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
self.failUnless(nFails < nFailsAllowed)
else:
print 'Problems with SMILES:', smi
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
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
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)
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)
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)
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()
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()
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
def crippen_molar_refractivity_contrib(a):
""" Hacky way of getting molar refractivity contribution. """
idx = a.GetIdx()
m = a.GetOwningMol()
return Crippen._GetAtomContribs(m)[idx][1]
def crippen_log_p_contrib(a):
""" Hacky way of getting logP contribution. """
idx = a.GetIdx()
m = a.GetOwningMol()
return Crippen._GetAtomContribs(m)[idx][0]