relax SVN archive

Expanded the description of the structure.rmsd user function.

Fix for the Noe.test_bug_21562_noe_replicate_fail system test.

This is for the changed behaviour of the structure.read_pdb user function. The problem is that the
PDB file read in this test has the chain ID set to X. This broken PDB causes molecule numbering
problems.

Expanded the displace_id argument for the structure.align user function.

This can now be a list of atom IDs, so that any atoms can be rotated together with the structure
being aligned. This is useful if the molecules argument is supplied.

Large improvement for the PDB molecule identification code.

This affects the structure.read_pdb user function. Now the chain ID code, if present in the PDB
file, is being used to determine which ATOM and HETATM records belong to which molecule. All of the
records for each molecule are stored until the end, when they are all yielded. This allows for
discontinuous chain IDs throughout the PDB file, something which occurs often with the HETATM
records.

Fix for the selective secondary structure reading of the structure.read_pdb user function.

The molecule index needs to incremented by 1 to be the molecule number.

Improvement for the merge argument of the structure.read_pdb user function.

This argument is now overridden if the molecule to merge to does not exist. This allows the merge
flag to be used together with read_mol and set_mol_name set to lists.

Improvement for the structure.read_pdb user function.

The helix and sheet secondary structure reading now takes the real_mol argument into account to
avoid reading in too much information.

Changes for water in the PDB file created by the structure.write_pdb user function.

The waters with the residue name 'HOH' are no longer output to HET records.

Fix for the displace_id and molecules arguments of the structure.align user function.

The atom ID used for the translations and rotations is now properly constructed from the molecule
names in the molecules list and the displace_id string.

Modified the Structure.test_align_molecules system test to catch a bug.

This is the failure of the displace_id argument of the structure.align user function when the
molecules argument is supplied - all atoms are being displaced instead of a subset.