Re: [h5md-user] Tuples and topology, the return

[Pierre de Buyl]

On Mon, Jul 14, 2014 at 09:06:50PM +0200, Konrad Hinsen wrote:
> --On 14 juillet 2014 11:37:29 +0200 Pierre de Buyl
> <address@hidden> wrote:
> 
> >>An mmCIF file contains everything. And H5MD cannot handle any of the
> >>information in a PDB entry. There is no overlap at the current stage
> >>of H5MD.
> >
> >There is. Storing properly [1] the position data is already a nice
> >feature of H5MD.
> 
> But H5MD can't store what the positions mean. I don't think any PDB
> client would be happy to have just a bunch of positions. At the very
> least, you need the chemical element and the occupancy, then you
> have at least a useable crystallographic model.

Just for clarity, by "chemical element" you simply refer to its atomic
name/number? This is really easy to put in a module (make 'species' mandatory
and clarify the meaning of the species integer value).

Occupancy? If that is a single additional variable, this is also a reasonable
addition to H5MD (be it via a module).

> Biologists still wouldn't care.

Will they ever? How can this be addressed?

> >In addition the positions, we are also able to store
> >successive sets of positions (an abuse that is sometimes made for PDB),
> >the species of the particles.
> 
> Right, that's where H5MD beats the PDB format (and also mmCIF) - but
> the PDB doesn't care about that. They have no time-dependent data.

All the PDB-abusers around would care, though.

P