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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