Basic force field and topology processing
Process bond and bend types as well
Add some TODO items
More robust molecule construction
Fix previous commit
Add torsion, both proper and improper
Add the `nfreq` parameter
Add support for frozen atoms with PIMD
Add support for ghost atoms with PIMD
Align screen output and clean up code a bit
Fix permissions
Avoid type mismatch
Merge pull request #18 from OndrejMarsalek/topology

Topology and force field processing.  Still needs to be made to work with the residue bonding utility.
Merge pull request #20 from OndrejMarsalek/frozen

Add support for frozen atoms with PIMD
Merge pull request #21 from OndrejMarsalek/ghosts

Add support for ghost atoms with PIMD
Merge pull request #22 from OndrejMarsalek/output

Align screen output and clean up code a bit
Merge pull request #24 from OndrejMarsalek/compile-PR

Better build settings for Linux
Add compile settings for Mac OS X
Merge pull request #29 from TuckermanGroup/osx

Add compile settings for Mac OS X
Fix Python build for new library location