fixed proline bug in DEEenergyCalculator, which stemmed from two issues:
1. the backbone HNs were being added to all rotamers, but they should have been added to only non-proline rotamers
2. the proline charges did not match the alanine and glycine charges.  when the poly-gly template is mutated to proline,
the backbone atom types change.  if the vdw/charge parameters for proline are different vs. gly, then there will be a problem.
I therefore set all the glycine, proline, and alanine types to the same vdw and charge values.  (There aren't any other types.)
Tests show that the energy is correct almost every time.  It's off occasionally, due to numeric imprecision, but it doesn't seem
to be a big deal.
javadoc corrections