Merge pull request #136 from RosettaCommons/JWLabonte/molfile_to_params
Minor Improvement to `molfile_to_params.py`: one can now specify the root and neighbor atoms from the command line.
This merge also includes some rider changes related to carbohydrates and lipids in the database:
* corrections to bond order in lipid topology files
* expansion of `dock_glycans.py`
carbohydrates integration test expected to change due to corrections in lipid bond orders.
molefile_to_params integration test expected to change due to output change.