Hi,
Sorry, I just checked and I have already deleted the J-coupling branch
(https://mail.gna.org/public/relax-commits/2010-02/msg00153.html).
This was also set up as a task (http://gna.org/task/?6328), which I
have just closed. Han's branch was first announced at
https://mail.gna.org/public/relax-devel/2008-11/msg00024.html.
The reading of XYZ files is something Han and I have discussed
extensively before as something that would be extremely useful for the
small molecule crowd, so that they don't have to convert their files
to the ugly protein specific PDB format first. I have already
discussed in person with her how we should implement this, but the
details might be a bit blurry as it was a while ago. I'll first
create a private branch called xyz, which can be checked out by
typing:
$ svn co http://svn.gna.org/svn/relax/branches/xyz
The first step would be to add an XYZ sample file, truncated to only a
few lines, to the test suite shared data directories. Then a system
test for reading the data would need to be added. Once this is
complete, then the functional code can be implemented step by step. I
would recommend creating the structure.read_xyz() user function. The
front end code in the 'prompt' directory can be duplicated from the
structure.read_pdb(). Implementing the back end will be a little more
complex and will require a little planning and discussion, once that
step is reached.
Cheers,
Edward
On 30 May 2011 13:26, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:
Hi,
My name is Han Sun and I am working now at the MPI in Göttingen. Edward and
I have worked last two years on the N-state model part of relax for the
stereochemistry analysis. There is one paper from this year discussing about
our work (http://dx.doi.org/10.1002/chem.201002520). Now I would like to add
a new branch to read the xyz file into relax. Since not every chemist is
familiar with the pdb-file, I think this function will be very useful for
them.
Another thing is that we have asked for adding a new brunch for the
dynamically averaged J-coupling analysis two years ago. Unfortunately, due
to several reasons this analysis was never developed. I think this branch
can now be deleted.
Best regards,
Han
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Re: XYZ structure reader