On Thu, Feb 25, 2016 at 2:16 AM, Brian Kelley <[email protected]> wrote:
> It is hard to tell if this is a bug or not, however:
>
> atomCompare=rdFMCS.AtomCompare.CompareAny,
> bondCompare=rdFMCS.BondCompare.CompareAny,
>
> Means that any atom matches any other atom and any bond matches any other
> bond. The smarts being returned does not have the appropriate wildcards.
>
> '[#6](:[#6](-[#6]):[#7]:[#7]:[#6]=[#8]):[#6]'
>
>
> The mcs you actually computed should have been something like:
>
>
> mcs = Chem.MolFromSmarts('[*](~[*](~[*])~[*]~[*]~[*]~[*])~[*]')
>
> print moli_noh.GetSubstructMatch(mcs)
> print molj_noh.GetSubstructMatch(mcs)
>
>
> (0, 1, 7, 9, 10, 2, 11, 12)
> (0, 1, 6, 8, 9, 5, 3, 2)
>
>
>
> So it looks like the smarts generation portion of the MCS code doesn't apply
> the rules of the mcs matcher. Bug? Maybe :)
>
>
Certainly not. It's a feature, and one I really like. There is definitely a
bug somewhere that's causing the problems with Gaetano's example, but
here's a small example that shows how it's supposed to work:
In [21]: mol1 = Chem.MolFromSmiles('Cc1nc(O)ccc1')
In [22]: mol2 = Chem.MolFromSmiles('Cc1cc(O)ccc1')
In [23]: mcs = rdFMCS.FindMCS([mol1,mol2],
timeout=20,
atomCompare=rdFMCS.AtomCompare.CompareAny,
bondCompare=rdFMCS.BondCompare.CompareAny,
matchValences=False,
ringMatchesRingOnly=True,
completeRingsOnly=False,
matchChiralTag=False)
In [25]: mcs.smartsString
Out[25]: '[#6]-[#6]1:[#7,#6]:[#6](-[#8]):[#6]:[#6]:[#6]:1'
The interesting atom here is the third one. When the MCS is found the
identity of the atoms is ignored while determining whether or not they
match each other, but the actual maximum common substructure of those two
molecules has either a N or a C as the third atom. This is what the SMARTS
tells you.
Gaetano, you have found a bug. We'll look into it.
-greg
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