relax SVN archive

Created the new vector_angle() library function.

This is located in the lib.geometry.vectors module. The function will calculate the angle between
two vectors with sign or direction using the atan2() function.

Merged revisions 22516 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22516 | bugman | 2014-03-21 11:09:18 +0100 (Fri, 21 Mar 2014) | 7 lines

Bug fix for all of the R1rho relaxation dispersion models.

The atan2() function is now being used rather than atan() for determining the rotating frame tilt
angle. This is to allow the angle to be in the correct quandrant - i.e. to have a sign or
direction.
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Bug fix for all of the R1rho relaxation dispersion models.

The atan2() function is now being used rather than atan() for determining the rotating frame tilt
angle. This is to allow the angle to be in the correct quandrant - i.e. to have a sign or
direction.

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

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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

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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.
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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.