Hi,
Thanks a lot for the reply! However, in this case, it looks like I would
have to somehow label the isotope in every query molecule, right? For
example:
```
template =
Chem.MolFromSmarts('[c]1(-[2S](=[3O])(=[3O])(-C)):[c]:[c]:[c]:[c]:[c]:1')
mol1 = Chem.MolFromSmiles('CS(=O)(=O)c1ccc(C2=C(c3ccccc3)CCN2)cc1')
compare = [template,mol1]
res = rdFMCS.FindMCS(compare,
atomCompare=rdFMCS.AtomCompare.CompareIsotopes,
bondCompare=rdFMCS.BondCompare.CompareAny,
ringMatchesRingOnly=False,
completeRingsOnly=False)
res.smartsString
```
returns: '[0*]1:[0*]:[0*]:[0*]:[0*]:[0*]:1', that is, it only picks the
ring but not the sulfone. I actually want the sulfone to be found, if it is
there. My problem is that I also want flexibility to change the ring atoms
and still find the ring as a match, while considering a match on the
sulfone only if it really is there. (e.g., CF3 should *not* match.) Does it
make sense?
Thanks a lot!
--
Gustavo Seabra.
On Thu, Jul 22, 2021 at 4:52 PM Andrew Dalke <da...@dalkescientific.com>
wrote:
> Hi Gustavo,
>
>
> > template =
> Chem.MolFromSmarts('[a]1(-[S](-*)(=[O])=[O]):[a]:[a]:[a]:[a]:[a]:1')
>
> Unless things have changed since I last looked at the algorithm, you can't
> meaningfully pass a SMARTS-based query molecule into the MCS program,
> outside of a few simple cases.
>
> It generates a SMARTS pattern based on the properties of the molecule. You
> asked it to CompareElements, but those [a] terms all have an atomic number
> of 0.
>
> >>> template =
> Chem.MolFromSmarts('[a#1]1(-[S](-*)(=[O])=[O]):[a#1]:[a#1]:[a#1]:[a#1]:[a#1]:1')
> >>> [a.GetAtomicNum() for a in template.GetAtoms()]
> [0, 16, 0, 8, 8, 0, 0, 0, 0, 0]
>
> That's why your CompareAny search returns the #0 terms, like:
>
>
> '[#16,#6](-[#0,#6])(=,-[#8,#9])(=,-[#8,#9])-[#0,#6]1:[#0,#6]:[#0,#6]:[#0,#6]:[#0,#6]:[#0,#7]:1'
>
> > I would appreciate some pointers on how it would be possible to find the
> maximum common substructure of 2 molecules, where in the template structure
> some atoms may be *any*, but some other atoms must be fixed.
>
> Perhaps with isotope labelling?
>
> That is, label the "any" atoms as isotope 1, and label your
> -[S](=[O])(=[O])- as -[2S](=[3O])(=[3O])-
>
> Then use rdFMCS.AtomCompare.CompareIsotopes .
>
> If there's anything you don't want to match at all, give each atom a
> unique isotope value.
>
> Best regards,
>
> Andrew
> da...@dalkescientific.com
>
>
>
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