relax SVN archive

svn+ssh://bugman@.../svn/relax/1.3

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r8186 | bugman | 2008-12-10 18:46:37 +0100 (Wed, 10 Dec 2008) | 3 lines

Added tests of structure.load_spins() to all the structure system tests.
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r8187 | bugman | 2008-12-11 10:33:32 +0100 (Thu, 11 Dec 2008) | 10 lines

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.
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r8188 | bugman | 2008-12-11 10:53:22 +0100 (Thu, 11 Dec 2008) | 8 lines

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.
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r8189 | bugman | 2008-12-11 11:14:00 +0100 (Thu, 11 Dec 2008) | 9 lines

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.
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