I believe that this is a bug, but it may be tricky to fix due to an
interaction with another feature.
Here's another simple example:
https://gist.github.com/greglandrum/a44f692bda8d110df309e561ea35f364
Input 6 is, analogous to what's happening to you Steve.
The normal process when running a reaction is to initialize a product
molecule with atoms from the product template and then to add the remaining
atoms/bonds from the reactant that are reachable from those matching atoms.
If there is a bond between matching atoms in the reactant but not in the
product template it will not be added to the product. This allows ring
opening reactions to happen (see input 10).
I think there's a way around this by adding bonds in the product if the
matching atoms are bonded in the reactant but not in the reactant template,
but I'm going to have to try it and see what the consequences are.
Here's the github issue:
https://github.com/rdkit/rdkit/issues/1387
-greg
On Thu, Mar 30, 2017 at 11:03 PM, Stephen Roughley <s.rough...@vernalis.com>
wrote:
> Thanks Brian.
>
> I think you have got to what I am trying to do - basically, trying to
> replace 2 identical groups in 2 separate parts of the molecule with the
> same second group, hence the component grouping in reagents and products.
> It works fine until the corner case shown. (Actually, it also fails if the
> dummy atoms [*:1] and [*:2] are required to match the same atom, as they
> would in e.g. c1ccccc1Oc1ccccc1, but that makes at least some more sense to
> me!)
>
> One possible workaround is to do the same reaction iteratively, to replace
> each group in turn. That would work in this case, but in a case where the
> reagent will match the product, it will give the wrong products, e.g. the
> transform:
>
> [C;H3]-!@[*:1]>>C-C-[*:1]
>
> I'm guessing this is probably a limitation of the rSMARTS definition,
> where the reaction products need to be something intermediate between
> SMARTS and SMILES.
>
> Steve
> ------------------------------
> *From:* Brian Kelley [fustiga...@gmail.com]
> *Sent:* 30 March 2017 17:59
> *To:* Stephen Roughley
> *Cc:* RDKit Discuss (rdkit-discuss@lists.sourceforge.net)
> *Subject:* Re: [Rdkit-discuss] RDKit Reaction gives disconnected
> components
>
> Correction here, you are not making two products because you are grouping
> the results ala:
>
> >>> rxn = AllChem.ReactionFromSmarts("([C:1][*][N:2])>>([C:1].[N:2])")
>
> >>> prods = rxn.RunReactants([Chem.MolFromSmiles("FC1ON1I")])
>
> >>> Chem.MolToSmiles(prods[0][0])
>
> 'CF.NI'
>
> However, it appears that you aren't mapping anything explicitly between
> [C:1] and [N:2] in some cases so the left hand side doesn't know what
> really to do.
>
> I'll have to dig into this a little more.
>
> Cheers,
> Brian
>
>
> On Thu, Mar 30, 2017 at 12:56 PM, Brian Kelley <fustiga...@gmail.com>
> wrote:
>
>> I have a feeling you may need to make two reactions. Let's consider a
>> dirt simple case:
>>
>> >>> rxn = AllChem.ReactionFromSmarts("[C:1][N:2]>>[C:1].[N:2]")
>>
>> >>> prods = rxn.RunReactants([Chem.MolFromSmiles("CN")])
>>
>> >>> Chem.MolToSmiles(prods[0][0])
>>
>> 'C'
>>
>> >>> Chem.MolToSmiles(prods[0][1])
>>
>> 'N'
>>
>> >>>
>>
>> Note that this reaction is explicitly breaking a bond. I think this is
>> what you are seeing with your example.
>>
>> Note that similar to the "." on the reagent side meaning multiple
>> reagents, the "." on the right hand side means there will be multiple
>> products.
>>
>> Does this help at all?
>>
>> Cheers,
>> Brian
>>
>> On Thu, Mar 30, 2017 at 12:07 PM, Stephen Roughley <
>> s.rough...@vernalis.com> wrote:
>>
>>> Dear Greg/RDKitters,
>>>
>>>
>>>
>>> This may be user error, or misunderstanding of rSMARTS, so can anyone
>>> throw some light on the following behaviour?
>>>
>>>
>>>
>>> First example works as expected – there are 2× Ph in m4, so we end up
>>> with 2×2×2 copies of the expected product:
>>>
>>>
>>>
>>> rSMARTS4='([*:1]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H
>>> 0]:1.[*:2]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:1)>
>>> >([*:1]-!@c:1:c:c(-F):c:c:c1.[*:2]-!@c:1:c:c(-F):c:c:c1)
>>> <http://UrlBlockedError.aspx>' #Replace 2× Ph-* with 2× 3-Fl-C6H4-*
>>>
>>> rxn4=AllChem.ReactionFromSmarts(rSMARTS4)
>>>
>>> rxn4
>>>
>>> m4=Chem.MolFromSmiles('c1ccccc1CCOCc1ccccc1')
>>>
>>> m4
>>>
>>> prodsbi=rxn4.RunReactants((m4,))
>>>
>>> for prod in prodsbi:
>>>
>>> Chem.SanitizeMol(prod[0])
>>>
>>> Draw.MolsToGridImage([prod[0] for prod in prodsbi],molsPerRow=4,
>>> subImgSize=(200,200))
>>>
>>>
>>>
>>> Now consider the following – the only difference I can think of is that
>>> the [*:1] and [*:2] atoms map to adjacent, directly bonded atoms – I cant
>>> see why that should matter…
>>>
>>>
>>>
>>> m3=Chem.MolFromSmiles('c1ccccc1COc1ccccc1')
>>>
>>> m3
>>>
>>> prodsbi=rxn4.RunReactants((m3,))
>>>
>>> for prod in prodsbi:
>>>
>>> Chem.SanitizeMol(prod[0])
>>>
>>> Draw.MolsToGridImage([prod[0] for prod in prodsbi],molsPerRow=8,
>>> subImgSize=(200,200))
>>>
>>>
>>>
>>> Just to be sure this is as I think it looks..
>>>
>>> prodsbi[0][0]
>>>
>>>
>>>
>>> Any suggestions as to why this happens, and whether it is the expected
>>> behaviour? (And how to avoid it?!)
>>>
>>> Thanks,
>>>
>>> Steve
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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