPkl(self):
" testing molecule pickle "
import tempfile
f, self.fName = tempfile.mkstemp(".pkl")
f = None
self.m = Chem.MolFromSmiles("CC(=O)CC")
outF = open(self.fName, "wb+")
cPickle.dump(self.m, outF)
outF.close()
inF = open(self.fName, "rb")
m2 = cPickle.load(inF)
inF.close()
try:
os.unlink(self.fName)
except:
pass
oldSmi = Chem.MolToSmiles(self.m)
newSmi = Chem.MolToSmiles(m2)
assert oldSmi == newSmi, "string compare failed"
开发者ID:steve-federowicz,项目名称:rdkit,代码行数:20,代码来源:UnitTestChem.py
示例11: ClusterFromDetails
def ClusterFromDetails(details):
""" Returns the cluster tree
"""
data = MolSimilarity.GetFingerprints(details)
if details.maxMols > 0:
data = data[:details.maxMols]
if details.outFileName:
try:
outF = open(details.outFileName, 'wb+')
except IOError:
error("Error: could not open output file %s for writing\n" % (details.outFileName))
return None
else:
outF = None
if not data:
return None
clustTree = ClusterPoints(data, details.metric, details.clusterAlgo, haveLabels=0, haveActs=1)
if outF:
cPickle.dump(clustTree, outF)
return clustTree
开发者ID:abradle,项目名称:rdkit,代码行数:23,代码来源:ClusterMols.py
示例12: WritePickledData
def WritePickledData(outName,data):
""" writes either a .qdat.pkl or a .dat.pkl file
**Arguments**
- outName: the name of the file to be used
- data: either an _MLData.MLDataSet_ or an _MLData.MLQuantDataSet_
"""
varNames = data.GetVarNames()
qBounds = data.GetQuantBounds()
ptNames = data.GetPtNames()
examples = data.GetAllData()
with open(outName,'wb+') as outFile:
cPickle.dump(varNames,outFile)
cPickle.dump(qBounds,outFile)
cPickle.dump(ptNames,outFile)
cPickle.dump(examples,outFile)
开发者ID:ASKCOS,项目名称:rdkit,代码行数:19,代码来源:DataUtils.py
示例13: MolViewer
cmpd = Chem.MolFromSmiles('C1=CC=C1C#CC1=CC=C1')
cmpd = Chem.AddHs(cmpd)
AllChem.EmbedMolecule(cmpd)
AllChem.UFFOptimizeMolecule(cmpd)
AllChem.CanonicalizeMol(cmpd)
print >>file('testmol.mol','w+'),Chem.MolToMolBlock(cmpd)
else:
cmpd = Chem.MolFromMolFile('testmol.mol')
builder=SubshapeBuilder()
if 1:
shape=builder.GenerateSubshapeShape(cmpd)
v = MolViewer()
if 1:
import tempfile
tmpFile = tempfile.mktemp('.grd')
v.server.deleteAll()
Geometry.WriteGridToFile(shape.grid,tmpFile)
time.sleep(1)
v.ShowMol(cmpd,name='testMol',showOnly=True)
v.server.loadSurface(tmpFile,'testGrid','',2.5)
v.server.resetCGO('*')
cPickle.dump(shape,file('subshape.pkl','w+'))
for i,pt in enumerate(shape.skelPts):
v.server.sphere(tuple(pt.location),.5,(1,0,1),'Pt-%d'%i)
if not hasattr(pt,'shapeDirs'): continue
momBeg = pt.location-pt.shapeDirs[0]
momEnd = pt.location+pt.shapeDirs[0]
v.server.cylinder(tuple(momBeg),tuple(momEnd),.1,(1,0,1),'v-%d'%i)
开发者ID:baoilleach,项目名称:rdkit,代码行数:29,代码来源:SubshapeBuilder.py
示例14: print
from rdkit.Chem.PyMol import MolViewer
from rdkit.Chem.Subshape import SubshapeBuilder, SubshapeObjects, SubshapeAligner
from rdkit.six.moves import cPickle
import copy
m1 = Chem.MolFromMolFile('test_data/square1.mol')
m2 = Chem.MolFromMolFile('test_data/square2.mol')
b = SubshapeBuilder.SubshapeBuilder()
b.gridDims = (10., 10., 5)
b.gridSpacing = 0.4
b.winRad = 2.0
if 1:
print('m1:')
s1 = b.GenerateSubshapeShape(m1)
cPickle.dump(s1, open('test_data/square1.shp.pkl', 'wb+'))
print('m2:')
s2 = b.GenerateSubshapeShape(m2)
cPickle.dump(s2, open('test_data/square2.shp.pkl', 'wb+'))
ns1 = b.CombineSubshapes(s1, s2)
b.GenerateSubshapeSkeleton(ns1)
cPickle.dump(ns1, open('test_data/combined.shp.pkl', 'wb+'))
