本文整理汇总了Python中rdkit.Chem.Crippen类的典型用法代码示例。如果您正苦于以下问题：Python Crippen类的具体用法？Python Crippen怎么用？Python Crippen使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Crippen类的11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: testDetails2
def testDetails2(self):
Crippen._Init()
inF = open(self.detailName2,'rb')
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)示例2: pySlogP_VSA_
def pySlogP_VSA_(mol, bins=None, force=1):
""" *Internal Use Only*
"""
if not force:
try:
res = mol._slogpVSA
except AttributeError:
pass
else:
if res.all():
return res
if bins is None:
bins = logpBins
Crippen._Init()
propContribs = Crippen._GetAtomContribs(mol, force=force)
volContribs = _LabuteHelper(mol)
ans = numpy.zeros(len(bins) + 1, 'd')
for i in range(len(propContribs)):
prop = propContribs[i]
vol = volContribs[i + 1]
if prop is not None:
bin = bisect.bisect_right(bins, prop[0])
ans[bin] += vol
mol._slogpVSA = ans
return ans示例3: testDetails
def testDetails(self):
Crippen._Init()
with open(self.detailName,'rb') as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)示例4: testDetails2
def testDetails2(self):
Crippen._Init()
with open(self.detailName2,'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
with io.BytesIO(buf) as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)示例5: _doDetailFile
def _doDetailFile(self,inF,nFailsAllowed=1):
done = 0
verbose=0
nFails=0
while not done:
if verbose: print('---------------')
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
done = 1
else:
refContribs = [x[0] for x in refContribs]
refOrder= numpy.argsort(refContribs)
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
contribs = [x[0] for x in contribs]
#
# we're comparing to the old results using the oelib code.
# Since we have some disagreements with them as to what is
# aromatic and what isn't, we may have different numbers of
# Hs. For the sake of comparison, just pop those off our
# new results.
#
while len(contribs)>len(refContribs):
del contribs[-1]
order = numpy.argsort(contribs)
for i in range(len(refContribs)):
refL = refContribs[refOrder[i]]
l = contribs[order[i]]
if not feq(refL,l):
print('%s (%s): %d %6.5f != %6.5f'%(smi,smi2,order[i],refL,l))
Crippen._GetAtomContribs(mol,force=1)
print('-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*')
nFails +=1
break;
else:
print('Problems with SMILES:',smi)
self.assertTrue(nFails<nFailsAllowed)示例6: pyPEOE_VSA_
def pyPEOE_VSA_(mol, bins=None, force=1):
""" *Internal Use Only*
"""
if not force:
try:
res = mol._peoeVSA
except AttributeError:
pass
else:
if res.all():
return res
if bins is None:
bins = chgBins
Crippen._Init()
#print('\ts:',repr(mol.GetMol()))
#print('\t\t:',len(mol.GetAtoms()))
rdPartialCharges.ComputeGasteigerCharges(mol)
#propContribs = [float(x.GetProp('_GasteigerCharge')) for x in mol.GetAtoms()]
propContribs = []
for at in mol.GetAtoms():
p = at.GetProp('_GasteigerCharge')
try:
v = float(p)
except ValueError:
v = 0.0
propContribs.append(v)
#print '\tp',propContribs
volContribs = _LabuteHelper(mol)
#print '\tv',volContribs
ans = numpy.zeros(len(bins) + 1, 'd')
for i in range(len(propContribs)):
prop = propContribs[i]
vol = volContribs[i + 1]
if prop is not None:
bin = bisect.bisect_right(bins, prop)
ans[bin] += vol
mol._peoeVSA = ans
return ans示例7: _writeDetailFile
def _writeDetailFile(self, inF, outF):
while 1:
try:
smi, refContribs = pickle.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)
pickle.dump((smi, contribs), outF)
else:
print('Problems with SMILES:', smi)示例8: CalculateMolMR
def CalculateMolMR(mol):
"""
#################################################################
Cacluation of molecular refraction value based on Crippen method
---->MR
Usage:
result=CalculateMolMR(mol)
Input: mol is a molecule object.
Output: result is a numeric value.
#################################################################
"""
return round(Crippen._pyMolMR(mol),3)示例9: 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()示例10: CalculateMolLogP2
def CalculateMolLogP2(mol):
"""
#################################################################
Cacluation of LogP^2 value based on Crippen method
---->LogP2
Usage:
result=CalculateMolLogP2(mol)
Input: mol is a molecule object.
Output: result is a numeric value.
#################################################################
"""
res=Crippen._pyMolLogP(mol)
return round(res**2,3)示例11: _writeDetailFile
def _writeDetailFile(self,inF,outF):
while 1:
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
break
else:
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
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