Hi Toby,
On Fri, Mar 7, 2014 at 11:57 AM, Toby Wright <toby.wri...@inhibox.com>wrote:
> Thanks Greg,
>
> The final strange behaviour I've noticed that could trip fellow users up
> is with matching kekule verses aromatic representations of the same
> molecule in SMARTS against SMILES. Most surprisingly C1=CC=CC=C1 is not a
> substructure of itself but has c1ccccc1 as a substructure (if the lefthand
> term is SMILES and the right is SMARTS in both cases).
> Code to demonstrate what I mean below:
>
> > aromatic_benzene_smiles = Chem.MolFromSmiles('c1ccccc1')
> > aromatic_benzene_smarts = Chem.MolFromSmarts('c1ccccc1')
> > kekule_benzene_smiles = Chem.MolFromSmiles('C1=CC=CC=C1')
> > kekule_benzene_smarts = Chem.MolFromSmarts('C1=CC=CC=C1')
> > aromatic_benzene_smiles.HasSubstructMatch(aromatic_benzene_smarts)
> True
> > aromatic_benzene_smiles.HasSubstructMatch(kekule_benzene_smiles)
> True
> > aromatic_benzene_smiles.HasSubstructMatch(kekule_benzene_smarts)
> False
> > kekule_benzene_smiles.HasSubstructMatch(kekule_benzene_smarts)
> False
> > kekule_benzene_smiles.HasSubstructMatch(aromatic_benzene_smiles)
> True
> > kekule_benzene_smiles.HasSubstructMatch(aromatic_benzene_smarts)
> True
>
> I think I can see why there is a difference in behaviour, a double bond is
> not the same thing as an aromatic bond. In the SMILES case a conversion can
> take place because the context is complete but in the SMARTS case it is not
> (or at least might not be). But I thought I'd point out the issue in any
> case. The workaround is to always explicitly make atoms aromatic in SMARTS
> if you wish them to match aromatic SMILES rather than relying on the kekule
> representation to sort it for you.
>
There have been a couple of discussion of related topics on the list
already. There is a nice discussion of this in the Daylight Theory Manual
page for SMARTS:
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html look for
"SMARTS versus SMILES"
-greg
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