Re: [bug #21599] allow import of nmr data from ccpn projects (optionally also export) -- February 06, 2014

Hello,

Justin will have a suitable project.

I can help on the software side (although I'll need some input from Rasmus as 
well).

I assume that Relax doesn't want to ship CCPN code so likely there would need 
to be an environment variable to indicate where the CCPN code exists, if it 
exists.  We use an environment variable CCPNMR_TOP_DIR to indicate where the 
top-level CCPN directory is, but we don't set it globally (e.g. in .cshrc or 
.bashrc) but instead it is set in a script that you run when you want to run 
the program.  But that doesn't mean it couldn't be set globally by someone 
who wants to use Relax + CCPN.  The relevant directory to add to the 
PYTHONPATH is then CCPNMR_TOP_DIR + '/ccpnmrX.Y/python', where X.Y = 
major.minor release.  Possibly we should just assume that that directory has 
been added to the PYTHONPATH so the imports then work, and if the imports 
don't work then there is no CCPN code (!).

Loading CCPN projects is one line of code so I can help with that.  The one 
issue that arises is how to pick out the data the user wants to use in Relax, 
and any other parameters that need setting.  Rasmus is working on a similar 
issue for programs like Cyana, so I will ask him about his thoughts.

Regards, Wayne

On 6 Feb 2014, at 10:14, Edward d'Auvergne wrote:

Hi Justin,

This is a great idea.  Would you happen to have such CCPN data?  Would
you be interested in helping with adding such support?  There are a
number of steps we can take for this and they do no need to all be
completed to be useful:

- This would be better as a task
(http://gna.org/task/?group=relax&status_id=0) rather than bug report.
Therefore I can create a task report with the text of this bug report
and then close this bug report (http://gna.org/bugs/?21599).  Once I
have created the task, as only relax developers can do this, then you
are free to add comments and upload files.

- Example files can be uploaded to the task.  This should consist of a
minimal data set.  The best would be to have data for two backbone NH
peaks and one Trp indole side chain NH peak.  These would then be used
for implementing the ideas via system tests.  I can add these files
directly to the relax test data directories.

- Create a relax branch for implementing CCPN reading support.  If you
have interest, you could be granted limited commit access to this
branch to play with the code.

- Incorporate the uploaded files into system tests for testing and
implementing the support.

- Implement the CCPN support.


The implementation itself would need to be discussed, and would depend
on the sample files.  For example for reading the spin information,
CCPN support could be added to the spectrum.read_spins user function.
For reading peak intensities, CCPN support could be added to the
spectrum.read_intensities user function.  For the structures I'm not
sure.  These two user functions might be sufficient, or at least they
would be very beneficial to have.

If you are thinking about pointing to a CCPN project and having
everything loaded into relax, then this would be more complex (I also
don't know the exact layout of the project).  But this could be
implemented as the spectrum.read_ccpn user function or something
similar.  This would then load the sequence, peak lists, structures,
etc sequentially by using the spectrum.read_spins,
spectrum.read_intensities, chemical_shift.read, structure.read_pdb...
user function backends.  So it might be best to implement the reading
of the data out of a CCPN project through the individual user
functions first, and then implement a very basic, all encompassing
user function at the end.

What do you think?

Cheers!

Edward


P. S.  The fact that CCPN is implemented in Python unfortunately does
not help relax in reading the CCPN project files in any way.



On 5 February 2014 11:20, Justin <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:

URL:
 <http://gna.org/bugs/?21599>

                Summary: allow import of nmr data from ccpn projects
(optionally also export)
                Project: relax
           Submitted by: jlec
           Submitted on: Wed 05 Feb 2014 10:20:57 AM GMT
               Category: None
Specific analysis category: None
               Priority: 5 - Normal
               Severity: 3 - Normal
                 Status: None
            Assigned to: None
        Originator Name:
       Originator Email:
            Open/Closed: Open
                Release: 3.1.5
        Discussion Lock: Any
       Operating System: All systems

   _______________________________________________________

Details:

It would be great if one could directly import nmrdata from ccpn projects,
like sequences, molecules, peaklists, structures....

As ccpn is written in python as well, with a good documentation of the data
model and the upstream is very cooperative, this should be  done within a
reasonable effort. And it would be truly an huge enhancement of the user
experience.




   _______________________________________________________

Reply to this item at:

 <http://gna.org/bugs/?21599>

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Re: [bug #21599] allow import of nmr data from ccpn projects (optionally also export)

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