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 <[email protected]> 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> >> >> _______________________________________________ >> Message sent via/by Gna! >> http://gna.org/ >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
