R1rho numeric models and MQ dispersion data support. -- July 23, 2013

Hi,

Note that I've started a new thread to make the discussions easier to follow in the archives (http://dir.gmane.org/gmane.science.nmr.relax.devel).

Added R1rho numeric models to relax would be great! If you look at the program or manual, you will see that only fast exchange R1rho models are currently implemented. The MQ dispersion code would also be an awesome addition. If you run the relax GUI, you should easily see where this would fit. This would mean that relax would be able to do more than any other dispersion software currently out there. Both analytic and numeric models for both CPMG-type and R1rho-type data (and maybe MQ-type data). This will allows users to directly test the absurdity of the arguments floating around about the benefits of the numeric verses analytic models ;) But it would really increase the citation count for the planned letter. It would be better if the code is in Python, but the Matlab could nevertheless be attached to the task (https://gna.org/task/?7712, even as just a permanent reference.

Here the key part for implementation would be good test data. Do you have test data sets which you have checked your code on? Has this data been tested against other software?

Cheers,

Edward

On 23 July 2013 10:41, Paul Schanda <paul.schanda@xxxxxx> wrote:

Hi Edward,

Thanks for your e-mails, and for this nice implementation. We are still in the process of getting everything running.

Concerning the copyright issues, can you please add Dominique Marion's name in the copyright section of all the files and functions, he developed the python scripts together with Mathilde, in 2013. Otherwise that's all fine for me.

Thanks.

As a side comment, if you feel very motivated to move on, I have numerical solutions of the Bloch-McConnell equations for the case of R1rho - but they are still in Matlab, I have not properly translated them to Python. There are also some MQ dispersion routines that we are working on.

Thanks a lot for all this great work. I am looking forward to playing around with the program.

paul

On 23.07.13 10:28, Edward d'Auvergne wrote:

Hi Paul, Mathilde and Dominique,

I would like to finalise the copyright notices in your code that is now in relax. This is in the lib/dispersion/ns_*.py files. If you have the subversion program installed on your machine (all operating systems are supported), you can get the code by typing at the terminal, cmd command prompt, etc:

$ svn co http://svn.gna.org/svn/relax/branches/relax_disp

At the end of this message, you will see the copyright statements from these files. But note that I have guessed the dates. And I have guessed who added or modified this code. Please carefully check the dates and if your name should be in the file - this information is incredibly important.

Cheers,

Edward

P. S. For Paul, I have the start date of 2010, as well as the additions of new comments from 2013. For Mathilde, I have simply guessed a copyright on all code and from 2013. I have added my name as I have modified the code to better suite relax and to be faster:

[edward@localhost relax_disp]$ head lib/dispersion/ns_*
==> lib/dispersion/ns_2site_3d.py <==
###############################################################################
#                                                                             #
# Copyright (C) 2010-2013 Paul Schanda (https://gna.org/users/pasa)           #
# Copyright (C) 2013 Mathilde Lescanne                                        #
# Copyright (C) 2013 Edward d'Auvergne                                        #
#                                                                             #
# This file is part of the program relax (http://www.nmr-relax.com).          #
#                                                                             #
# This program is free software: you can redistribute it and/or modify        #
# it under the terms of the GNU General Public License as published by        #

==> lib/dispersion/ns_2site_expanded.py <==
###############################################################################
#                                                                             #
# Copyright (C) 2010-2013 Paul Schanda (https://gna.org/users/pasa)           #
# Copyright (C) 2013 Mathilde Lescanne                                        #
# Copyright (C) 2013 Edward d'Auvergne                                        #
#                                                                             #
# This file is part of the program relax (http://www.nmr-relax.com).          #
#                                                                             #
# This program is free software: you can redistribute it and/or modify        #
# it under the terms of the GNU General Public License as published by        #

==> lib/dispersion/ns_2site_star.py <==
###############################################################################
#                                                                             #
# Copyright (C) 2010-2013 Paul Schanda (https://gna.org/users/pasa)           #
# Copyright (C) 2013 Mathilde Lescanne                                        #
# Copyright (C) 2013 Edward d'Auvergne                                        #
#                                                                             #
# This file is part of the program relax (http://www.nmr-relax.com).          #
#                                                                             #
# This program is free software: you can redistribute it and/or modify        #
# it under the terms of the GNU General Public License as published by        #

==> lib/dispersion/ns_matrices.py <==
###############################################################################
#                                                                             #
# Copyright (C) 2013 Mathilde Lescanne                                        #
# Copyright (C) 2013 Edward d'Auvergne                                        #
#                                                                             #
# This file is part of the program relax (http://www.nmr-relax.com).          #
#                                                                             #
# This program is free software: you can redistribute it and/or modify        #
# it under the terms of the GNU General Public License as published by        #
# the Free Software Foundation, either version 3 of the License, or           #
[edward@localhost relax_disp]$

-- Paul Schanda, Ph.D. Biomolecular NMR group Institut de Biologie Structurale Jean-Pierre Ebel (IBS) 41, rue Jules Horowitz F-38027 Grenoble France +33 438 78 95 55 paul.schanda@xxxxxx http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en

R1rho numeric models and MQ dispersion data support.

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