Ideally, I'd like to treat these pseudoatoms as similarly to normal atoms as
possible. I would mostly want to use them for substructure matching, running
reactions, and also display purposes. Also, basic atom queries, such as
getting a mapping number or a atom symbol.
I was thinking that maybe this could be done by just defining the CoA atom type
(for example) just as the carbon or oxygen atom types are defined (setting
atomic weight, valences, etc.).
Does this make sense?
- Kovas
________________________________
From: Greg Landrum <greg.land...@gmail.com>
Sent: Wednesday, September 27, 2017 2:27:04 AM
To: Kovas Palunas
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit
Where would you want to use this?
Is it for depiction (i.e. drawing molecules) or something else?
-greg
On Tue, Sep 26, 2017 at 10:12 PM, Kovas Palunas
<kovas.palu...@arzeda.com<mailto:kovas.palu...@arzeda.com>> wrote:
Hi all,
Has anyone tried implementing or using a group to atom masking strategy in
RDKit? By this I mean taking a piece of a molecule and representing it as a
single atom. Here is an example:
CCCCO could be represented as [But]O, where the atom [But] represents the
four carbon chain.
In my case I'm particularly interested is using this strategy to represent
large biological molecules / molecule pieces, such as coenzyme A.
If I were to implement this myself, is there a place in RDKit where atom types
can be defined?
Thanks!
- Kovas
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