Re: [Rdkit-discuss] Masking groups as atoms in RDKit

[Kovas P. <kov...@ar...>]

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 <gre...@gm...>
Sent: Wednesday, September 27, 2017 2:27:04 AM
To: Kovas Palunas
Cc: rdk...@li...
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 <kov...@ar...<mailto:kov...@ar...>> 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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