Thanks Rafael.
Best,
Ming
On Mon, May 16, 2022 at 2:27 AM Rafael L <rafael.lame...@usp.br> wrote:
> To find all compounds that match the ester substructure, you can use
> GetSubstructMatches. I would do the following (I'm supposing you have all
> your structures in a Pandas dataframe, and that you converted SMILES to
> RDKit Mol):
>
> ester_pattern = Chem.MolFromSmarts("COC(C)=O")
>
> # in a pandas dataframe with a column containing your structures as RDKit
> Mol objects
> df["is_ester"] = df["rdkit_mol"].apply(lambda x:
> bool(x.GetSubstructMatches(ester_pattern)))
>
> This will give you a column with 0s and 1s that you can use as a mask. Of
> course, there are other ways to do this, like using a for loop.
> Now, to replace the esters by the disulfide group, if you can't manage to
> work with reaction SMARTS, you could try using Python strings' replace()
> method on SMILES. I believe esters can be represented in two ways (left to
> right and right to left), so keep that in mind. You can always use
> GetSubstructMatches later to see if any ester was left behind.
> Regards.
>
> On Sun, May 15, 2022 at 1:33 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
>>
>
>
> --
> *Rafael da Fonseca Lameiro *
> PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED)
> São Carlos Institute of Chemistry - University of São Paulo - Brazil
> [image: orcid logo 16px] https://orcid.org/0000-0003-4466-2682
>
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