relax SVN archive

Merged revisions 26791 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26791 | bugman | 2014-11-27 19:11:38 +0100 (Thu, 27 Nov 2014) | 11 lines

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.
........

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.

Added systemtest Nmrglue.xtest_plot_contour to test the functionality of contour plotting.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Fixes for the Frame_order.test_simulate_rotor_z_axis system test.

Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is
required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at
[1, 0, 0] so that the axis alpha angle of pi/2 creates an axis parallel to Z. The origin to atom
distance check has also been loosened due to the PDB truncation artifact.

Added the initial systemtest Nmrglue.test_nmrglue_read to read spectrum files via nmrglue.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added the user funcion spectrum.nmrglue_read to read spectrum files via nmrglue.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added a class instance object for handling and storing nmrglue data.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added the initial pipe_control and lib.software modules, for the wrapper functions to nmrglue.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Created an initial version of the Frame_order.test_simulate_rotor_z_axis system test.

This is to check the frame_order.simulate user function rotor model along the z-axis. It currently
fails due to a bug in the user function.

Merged revisions 26782 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26782 | bugman | 2014-11-27 15:16:48 +0100 (Thu, 27 Nov 2014) | 8 lines

Modified the printouts from the structure.write_pdb user function if models are present.

Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each model, the header 'MODEL
records' is printed followed by a single '.' character for each model. For structures with many models,
this results in a huge speed up of the user function which is strongly limited by how fast the
terminal can display text.
........