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)' #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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