There's currently no way to add to the periodic table. I'm somewhat
uncomfortable with the idea (there's a lot that can go wrong), but your use
case isn't that uncommon (using custom atom types to represent amino acids
has come up before), so it's worth thinking about how to do something like
this.

-greg


On Thu, Sep 28, 2017 at 8:00 AM, Kovas Palunas <kovas.palu...@arzeda.com>
wrote:

> The way i was thinking about it, the smarts of OCC would not match the
> O[but] because [but] is a totally new atom that is not related to carbon at
> all.  This doesn't really make sense in this example, but it does (i think)
> for most of my purposes (where i want to mask away a biological
> macromolecule that i do not want to interact with).
>
> There are probably still edge cases i'm not seeing... but maybe it's still
> worth a try?  I saw there was a periodic table module in RDKit.  Is it
> possible to add these atoms there?
>
> - Kovas
>
>
> From: Greg Landrum
> Sent: Wednesday, September 27, 10:13 PM
> Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit
> To: Kovas Palunas
> Cc: rdkit-discuss@lists.sourceforge.net
>
>
>
> I'm afraid that there's likely to be rather a lot of devil hiding in the
> details (as is so often the case).
>
> A simple example of one problem: let's take your [But]O case. Suppose you
> do a substructure search for the molecule defined by the SMARTS "OCC". Does
> that match "[But]O"?  What does it return when I ask for the substructure
> matches (this function, if you aren't familiar with it, returns the indices
> of the matching atoms)? What about the SMARTS "CC"?
>
> One solution to this that works with substructure searching is to have the
> molecule contain all the atoms - "CCCCO" in your example - but to have the
> four C atoms marked as a group so that drawings of the molecule display
> "[But]O". Supporting this type of functionality is on the To Do list (it's
> part of supporting S Groups from Mol files).
>
> If you just want to indicate that there is a [But] group there but not
> really do anything with the group's structure, there's are probably already
> ways to handle this using dummy atoms and custom labels.
>
> -greg
>
>
>
>
> On Wed, Sep 27, 2017 at 9:26 PM, Kovas Palunas <kovas.palu...@arzeda.com>
> wrote:
>
> 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 <rdkit-discuss@lists.sourceforge.net>-discuss@lists.
> sourceforge.net <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>
> 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
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit <Rdkit-discuss@lists.sourceforge.net>-disc...@lists.sourceforge.net
> <Rdkit-discuss@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>listinfo
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>/
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>rdkit
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>-discuss
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
>
>
>
>
>
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to