Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.
Merge pull request #90 from peastman/master

Moved Python app layer tests into the main source tree
Merge pull request #87 from peastman/molecules

Eliminated a potential stack overflow when identifying molecules
Speed optimization to GromacsTopFile
Merge branch 'master' of https://github.com/SimTk/openmm