HI Greg,
Ideally I’d like the output to be one ring cleaved from the molecule, which
then can be attached to another similar molecule. Nicks code yesterday allowed
me to cleave a ring pretty easily, just have to reattach it now.
Example output would be like this: n1ccc2nc3cc4cc5ccncc5cc4nc3nc2c1 =
c1ccncc1 + rest of molecule.
Josh
From: Greg Landrum [mailto:[email protected]]
Sent: 10 December 2014 02:41
To: Campbell J.E.
Cc: [email protected]
Subject: Re: [Rdkit-discuss] Chopping and recombining molecules
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]<mailto:[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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