Hi all,
I'm back again with what seems to me like puzzling behaviour from the
rdfMCS.findMCS function when dealing with fused ring systems:
> mol3RA = Chem.MolFromSmiles('c1ccc2cc3ccccc3cc2c1')
> mol3RB = Chem.MolFromSmiles('c1ccc2c(c1)ccc1ccccc21')
> rdFMCS.FindMCS([mol3RA, mol3RB], matchValences=True,
matchChiralTag=True,
ringMatchesRingOnly=True,
completeRingsOnly=True # False will return the same result
).smartsString
'[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'
Or, in pictures:
[cid:image004.png@01D1C8B5.3839E890]
The MCS shown above is the same whether or not I turn on the 'completeRingsOnly
flag.
So, the atoms are all there, but the MCS ring can't be closed because the
attachment point doesn't match.
Since we're requesting completeRingsOnly, wouldn't make sense for the MCS be
reduced to just a naphthalene?
What's the rationale behind the current implementation? Is there a way to force
it to drop the open circle?
And another, related, question: is there a way to make the MCS computation even
more restrictive,
only returning a ring as part of the MCS if the whole fused system is matched,
not just a portion (albeit a complete ring by itself?). In the example
described above, there would be no MCS.
I'd be fine with some post-processing to the same aim. Another example:
[cid:image006.png@01D1C8B5.3839E890]
Thanks in advance,
Luca
Luca Fenu - Computational Chemist
Computational Chemist, CADD Group, Chemistry
Eli Lilly and Company Limited
Erl Wood Manor, Sunninghill Road, Windlesham, Surrey, GU20 6PH
012.764.83354 (office) | 07858.701.646 (mobile)
fenu_l...@network.lilly.com<mailto:surname_n...@network.lilly.com> |
www.lilly.co.uk<http://www.lilly.co.uk>
[cid:image005.jpg@01D0842C.DF674960]
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