relax SVN archive

The CaM frame order system tests for the rotor models are converted to the new axis_alpha parameter.

The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle
alpha.

Improvements for the centre of mass calculation for the frame order model optimisation.

This is now only calculated for the rotor models. The CoM is also printed out for better user feedback.

Merged revisions 22512 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22512 | bugman | 2014-03-19 15:32:34 +0100 (Wed, 19 Mar 2014) | 6 lines

The verbosity flag is now used in the centre of mass calculations.

The pipe_control.structure.mass.pipe_centre_of_mass() function now passes the verbosity argument
into the lib.structure.mass.centre_of_mass() function.
........

The verbosity flag is now used in the centre of mass calculations.

The pipe_control.structure.mass.pipe_centre_of_mass() function now passes the verbosity argument
into the lib.structure.mass.centre_of_mass() function.

The AXIS_ALPHA parameter is now initialised in the CaM frame order system test base script.

The base script was broken a while back (r22192) due to AXIS_ALPHA not being defined but being
checked for.

Merged revisions 22508-22509 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22508 | bugman | 2014-03-19 08:37:35 +0100 (Wed, 19 Mar 2014) | 7 lines

Created the Structure.test_bug_21814_pdb_no_80_space_padding system test.

This is for catching bug #21814 (https://gna.org/bugs/?21814), the PDB reading failure when the PDB
records are not padded to 80 spaces. The PDB file used for the test is the same file as attached to
the bug report.
........
r22509 | bugman | 2014-03-19 08:53:20 +0100 (Wed, 19 Mar 2014) | 9 lines

Fix for bug #21814 (https://gna.org/bugs/?21814).

This is the PDB reading failure when the PDB records are not padded to 80 spaces. The fix is
simple, all PDB records are pre-validated. This includes removing all newline characters and
padding each PDB record to 80 spaces when needed. This will however add an overhead cost -- the
internal PDB reader will now be slower. However corrupted PDB files, produced by MODELLER for
example, not padded to 80 spaces will now be better supported.
........

Fix for bug #21814 (https://gna.org/bugs/?21814).

This is the PDB reading failure when the PDB records are not padded to 80 spaces. The fix is
simple, all PDB records are pre-validated. This includes removing all newline characters and
padding each PDB record to 80 spaces when needed. This will however add an overhead cost -- the
internal PDB reader will now be slower. However corrupted PDB files, produced by MODELLER for
example, not padded to 80 spaces will now be better supported.

Created the Structure.test_bug_21814_pdb_no_80_space_padding system test.

This is for catching bug #21814 (https://gna.org/bugs/?21814), the PDB reading failure when the PDB
records are not padded to 80 spaces. The PDB file used for the test is the same file as attached to
the bug report.

Merged revisions 22492,22498-22499,22501-22502 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22492 | tlinnet | 2014-03-17 14:30:51 +0100 (Mon, 17 Mar 2014) | 4 lines

Replaced funtion atan(omega1 / Delta_omega) with atan2(omega1 , Delta_omega), to make sure returned theta values are between 0 and pi.

This was done in the function return_offset_data() in the specific_analyses of relax_disp.
This was discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5210.
........
r22498 | tlinnet | 2014-03-17 18:18:59 +0100 (Mon, 17 Mar 2014) | 1 line

Changed a unit test and systemtest, where a change from the atan to atan2 function to calculate theta can give differences to the 15 decimal.
........
r22499 | tlinnet | 2014-03-17 18:19:01 +0100 (Mon, 17 Mar 2014) | 4 lines

Replaced how a global analysis average results from a previous run to instead take the median.

This is to prevent averaging extreme outliers, and instead take the median of the previous result.
This was discussed in: https://mail.gna.org/public/relax-devel/2013-10/msg00009.html.
........
r22501 | tlinnet | 2014-03-18 16:06:01 +0100 (Tue, 18 Mar 2014) | 1 line

Modified systemtest Relax_disp.test_r1rho_kjaergaard to use input guess values of phi_ex in units of ppm^2 instead of rad^2/s^2.
........
r22502 | tlinnet | 2014-03-18 16:47:56 +0100 (Tue, 18 Mar 2014) | 4 lines

Small change to systemtest Relax_disp.test_r1rho_kjaergaard.

The outcome of kex from systemtest is in the area of 4-5000. The expected value is 13000.
A deeer analysis of the input is needed, to judge what is the correct value.
........

Merged revisions 22491 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22491 | bugman | 2014-03-17 14:09:45 +0100 (Mon, 17 Mar 2014) | 6 lines

Shifted two functions from pipe_control.angles into the new lib.geometry.angles module.

This is the fold_spherical_angles() and wrap_angles() functions which are not related to the relax
data store and hence can be made independent.
........