Ming,
I’m not at my computer now, but I think you may be better served with using
the reaction functionality instead of replacing substructures via
ReplaceSubstructs. You can probably create a reaction SMARTS string for
converting a generic ester to a generic disulfide (
https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html).
On Sun, May 15, 2022 at 12:31 AM Ming Hao <haom.ni...@gmail.com> wrote:
> Hi All,
>
> I want to replace the ester structure ('COC(C)=O') with disulfide ('CSSC')
>
> [image: image.png]
>
> Here is what I did, but it does not work. It seems to need specified
> methods to replace the original structure with the new one, not just put
> individual SMILES there.
>
> ##############################################################
> from rdkit import Chem
> from rdkit.Chem import AllChem, Draw
> from rdkit.Chem.Draw import IPythonConsole
>
> orgsmi = 'CCOC(=O)CCCCCN(CC)CCCCCCCC(=O)OC(C)CC'
> m = Chem.MolFromSmiles(orgsmi)
> m
>
> pat = Chem.MolFromSmiles('COC(C)=O')
> pat
>
> rep = Chem.MolFromSmiles('CSSC')
> rep
>
> new = AllChem.ReplaceSubstructs(m, pat, rep)
> new[0] # The structure was separated
> new[1] # The structure was separated
> len(new)
> #################################################################
>
> Can you help me with this? By the way, I have 10K structures, and first I
> need to find the compounds with the pattern (ester, COC(C)=O) and replace
> them with disulfide ('CSSC'). What is a good way to do this?
>
> Thanks.
> Ming
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>
--
-Christopher Mayer-Bacon (*he/him/his*)
PhD student
Department of Biological Sciences
University of Maryland, Baltimore County
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