corrected caught exception, this exception changed in commit: 1ef89fb0
when IMolecule was removed (27c6f7df) this conditional was broken. ICrystal was not a subclass of IMolecule but it is a subclass of IAtomContainer and so the first condition will match and writeCrystal is never called.
setting mass number in addition to exact mass
using array list instead of vector
removed settable input stream, this could be reintroduced but should be done via a constructor. the configFile path was corrected and renamed, several small tidy ups to the loading code
moved configuration of MM2 into a single (previous broken) method - resolves unit test in error