else:
s1 = cPickle.load(open('test_data/square1.shp.pkl', 'rb'))
s2 = cPickle.load(open('test_data/square2.shp.pkl', 'rb'))
#ns1 = cPickle.load(file('test_data/combined.shp.pkl','rb'))
ns1 = cPickle.load(open('test_data/combined.shp.pkl', 'rb'))
v = MolViewer()
SubshapeObjects.DisplaySubshape(v, s1, 'shape1')
SubshapeObjects.DisplaySubshape(v, ns1, 'ns1')
开发者ID:abradle,项目名称:rdkit,代码行数:31,代码来源:testCombined.py
示例15: RunOnData
def RunOnData(details, data, progressCallback=None, saveIt=1, setDescNames=0):
if details.lockRandom:
seed = details.randomSeed
else:
import random
seed = (random.randint(0, 1e6), random.randint(0, 1e6))
DataUtils.InitRandomNumbers(seed)
testExamples = []
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data, shuffle=1, runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data, shuffle=0, runDetails=details)
namedExamples = data.GetNamedData()
if details.splitRun == 1:
trainIdx, testIdx = SplitData.SplitIndices(
len(namedExamples), details.splitFrac, silent=not _verbose)
trainExamples = [namedExamples[x] for x in trainIdx]
testExamples = [namedExamples[x] for x in testIdx]
else:
testExamples = []
testIdx = []
trainIdx = list(range(len(namedExamples)))
trainExamples = namedExamples
if details.filterFrac != 0.0:
# if we're doing quantization on the fly, we need to handle that here:
if hasattr(details, 'activityBounds') and details.activityBounds:
tExamples = []
bounds = details.activityBounds
for pt in trainExamples:
pt = pt[:]
act = pt[-1]
placed = 0
bound = 0
while not placed and bound < len(bounds):
if act < bounds[bound]:
pt[-1] = bound
placed = 1
else:
bound += 1
if not placed:
pt[-1] = bound
tExamples.append(pt)
else:
bounds = None
tExamples = trainExamples
trainIdx, temp = DataUtils.FilterData(tExamples, details.filterVal, details.filterFrac, -1,
indicesOnly=1)
tmp = [trainExamples[x] for x in trainIdx]
testExamples += [trainExamples[x] for x in temp]
trainExamples = tmp
counts = DataUtils.CountResults(trainExamples, bounds=bounds)
ks = counts.keys()
ks.sort()
message('Result Counts in training set:')
for k in ks:
message(str((k, counts[k])))
counts = DataUtils.CountResults(testExamples, bounds=bounds)
ks = counts.keys()
ks.sort()
message('Result Counts in test set:')
for k in ks:
message(str((k, counts[k])))
nExamples = len(trainExamples)
message('Training with %d examples' % (nExamples))
nVars = data.GetNVars()
attrs = list(range(1, nVars + 1))
nPossibleVals = data.GetNPossibleVals()
for i in range(1, len(nPossibleVals)):
if nPossibleVals[i - 1] == -1:
attrs.remove(i)
if details.pickleDataFileName != '':
pickleDataFile = open(details.pickleDataFileName, 'wb+')
cPickle.dump(trainExamples, pickleDataFile)
cPickle.dump(testExamples, pickleDataFile)
pickleDataFile.close()
if details.bayesModel:
composite = BayesComposite.BayesComposite()
else:
composite = Composite.Composite()
composite._randomSeed = seed
composite._splitFrac = details.splitFrac
composite._shuffleActivities = details.shuffleActivities
composite._randomizeActivities = details.randomActivities
if hasattr(details, 'filterFrac'):
composite._filterFrac = details.filterFrac
if hasattr(details, 'filterVal'):
composite._filterVal = details.filterVal
composite.SetModelFilterData(details.modelFilterFrac, details.modelFilterVal)
composite.SetActivityQuantBounds(details.activityBounds)
#.........这里部分代码省略.........
