Hi,
This post starts a new thread in relax-devel, but it follows on from
the relax-users post at
https://mail.gna.org/public/relax-users/2008-04/msg00005.html. The
parent of the previous thread is located at
https://mail.gna.org/public/relax-users/2008-04/msg00001.html.
On Wed, Apr 2, 2008 at 7:11 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
[snip]
It seems the mfout (which are all located in their respective folder : m1,
m2 , m3, m4 and m5) are not loaded properly...
Do you have any clue about this issue ?
Unfortunately I don't know what is happening. There is obviously data
missing from the relax data store, but what it is, I'm not sure. If
you'd like to try to fix and improve the situation, please feel free
to play with the code. I think the 1.3 line would be best for any
changes in this code. Almost all of the user functions you've used
here have been updated to the new relax design and the rest should
simply involve the removal of the run object from the relevant
functions.
Also, is there a way of extracting information from a mfout with relax
without inputing any sequence, diffusion tensor, or data..? I thought it
would be possible to use palmer.extract() in a short script like this :
As of yet, no. The parser behind palmer.extract() will need to be
significantly improved. It currently only reads in the results from
optimisation, all of the setup details are skipped. The mfout file is
STAR (Self Defining Text Archival and Retrieval) formatted. But the
parser for this format is very basic and hacky. If the mfout file is
not as expected, palmer.extract() will fail.
The star format is used in a number of other places as well. For
example I plan to better incorporate relax with the BRMB
(http://www.bmrb.wisc.edu) which uses the STAR format. And CIF files
are also STAR formatted. So, ideally in the end I would like to
create a STAR format writer and parser for relax. Or if there is a
STAR format reader already that is open source and can easily be
imported into relax, then bundle that with the relax download. As far
as I can tell, there is unfortunately no official python package for
reading and writing this format.
But this will take time and will be very incremental. So if you would
like to update the current code quickly to read more of the mfout file
details, please feel free. This STAR parser part in
generic_fns/palmer.py could be spun out to a file called say
generic_fns/star.py. And anything can be done with the code -
directly within the 1.3 line. Because of the run argument,
palmer.extract() is still using the old relax design and is not
functioning, so really nothing can be broken because it already is
broken.
In the end, my plan is that the parser will be able to read any star
formatted file and generate a python object containing the data of
that star file. Then the code in generic_fns.palmer, etc. will read
what it needs from this object. I'm only describing this idea so that
any code changes do not evolve too far from this concept.
Cheers,
Edward
STAR format file writer and parser - generating output for BMRB submission, reading the data out of the Palmer's Modefree mfout file, and parsing CIF files.