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<http://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<mailto: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<mailto: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&!H0]: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)<UrlBlockedError.aspx>'
#Replace 2× Ph-* with 2× 3-Fl-C6H4-*
rxn4=AllChem.ReactionFromSmarts(rSMARTS4)
rxn4
[cid:image001.png@01D2A957.14773010]
m4=Chem.MolFromSmiles('c1ccccc1CCOCc1ccccc1')
m4
[cid:image002.png@01D2A957.14773010]
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))
[cid:image003.png@01D2A957.14773010]
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
[cid:image004.png@01D2A957.14773010]
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))
[cid:image005.png@01D2A957.7D27E0A0]
Just to be sure this is as I think it looks..
prodsbi[0][0]
[cid:image006.png@01D2A957.7D27E0A0]
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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