relax SVN archive

Final fixes for bug #12735 (https://gna.org/bugs/index.php?12735).

The last problem was again triggered by the Scientific python PDB reader weirdness. Residues ending
in '+' were being treated by the PDB reader as a different molecule. But then the molecule names
LYS+, ARG+, etc. were causing problems as '+' was being treated as regular expression when matching
molecule names. Therefore the '+' character has been stripped from all molecule, residue, and atom
names.

Another partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).

This problem was trigged by the internal reader (where the problem lies) together with the
gromacs_phthalic_acid.pdb file. The issue was that the __fill_object_from_pdb() was operating on
all structures currently loaded into relax. Hence with the 2 models of this PDB file, the first
molecule had all the atoms of the first and second PDB models combined.

Partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).

The problem fixed here is that of the missing molecule container. This was caused by the weirdness
of the Scientific python PDB reader splitting one modified lactose molecule into 2 molecules. The
lactose part was unnamed, while the modifier was named after the residues 'UNK'. The
generic_fns.mol_res_spin.return_molecule() function was having problems with this concept of the
first molecule unnamed and the second named. This is now fixed and the unnamed molecule can be
retrieved.

Added tests of structure.load_spins() to all the structure system tests.

Merged revisions 8180,8183 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r8180 | bugman | 2008-12-10 14:15:47 +0100 (Wed, 10 Dec 2008) | 6 lines

Bug fix for the vector_dist() function.

The PyMOL structure loading command should not use the file root but the full file name!!! A few
unused 'id' file root variables were also deleted.
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r8183 | bugman | 2008-12-10 18:35:05 +0100 (Wed, 10 Dec 2008) | 3 lines

Added a print out for the loading of PDB models.
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Initialized merge tracking via "svnmerge" with revisions "1-8160" from
svn+ssh://bugman@.../svn/relax/1.3

Added a print out for the loading of PDB models.

Added some more code to the read_restraints() function.

Added a missing import.

Bug fix for the vector_dist() function.

The PyMOL structure loading command should not use the file root but the full file name!!! A few
unused 'id' file root variables were also deleted.