Specify water box dimensions with JS enhanced padding field

Fix issue with mutations when chain appears in multiple places in PDB file

Fix issue with mutations when chain appears in multiple places in PDB file separated by other chains.

[WIP] Added support for loading PDBx/mmCIF files

Removed the remaining internal dependence on PdbStructure

Fix issues with travis-ci and binstar upload of dev package.

Fixed error when _addAtomsToTopology() added bonds but not atoms

Migrate to the new container architecture.

Test case doesn't download PDB as many times

Added --pdbid, --url, and --verbose flags.

* Users can now specify '--pdbid pdbid' flag in command-line to retrieve PDB file from RCSB
* Users can also specify '--url URL' to retrieve from custom URL.
* --vebose flag for command-line now prints out some information about what is going on; maybe we can convert this to logging later

Cowardly refuse to install unless openmm >= 6.3 is installed