It seems the bins for the distances (tuple (0,2,0)) did not pass the triangle
inequality test and was deemed invalid. Setting `trianglePruneBins` to False
when you construct the SigFactory should fix it:
> sigFactory =
> SigFactory(featFactory,minPointCount=2,maxPointCount=3,trianglePruneBins=False)
Hope it helps.
Eddie
On Sep 3, 2013, at 11:26 AM, Patrick Walters <wpwalt...@gmail.com> wrote:
> 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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