Improvements:

- General code revision

- Conversion of docstrings to epytext

- NumPy 1.2 compatibility fixes

- AtomCluster objects have a default name (the empty string)

- PDBMoleculeFactory guarantees that ADP tensors are exactly symmetric

- New method Trajectory.flush()


Bug fixes:

- Dihedral restraints lead to a segmentation fault.

- Dihedral restraints for angles close to pi/-pi caused instabilities.

- Multiple assignments to the same attribute of a universe lead to
  all the objects being added to the universe, with the last assignment
  defininge the value of the attribute. For consistency with assignment
  semantics, an assignment now removes the previous value of the attribute
  from the universe.

- Under certain conditions, nucleic acid chains in PDB files were
  wrongly identified as peptide chains.

- Wrong import in MMTK.InternalCoordinates

- Visualization of periodic universes with undefined atom positions
  didn't work.

- Creation of AtomCluster objects from PDB files was sometimes 
  incomplete (mission positions)

- Opening a trajectory with undefined atom positions lead to a crash.