Hello,
I found two issues which are reproducible in 2016.09 and 2017.3 conda
builds.
0. The first issue is related to PostgreSQL. If I try to install it
from conda it asks me to downgrade rdkit to 2016.3. After downgrading of
rdkit psql works well.
1. Generation of 2D pharmacophore fingerprints using default
parameters returns errors for some molecules. However if I add
trianglePruneBins=False option to initialization procedure of a
signature factory it starts working. It seems that Gen2DFingerprint
ignores trianglePruneBins parameter. Below is a code example:
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem.Pharm2D import Generate
import os
fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef')
factory = ChemicalFeatures.BuildFeatureFactory(fdefName)
sigFactory = SigFactory(factory, minPointCount=2, maxPointCount=3,
trianglePruneBins=True) # replace to False and the error will
disappear(True is a default value)
sigFactory.SetBins([(0,2),(2,5),(5,8)])
sigFactory.Init()
mol = Chem.MolFromSmiles('Cc1nc(CN(C)c2ncnc3ccc(-c4ccc5c(c4)OCO5)cc23)cs1')
fp = Generate.Gen2DFingerprint(mol, sigFactory)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/home/pavlo/anaconda3/envs/rdk_2017_3/lib/python3.6/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
in GetBitIdx(self, featIndices, dists, sortIndices)
249 print('\tbins:', repr(self._bins), type(self._bins))
--> 250 bin_ = self._findBinIdx(dists, self._bins,
self._scaffolds[len(dists)])
251 except ValueError:
/home/pavlo/anaconda3/envs/rdk_2017_3/lib/python3.6/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
in _findBinIdx(self, dists, bins, scaffolds)
169 whichBins[i] = where
--> 170 res = scaffolds.index(tuple(whichBins))
171 if _verbose:
ValueError: (2, 0, 0) is not in list
During handling of the above exception, another exception occurred:
IndexError Traceback (most recent call last)
<ipython-input-8-0e6b1a52de56> in <module>()
1 # from rdkit.Chem.Pharm2D import Generate
2 mol =
Chem.MolFromSmiles('Cc1nc(CN(C)c2ncnc3ccc(-c4ccc5c(c4)OCO5)cc23)cs1')
----> 3 fp = Generate.Gen2DFingerprint(mol, sigFactory)
/home/pavlo/anaconda3/envs/rdk_2017_3/lib/python3.6/site-packages/rdkit/Chem/Pharm2D/Generate.py
in Gen2DFingerprint(mol, sigFactory, perms, dMat, bitInfo)
160 for match in matchesToMap:
161 if sigFactory.shortestPathsOnly:
--> 162 idx = _ShortestPathsMatch(match, perm, sig, dMat,
sigFactory)
163 if idx is not None and bitInfo is not None:
164 l = bitInfo.get(idx, [])
/home/pavlo/anaconda3/envs/rdk_2017_3/lib/python3.6/site-packages/rdkit/Chem/Pharm2D/Generate.py
in _ShortestPathsMatch(match, featureSet, sig, dMat, sigFactory)
71 dist[i] = d
72
---> 73 idx = sigFactory.GetBitIdx(featureSet, dist, sortIndices=False)
74 if _verbose:
75 print('\t', dist, minD, maxD, idx)
/home/pavlo/anaconda3/envs/rdk_2017_3/lib/python3.6/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
in GetBitIdx(self, featIndices, dists, sortIndices)
253 fams = [fams[x] for x in featIndices]
254 raise IndexError('distance bin not found: feats: %s;
dists=%s; bins=%s; scaffolds: %s' %
--> 255 (fams, dists, self._bins, self._scaffolds))
256
257 return startIdx + offset + bin_
IndexError: distance bin not found: feats: ['Acceptor', 'Aromatic',
'Aromatic']; dists=[5, 1, 1]; bins=[(0, 2), (2, 5), (5, 8)]; scaffolds:
[0, [(0,), (1,), (2,)], 0, [(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1),
(0, 1, 2), (0, 2, 1), (0, 2, 2), (1, 0, 0), (1, 0, 1), (1, 0, 2), (1, 1,
0), (1, 1, 1), (1, 1, 2), (1, 2, 0), (1, 2, 1), (1, 2, 2), (2, 0, 1),
(2, 0, 2), (2, 1, 0), (2, 1, 1), (2, 1, 2), (2, 2, 0), (2, 2, 1), (2, 2,
2)], 0]
Kind regards,
Pavel.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
