relax SVN archive

Fix for the software verification tests.

The recent expansion and improvements of the REMARK records created by the internal structural
object PDB writing method imported the relax version to place this information into the PDB files.
However this breaks the relax library design, as shown by the verification tests. Instead the relax
version information is being taken from the lib.structure.internal.object.RELAX_VERSION variable.
This defaults to None, however the version module now sets this variable directly when it is
imported so that it is always set to the current relax version when running relax.

Started to redesign the frame_order.pdb_model user function.

Instead of having the positive and negative representations in different PDB models, and the Monte
Carlo simulations in different molecules, these will now all be shifted into separate files.

For this to be possible, the file root rather than file names must now be supplied to the
frame_order.pdb_model user function. To allow for different file compression, the compress_type
argument is now used. The backend code correctly handles the file root change, but the multiple
files are not created yet.

Merged revisions 24361,24365,24380-24383 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24361 | bugman | 2014-06-30 10:16:57 +0200 (Mon, 30 Jun 2014) | 5 lines

Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded module docstring.

This is to better separate the original scripts used to document the code evolution.
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r24365 | bugman | 2014-06-30 18:10:09 +0200 (Mon, 30 Jun 2014) | 6 lines

Created the very basic structure.com user function for calculating the centre of mass.

This is to simply allow an easy interface to the pipe_control.structure.mass.pipe_centre_of_mass()
function.
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r24380 | bugman | 2014-07-01 17:04:41 +0200 (Tue, 01 Jul 2014) | 6 lines

Empty lines are now handled by the lib.structure.pdb_write.record() function.

By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file.
This can be used for nicer formatting.
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r24381 | bugman | 2014-07-01 17:08:16 +0200 (Tue, 01 Jul 2014) | 8 lines

Expansion of the REMARK section of the PDB file created for the internal structural object.

This is visible when using the structure.write_pdb user function, as well as the many other user
functions which create PDB files. The relax version as well as the file creation date are now
recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK
section improve the formatting.
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r24382 | bugman | 2014-07-01 17:16:30 +0200 (Tue, 01 Jul 2014) | 5 lines

Fixes for the Diffusion_tensor system tests due to the recent PDB file changes.

Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.
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r24383 | bugman | 2014-07-01 17:30:56 +0200 (Tue, 01 Jul 2014) | 6 lines

Fixes for all system tests failing due to the expanded and improved PDB REMARK section.

The system tests now remove all REMARK records prior to comparing file contents. The special
strip_remarks() system test method has been created to simplify the stripping process.
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Fixes for all system tests failing due to the expanded and improved PDB REMARK section.

The system tests now remove all REMARK records prior to comparing file contents. The special
strip_remarks() system test method has been created to simplify the stripping process.

Fixes for the Diffusion_tensor system tests due to the recent PDB file changes.

Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.

Expansion of the REMARK section of the PDB file created for the internal structural object.

This is visible when using the structure.write_pdb user function, as well as the many other user
functions which create PDB files. The relax version as well as the file creation date are now
recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK
section improve the formatting.

Empty lines are now handled by the lib.structure.pdb_write.record() function.

By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file.
This can be used for nicer formatting.

Fix for the pymol.frame_order user function.

The representation function for the rotor objects was hiding all parts of the representation, hence
the pivot labels where being hidden. To fix this, the hiding of the geometric object now occurs in
the base frame_order_geometric() function prior to setting up the representations for the various
objects.

Fixes for the cone geometric object created by the frame_order.pdb_model user function.

This was broken by the code refactoring and now works again for the pseudo-ellipse models.

Redesign of the axis geometric representation for the frame order motions.

This is now much more model dependent to avoid clashes with the rotor objects and other
representations:

- For the torsionless isotropic cone, a single z-axis is created.

- For the double rotor, a single z-axis is produced connecting the two pivots, from pivot2 to pivot1.

- For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are created.

- For the torsionless pseudo-ellipse, all three x, y and z-axes are created.

- For all other models, no axis system is produced as this has been made redundant by the rotor
objects.