Hi Josh,
This looks like it might be doable, but before I start guessing: can you
please give examples(s) of what you would like to have as output for the
molecule below?
-greg
On Tue, Dec 9, 2014 at 3:23 PM, Campbell J.E. <[email protected]> wrote:
> Hi rdkit users,
>
>
>
> I have some linear ring molecules (such as pentacene, anthracene etc) with
> various substitutions that I want to fragment into individual rings and
> recombine as a new molecule. What’s the best way to do this in rdkit? I’ve
> been trying to use EditableMol but I can’t access all the fragments, or
> remove more bond at once. Here’s my code so far:
>
>
>
> #n1ccc2nc3cc4cc5ccncc5cc4nc3nc2c1
>
> break_atoms = [list(x) for x in
> m3.GetSubstructMatches(Chem.MolFromSmarts('[R2]'))]
>
> break_bonds = ((3,20), (5,18), (7,16), (9,14))
>
> em = Chem.EditableMol(m3)
>
> em.RemoveBond(3,20)
>
> nm = em.GetMol()
>
> frags = Chem.GetMolFrags(nm,asMols=True)
>
> [Chem.MolToSmiles(x,True) for x in frags]
>
>
>
> I’ve had a look at the substructure replace function as well but I guess
> I’d need to identify the ring substructures first? Thanks for any help.
>
>
>
> Josh Campbell
>
>
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