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

[Konrad Hinsen]

--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. Biologists still wouldn't care.

> 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.

Konrad.