Thanks Christopher. I will try that. Best, Ming
On Sun, May 15, 2022 at 12:40 AM Christopher Mayer-Bacon <cmaye...@umbc.edu> wrote: > 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 >> > _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > >> -- > -Christopher Mayer-Bacon (*he/him/his*) > PhD student > Department of Biological Sciences > University of Maryland, Baltimore County >
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