I meant the smarts not matching the atom comparisons might be a bug, the "or"
approach for combining atoms and bonds is much cleaner and makes a lot more
sense. I can see use cases for both actually.
----
Brian Kelley
> On Feb 25, 2016, at 1:31 AM, Greg Landrum <[email protected]> wrote:
>
>
>
>> 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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