Hi All,
I was working through the 2D pharmacophore example in the "Getting Started"
docs
http://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints
and I threw an exeception that I don't understand. Here's my code
==================================
#!/usr/bin/env python
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem.Pharm2D import Generate
mol = Chem.MolFromSmiles("CC12CCC3C(CCc4cc(O)ccc34)C2CC(O)C1O")
fdefName = 'MinimalFeatures.fdef'
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefName)
sigFactory = SigFactory(featFactory,minPointCount=2,maxPointCount=3)
sigFactory.SetBins([(0,2),(2,5),(5,8)])
sigFactory.Init()
print sigFactory.GetSigSize()
Generate.Gen2DFingerprint(mol,sigFactory)
==================================
MinimalFeatures.fdef comes from $RDBASE/Docs/Book/data/MinimalFeatures.fdef
Here's the exception
===================================
File "./test2.py", line 18, in <module>
Generate.Gen2DFingerprint(mol,sigFactory)
File
"/Users/walters/software/RDKIT/2013_09_01/rdkit-master/rdkit/Chem/Pharm2D/Generate.py",
line 154, in Gen2DFingerprint
_ShortestPathsMatch(match,perm,sig,dMat,sigFactory)
File
"/Users/walters/software/RDKIT/2013_09_01/rdkit-master/rdkit/Chem/Pharm2D/Generate.py",
line 69, in _ShortestPathsMatch
idx = sigFactory.GetBitIdx(featureSet,dist,sortIndices=False)
File
"/Users/walters/software/RDKIT/2013_09_01/rdkit-master/rdkit/Chem/Pharm2D/SigFactory.py",
line 248, in GetBitIdx
raise IndexError,'distance bin not found: feats: %s; dists=%s; bins=%s;
scaffolds: %s'%(fams,dists,self._bins,self._scaffolds)
IndexError: distance bin not found: feats: ['Acceptor', 'Aromatic',
'Donor']; 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]
======================================
Can someone tell me what I'm doing wrong? At first I thought I just needed
to increase the maximum of the last bin boundary, but that doesn't seem to
do it.
Thanks in advance,
Pat
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