Re: [Rdkit-discuss] Exhaustive fragmentation of molecules

[Paolo T. <pao...@gm...>]

Dear Puck,

You may break a bond by creating a Chem.RWMol out of your Chem.Mol, and 
then calling the RemoveBond() method on your Chem.RWMol, or you may use 
dedicated functions in the rdmolops module. Individual fragments can 
then be obtained by calling rdmolops.GetMolFrags().

I have put together a gist here:

https://gist.github.com/ptosco/3fb93b7c09dac15b6d355eb0ad29f532

to show examples of the above; I hope this will help get you started on 
your task.

Cheers,
p.

On 08/01/2020 10:39, Puck van Gerwen wrote:
> Dear rdkit community,
>
> I am looking to start from a mol object (loaded from an .xyz file) and 
> return all possible fragments (as mol objects) generated from breaking 
> one bond (any bond order). I don't want any pre-encoded rules about 
> which bonds to break as in BRICS. I saw some discussions on the forum 
> about using EditableMol or other mol types. Would you be able to point 
> me to the best way to do this?
> Thanks very much.
>
> -- 
> Puck van Gerwen
> Doktorandin
> Gruppe von Anatole von Lilienfeld
> Universität Basel
>
>
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