Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom

[Bin S. <bin...@pr...>]

Hello Paul,

I will take a look at your code. Thank you.









-------- Original Message --------
Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
Local Time: October 14, 2016 1:12 AM
UTC Time: October 13, 2016 5:12 PM
From: pe...@mr...
To: rdk...@li...

On 13/10/2016 05:04, Bin Song wrote:
> Hello everyone,
>
> A new user of Rdkit and new subscriber of the mailing list reporting here.
>
> I have a question to ask, as stated in the subject. I have googled and consulted the
> documentation of rdkit, but found no answer. Basically, I want to run a search with a smarts
> string on my molecule. I am interested in the hydrogen atoms bonded to an atom that is part
> of the match, as GetSubstructMatches does not return the idx of hydrogens. Because I am
> looking at crystal structures, I want the idx of hydrogen so that I get the 3D coordinates
> of the hydrogen to perform further computations. If anyone has any tips and good ideas,
> please let me know.

Are you sure? I use HasSubstrMatch to match hydrogens.

see set_atom_type() here:

https://github.com/pemsley/coot/blob/master/pyrogen/atom_types.py

I think that this is more or less what you want to do.

(As you might be able to work out, I too have an interest in hydrogens on ligands in protein
ligand crystal structures.)

Paul.


------------------------------------------------------------------------------
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
Rdk...@li...
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss