You can match a dummy atom (*) with the SMARTS [#0]
Steve
On 16 Mar 2017 16:43, "Chris Earnshaw" <cgearns...@gmail.com> wrote:
> 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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>
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