On Fri, Feb 14, 2014 at 12:03 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > I have a number of multimolecular complexes that I'm converting into
> canonical SMILES. Some of these molecules are carbon monoxide, and I am
> noticing that sometimes they are written as [C]=O, and sometimes as O=[C].
> >
> > Is the expected behavior of canonical SMILES - or should it instead be
> canonicalizing each molecule in the complex?
>
> I'm not sure that there is specific code in place for multi molecular
> systems. What you describe (that each fragment have a canonical ordering)
> is a useful idea, since it makes it much easier to parse the string into
> canonical pieces.
>
The original canonicalizer worked this way -- each fragment's symmetry was
computed independently and the labels generated such that a fragment would
canonicalize the same way no matter whether it appeared alone or as part of
a larger molecule. It must have changed at the last major release.
This is actually a pretty bad thing. But it may not be that easy to fix,
and would result in a major change to the SMILES that OpenBabel produces
(very unfortunate, as it requires large databases to be completely
re-canonicalized).
Craig
>
> Could you file a bug to remind me to get through this before the next
> release? Basically, I'd just make sure that in a multi-fragment SMILES,
> each fragment is canonicallized separately and then the result is put into
> a canonical ordering of fragments.
>
> Thanks,
> -Geoff
>
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