Re: [Rdkit-discuss] PathToSubmol on atom indices?

[Michal Krompiec]

Dear Kangway,
Thank you very much!
M.

On Thu, Jun 4, 2020 at 6:56 PM Chuang, Kangway 
wrote:

> Hi Michal,
>
> You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related
> MolFragmentToSmarts) and specify an atom id list with "atomsToUse":
>
> e.g.
>
> rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15])
>
> Kangway
> --
> *From:* Michal Krompiec 
> *Sent:* Thursday, June 4, 2020 10:45 AM
> *To:* RDKit Discuss 
> *Subject:* [Rdkit-discuss] PathToSubmol on atom indices?
>
> Hello, I noticed this was discussed before and I'm wondering if anything's
> changed.
> Is it possible to extract a substructure from a molecule, based on atom
> indices? I understand that Chem.PathToSubmol does something similar, but
> takes bond indices.
> Best,
> Michal
>
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Re: [Rdkit-discuss] PathToSubmol on atom indices?

[Chuang, Kangway]

Hi Michal,

You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related 
MolFragmentToSmarts) and specify an atom id list with "atomsToUse":

e.g.

rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15])

Kangway

From: Michal Krompiec 
Sent: Thursday, June 4, 2020 10:45 AM
To: RDKit Discuss 
Subject: [Rdkit-discuss] PathToSubmol on atom indices?

Hello, I noticed this was discussed before and I'm wondering if anything's 
changed.
Is it possible to extract a substructure from a molecule, based on atom 
indices? I understand that Chem.PathToSubmol does something similar, but takes 
bond indices.
Best,
Michal
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[Rdkit-discuss] PathToSubmol on atom indices?

[Michal Krompiec]

Hello, I noticed this was discussed before and I'm wondering if anything's
changed.
Is it possible to extract a substructure from a molecule, based on atom
indices? I understand that Chem.PathToSubmol does something similar, but
takes bond indices.
Best,
Michal
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss