relax SVN archive

Fix for the lib.structure.geometric.generate_vector_residues() function.

The atom numbers are no longer read from the internal structural object, as these are not reliable.
If another geometric representation exists in the object, then the atom numbers could be None. Or
loading structures from multiple PDB files can cause the numbering to be repeated or out of order.

Fixes for the lib.structure.represent.cone module.

The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with
the cone() function in the module namespace.

Completed the frame_order.pdb_model user function backend for the frame order PDB representation.

Most of this backend, including the axes and cone representations, had been broken for quite a while
and were being skipped with an early return statement. This has now been made functional and a few
fixes have been made.

For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model
is produced in the final frame order PDB representation file. For all other models, the rotor
representation is no longer centred to the point on axis closest to the centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger in these models so
that it is outside of the cone, and the propeller blades are now staggered.

Fix for the heterogen section of the internal structural object write_pdb() method.

A number of checks were performed to see if the PDB heterogen records were the same for all
structures, but this is meaningless as the structures can of course be different.

Deletion of the pipe_control.structure.main.create_cone_pdb() function.

This is only used in the frame order analysis, but has been made redundant by the
lib.structure.represent.cone.cone() function.

Modified that unit tests having different r20a and r20b values is checking if the correct one is returned.

This is the preparation for merging back disp_speed branch into trunk.
This follows post http://article.gmane.org/gmane.science.nmr.relax.devel/5948.

Merged revisions 23468,23470 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23468 | bugman | 2014-05-27 15:51:08 +0200 (Tue, 27 May 2014) | 6 lines

Shifted some functions from lib.structure.geometric into their own modules.

The angles_regular() and angles_uniform() functions are now in the lib.structure.angles module, and
the get_proton_names in lib.structure.conversion.
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r23470 | bugman | 2014-05-27 16:30:56 +0200 (Tue, 27 May 2014) | 6 lines

Fix for the lib.geometry.lines.closest_point_ax() function for when the two points are the same.

If the point on the line and point in the 3D space are the same, then this function used to return
an array of NaN values. This situation is now caught and the point in the 3D space is returned.
........

Merged revisions 23470 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23470 | bugman | 2014-05-27 16:30:56 +0200 (Tue, 27 May 2014) | 6 lines

Fix for the lib.geometry.lines.closest_point_ax() function for when the two points are the same.

If the point on the line and point in the 3D space are the same, then this function used to return
an array of NaN values. This situation is now caught and the point in the 3D space is returned.
........

Fix for the lib.geometry.lines.closest_point_ax() function for when the two points are the same.

If the point on the line and point in the 3D space are the same, then this function used to return
an array of NaN values. This situation is now caught and the point in the 3D space is returned.

Merged revisions 23468 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23468 | bugman | 2014-05-27 15:51:08 +0200 (Tue, 27 May 2014) | 6 lines

Shifted some functions from lib.structure.geometric into their own modules.

The angles_regular() and angles_uniform() functions are now in the lib.structure.angles module, and
the get_proton_names in lib.structure.conversion.
........