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)