Fix OUTPDB model to show same side chain configurations as dock file.

[primaryodors]

• The Protein objects are now retained until the program finishes, and reused for writing the model PDB(s);
• It was still necessary to save the side chain positions into Pose objects and restore them before writing the model(s);
• The Pose object now allows restoring to a different Molecule from the original saved-from Molecule, provided the two molecules have compatible atoms.

All master tests are succeeding.