relax SVN archive

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.

Fixes for the Structure.test_superimpose_fit_to_mean system test for the displace_id argument.

Added the displace_id argument to the structure.align and structure.superimpose user functions.

This gives both of these user functions finer control over which atoms are translated and rotated by
the algorithm. This allows, for example, to align structures based on a set of backbone heavy atoms
while the protons and side chains are displaced by default. Or if a domain is aligned, then just
that domain can be displaced.

Modified some system tests of the structure.align and structure.superimpose user functions.

The displace_id argument has been introduced for both of these user functions for finer control over
which atoms are translated and rotated by the algorithm. This allows, for example, to align
structures based on a set of backbone heavy atoms while the protons and side chains are displaced by
default. Or if a domain is aligned, then just that domain can be displaced.