Hi,
I’m trying to generate 2Dpharmacophore fingerprints as described here
https://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints
<https://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints>
For the majority of molecules this works fine but for a few I get this
error, any idea what the issue is?
Chris
qmol =
Chem.MolFromSmiles('COc1ccc(C(C)C)cc1CN[C@H]1C2CCN(CC2)[C@H]1C(c1ccccc1)c1ccccc1')
fpquery = Generate.Gen2DFingerprint(qmol,sigFactory)
fpquery
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
inGetBitIdx(self, featIndices, dists, sortIndices)
248 print('\tbins:', repr(self._bins), type(self._bins))
--> 249bin_= self._findBinIdx(dists, self._bins, self._scaffolds[len(dists)])
250 except ValueError:
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
in_findBinIdx(self, dists, bins, scaffolds)
167 whichBins[i] = where
--> 168res= scaffolds.index(tuple(whichBins))
169 if _verbose:
ValueError: (0, 2, 0) is not in list
During handling of the above exception, another exception occurred:
IndexError Traceback (most recent call last)
<ipython-input-23-254e36ab25ba> in<module>
1 qmol=
Chem.MolFromSmiles('COc1ccc(C(C)C)cc1CN[C@H]1C2CCN(CC2)[C@H]1C(c1ccccc1)c1ccccc1')
----> 2fpquery= Generate.Gen2DFingerprint(qmol,sigFactory)
3 fpquery
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/Generate.py
inGen2DFingerprint(mol, sigFactory, perms, dMat, bitInfo)
160 for matchin matchesToMap:
161 if sigFactory.shortestPathsOnly:
--> 162idx= _ShortestPathsMatch(match, perm, sig, dMat, sigFactory)
163 if idxis not None and bitInfois not None:
164 l= bitInfo.get(idx, [])
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/Generate.py
in_ShortestPathsMatch(match, featureSet, sig, dMat, sigFactory)
71 dist[i] = d
72
---> 73idx= sigFactory.GetBitIdx(featureSet, dist, sortIndices=False)
74 if _verbose:
75 print('\t', dist, minD, maxD, idx)
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py
inGetBitIdx(self, featIndices, dists, sortIndices)
252 fams= [fams[x] for xin featIndices]
253 raise IndexError('distance bin not found: feats: %s; dists=%s;
bins=%s; scaffolds: %s' %
--> 254(fams, dists, self._bins, self._scaffolds)) 255
256 return startIdx+ offset+ bin_
IndexError: distance bin not found: feats: ['Acceptor', 'Aromatic',
'Hydrophobe']; dists=[1, 5, 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]
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