Improvements:

- ParticleProperty objects (including ParticleScalar, ParticleVector,
  and Configuration objects) have a new method selectAtoms. Its argument
  is a function that is called with the property of one particle and returns
  a boolean deciding whether or not that particle is part of the selection.

- CalphaForceField has a new option (version=2) for the pair force constants.
  For reasonable input structures, it is equivalent to the default, version=1.
  It adds a threshold for small nearest-neighbour C-alpha distances: for 
  distances less than 0.37 nm, the force constant does not decrease below
  its value at 0.37 nm. This ensures that the Hessian remains positive
  semi-definite for proteins with unrealistically short C-alpha distances.

- MMTK.Subspae.Subspace has a new method complement() which returns the
  orthogonal complement.

- Two new example scripts:
  -  Miscellaneous/bad_contacts.py
  -  Miscellaneous/two_models.py

- Protein friction constants for Brownian Dynamics (module MMTK.ProteinFriction)
  are calculated with a threshold that assures a minimal value of
  1000/ps. Without this threshold, friction constants could become negative
  for solvent-exposed loops.

Bug fixes:

- The VelocityVerletIntegrator could crash, or produce NaN results,
  for systems with distance constraints and a thermostat but no barostat.

- All examples now work with recent releases of NumPy.

- Installation could break on systems whose C compiler's sizeof returns
  another type than "int".

- Trajectory actions of type "function" could crash integrators.