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

Preserve residue and chain IDs

Fixed a test failure under Python 3