João,
The function you're looking for is:
void ObjectMoleculeAddSeleHydrogens(ObjectMolecule * I, int sele, int state)
in layer2/ObjectMolecule.c line 3629 (or thereabouts). PyMOL has a
connectivity table that determines which atoms are bound to which
others. Read over that function and see if that clarifies things for
you.
Good luck,
-- Jason
On Thu, Jul 1, 2010 at 10:54 AM, João Rodrigues <anar...@gmail.com> wrote:
> Hey Jason!
>
> Thanks for the reply, no problem at all with the delay :)
>
> I got my hands around the code and I *think* I got it to add hydrogens to a
> protein (including checking that random effect).
>
> My only question is, how PyMol determines which atoms lack hydrogens. I
> checked the hetatm.py and protein.py files and they seems to compare the
> structure with a pre-defined database of bonds for each residue. However,
> this works for proteins only right?
>
> How does it work for methane? How does it recognize that is lacks 4 atoms?
> If you can point me to the file where that part is described, that would be
> amazing! I've lost two weeks trying to figure it out already and I can't...
>
> Best!
>
> João
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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