开发者ID:connorcoley,项目名称:rdkit,代码行数:101,代码来源:BuildComposite.py
示例16: message
cat = None
obls = None
if details.doBuild:
if not suppl:
message("We require inData to generate a catalog\n")
sys.exit(-2)
message("Building catalog\n")
t1 = time.time()
cat = BuildCatalog(suppl, maxPts=details.numMols, minPath=details.minPath,
maxPath=details.maxPath)
t2 = time.time()
message("\tThat took %.2f seconds.\n" % (t2 - t1))
if details.catalogName:
message("Dumping catalog data\n")
cPickle.dump(cat, open(details.catalogName, 'wb+'))
elif details.catalogName:
message("Loading catalog\n")
cat = cPickle.load(open(details.catalogName, 'rb'))
if details.onBitsName:
try:
obls = cPickle.load(open(details.onBitsName, 'rb'))
except Exception:
obls = None
else:
if len(obls) < (inD.count('\n') - 1):
obls = None
scores = None
if details.doScore:
if not suppl:
message("We require inData to score molecules\n")
开发者ID:connorcoley,项目名称:rdkit,代码行数:30,代码来源:BuildFragmentCatalog.py
示例17: Pickle
def Pickle(self, fileName='foo.pkl'):
""" Pickles the tree and writes it to disk
"""
with open(fileName, 'wb+') as pFile:
cPickle.dump(self, pFile)
开发者ID:connorcoley,项目名称:rdkit,代码行数:6,代码来源:Tree.py
示例18: clear
# create a logged canvas and draw on it
sz = (300,300)
c1 = Logger.Logger(pidSVG.SVGCanvas,sz,'foo.svg',loggerFlushCommand='clear')
c1.drawPolygon([(100,100),(100,200),(200,200),(200,100)],fillColor=pid.Color(0,0,1))
c1.drawLines([(100,100,200,200),(100,200,200,100)],color=pid.Color(0,1,0),width=2)
# because the log has been instantiated with clear() as the loggerFlushCommand,
# this will blow out the log as well as the contents of the canvas.
c1.clear()
# draw some more stuff
c1.drawPolygon([(100,100),(100,200),(200,200),(200,100)],fillColor=pid.Color(1,0,0))
c1.drawLines([(100,100,200,200),(100,200,200,100)],color=pid.Color(0,0,0),width=2)
# and write the resulting file.
c1.save()
# save the log by pickling it.
from rdkit.six.moves import cPickle
cPickle.dump(c1._LoggerGetLog(),open('foo.pkl','wb+'))
# create a new canvas
c2 = pidPIL.PILCanvas(sz,'foo.png')
# read the pickled log back in
t = cPickle.load(open('foo.pkl','rb'))
# and play the log on the new canvas
Logger.replay(t,c2)
# there should now be a file 'foo.png' with the image
开发者ID:Acpharis,项目名称:rdkit,代码行数:27,代码来源:SpingDemo.py
示例19: FingerprintsFromDetails
def FingerprintsFromDetails(details, reportFreq=10):
data = None
if details.dbName and details.tableName:
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo
from rdkit.ML.Data import DataUtils
try:
conn = DbConnect(details.dbName, details.tableName)
except Exception:
import traceback
error('Problems establishing connection to database: %s|%s\n' % (details.dbName,
details.tableName))
traceback.print_exc()
if not details.idName:
details.idName = DbInfo.GetColumnNames(details.dbName, details.tableName)[0]
dataSet = DataUtils.DBToData(details.dbName, details.tableName,
what='%s,%s' % (details.idName, details.smilesName))
idCol = 0
smiCol = 1
elif details.inFileName and details.useSmiles:
from rdkit.ML.Data import DataUtils
conn = None
if not details.idName:
details.idName = 'ID'
try:
dataSet = DataUtils.TextFileToData(details.inFileName,
onlyCols=[details.idName, details.smilesName])
except IOError:
import traceback
error('Problems reading from file %s\n' % (details.inFileName))
traceback.print_exc()
idCol = 0
smiCol = 1
elif details.inFileName and details.useSD:
conn = None
dataset = None
if not details.idName:
details.idName = 'ID'
dataSet = []
try:
s = Chem.SDMolSupplier(details.inFileName)
except Exception:
import traceback
error('Problems reading from file %s\n' % (details.inFileName))
traceback.print_exc()
else:
while 1:
try:
m = s.next()
except StopIteration:
break
if m:
dataSet.append(m)
if reportFreq > 0 and not len(dataSet) % reportFreq:
message('Read %d molecules\n' % (len(dataSet)))
if details.maxMols > 0 and len(dataSet) >= details.maxMols:
break
for i, mol in enumerate(dataSet):
if mol.HasProp(details.idName):
nm = mol.GetProp(details.idName)
else:
nm = mol.GetProp('_Name')
dataSet[i] = (nm, mol)
else:
dataSet = None
fps = None
if dataSet and not details.useSD:
data = dataSet.GetNamedData()
if not details.molPklName:
fps = apply(FingerprintsFromSmiles, (data, idCol, smiCol), details.__dict__)
else:
fps = apply(FingerprintsFromPickles, (data, idCol, smiCol), details.__dict__)
elif dataSet and details.useSD:
fps = apply(FingerprintsFromMols, (dataSet, ), details.__dict__)
if fps:
if details.outFileName:
outF = open(details.outFileName, 'wb+')
for i in range(len(fps)):
cPickle.dump(fps[i], outF)
outF.close()
dbName = details.outDbName or details.dbName
if details.outTableName and dbName:
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbUtils, DbModule
conn = DbConnect(dbName)
#
# We don't have a db open already, so we'll need to figure out
# the types of our columns...
#
colTypes = DbUtils.TypeFinder(data, len(data), len(data[0]))
typeStrs = DbUtils.GetTypeStrings([details.idName, details.smilesName], colTypes,
keyCol=details.idName)
cols = '%s, %s %s' % (typeStrs[0], details.fpColName, DbModule.binaryTypeName)
# FIX: we should really check to see if the table
# is already there and, if so, add the appropriate
#.........这里部分代码省略.........
开发者ID:connorcoley,项目名称:rdkit,代码行数:101,代码来源:FingerprintMols.py
示例20: print
for example in examples:
res = net.ClassifyExample(example[:-1])
print("%f -> %f" % (example[-1], res))
return net
def runProfile(command):
import random
random.seed(23)
import profile, pstats
datFile = "%s.prof.dat" % (command)
profile.run("%s()" % command, datFile)
stats = pstats.Stats(datFile)
stats.strip_dirs()
stats.sort_stats("time").print_stats()
if 0:
net = testXor()
print("Xor:", net)
from rdkit.six.moves import cPickle
outF = open("xornet.pkl", "wb+")
cPickle.dump(net, outF)
outF.close()
else:
# runProfile('testLinear')
net = testLinear()
# net = testOr()
开发者ID:maxpillong,项目名称:rdkit,代码行数:30,代码来源:Trainers.py
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