Hi Brian
I'm by no means an expert in RDKit with Python, but until someone else
comes along, here are a few thoughts.
Your reaction SMARTS specifically defines aromatic carbons joined by single
bonds which won't match an incoming benzene ring, and it's a bit redundant
to specify that aromatic carbons are in rings. It's possibly also neater to
specify the ring closure if you want to include the whole ring. Finally, I
don't think that you can specify dummy atoms in a reaction SMARTS as you're
attempting (it certainly doesn't work for me with R and R1) but you
certainly can specify 'placeholder' atoms using real elements. I've found
U, V & W handy for this in the past.
A small Python script with a modified SMARTS which works for me is -
from rdkit import Chem
from rdkit.Chem import AllChem
rxn =
AllChem.ReactionFromSmarts('[c:1]1[c:2][c:3][c:4][c:5]([U:7])[c:6]1.[V:8]-[*:9]
>> [c:1]1[c:2][c:3][c:4][c:5](-[*:9])[c:6]1')
ps =
rxn.RunReactants((Chem.MolFromSmiles('c1ccccc1[U]'),Chem.MolFromSmiles('[V]Cl')))
Chem.MolToSmiles(ps[0][0])
This returns 'Clc1ccccc1'.
Unless you have some specific reason to include the complete benzene ring,
the reaction SMARTS can be simplified a lot further, to -
[c:1][U:2].[V:3]-[*:4] >> [c:1]-[*:4]
This will carry out your virtual reaction on any aromatic carbon carrying
the appropriate placeholder element.
I'd be interested to learn if there is an approved way to mark substitution
positions in reactions like this without having to resort to the cheat of
using obscure elements.
Regards,
Chris
On 15 March 2017 at 23:20, Bennion, Brian <benni...@llnl.gov> wrote:
> Hello All,
>
>
>
> I have looked around the email list and studied the daylight guide as well
> as the opensmiles website in hopes of solving my problem. External
> r-groups is a proposed extension but that is all I could find.
>
>
>
> It is possible that I have made it too complicated though.
>
>
>
> In discussions with my synthetic chemist we came up with 27 substituents
> two place around our molecule scaffold.
>
> I labeled the scaffolds with R1 in the position that the substitution will
> occur and attached a dummy label to the substituents. I thought that I
> could do a simple replacement rxn. However, I have not been successful.
>
>
>
> The smarts string so far is listed below.
>
>
>
> AllChem.ReactionFromSmarts('[c;R:1]-[c;R:2]-[c;R:3]-[c;R:4]
> -[c;R:5]([R1;!R:7])-[c;R:6].[R:8]-[*:9] >> [c;R:1]-[c;R:2]-[c;R:3]-[c;R:
> 4]-[c;R:5]([*:9])-[c;R:6]')
>
>
>
> Basically just adding a group to positions along a benzene ring
>
>
>
> Thanks
>
> Brian Bennion
>
>
>
>
>
>
>
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