Hi Greg,
Greg wrote:
> You actually don't need to add the Hs:
> >>> p1 = Chem.MolFromSmarts('[#7,#8;H1]')
> >>> p2 = Chem.MolFromSmarts('[#7,#8;H2]')
> >>> p3 = Chem.MolFromSmarts('[#7,#8;H3]') m =
> >>> Chem.MolFromSmiles('CC(=O)N')
> >>> m2 = Chem.MolFromSmiles('OCC(=O)N')
> >>> def NHOHCount(mol): return
> >>>
> len(mol.GetSubstructMatches(p1))+2*len(mol.GetSubstructMatches(p2))+
> >>> 3*len(mol.GetSubstructMatches(p3))
> ...
> >>> NHOHCount(m)
> 2
> >>> NHOHCount(m2)
> 3
I think this system works well in almost all cases : ) However, I had a
nagging concern over a couple of 'edge' cases - namely water, and
ammonia (and for that matter, the oxonium and ammonium ions).
I guess the simple inclusion of P4 = Chem.MolFromSmarts('[#8;H4]') would
make sure all cases were covered(?).
Out of interest, I decided to compile a small list of 'normal' and
'edge' case SMILES, and ran it through the MOE descriptor node in KNIME.
For all these cases, lip_don behaves as I would expect (tab-separated
output included below)
Kind regards
James
"SMILES" "a_acc" "a_don" "lip_acc" "lip_don"
"CO" 1.0 1.0 1.0 1.0
"C(=O)N" 1.0 1.0 2.0 2.0
"O" 1.0 1.0 1.0 2.0
"CN" 1.0 1.0 1.0 2.0
"[O+]" 1.0 0.0 1.0 3.0
"C[O+]" 1.0 0.0 1.0 2.0
"[N+]" 0.0 0.0 1.0 4.0
"C[N+]" 0.0 0.0 1.0 3.0
"[N-]" 0.0 1.0 1.0 2.0
"[O-]" 0.0 1.0 1.0 1.0
"C(=O)[N-]" 0.0 1.0 2.0 1.0
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