Re: [h5md-user] Another HDF5-based trajector format

[pdebuyl]

Hi Konrad,

On Mon, Sep 01, 2014 at 11:58:27AM +0200, Konrad Hinsen wrote:
> I found this description somewhat accidentally:
> 
>   http://mdtraj.org/latest/hdf5_format.html
> 
> It looks like a complete definition of an HDF5-based trajectory
> format for biomolecular systems, but it also looks like tailor-made
> for the needs of a particular library.

This is very interesting indeed. From browsing the history (I just love that you
can do that) [1] the HDF5 support is from a bit more than a year ago, that is
later than my extensive web searches. I had found H5Part [2] but it was not
satifactory. I'll have a closer look at mdtraj.

As you mention, it is program-specific. Also, the structure seems really rigid 
(no
groups, for instance).

The topology [their own word, we use connectivity now I think :-) ] storage is a
bit awkward, as it is a json text files embedded in a HDF5 dataset. But at least
they have connectivity information.

With respect to MOSAIC, it also seems more rigid for the same reasons as above:
one single entity in the file.

> An interesting aspect is the use of compression. Did anyone try this
> in H5MD? 

Only a few times, without much gain (from memory, less than 10% gain with gzip).
I don't have a good automated strategy to test this.

Pierre

[1] https://github.com/rmcgibbo/mdtraj/commits/master/docs/hdf5_format.rst
[2] http://vis.lbl.gov/Research/H5Part/