Ommprotocol

- Add distance-based restraints (see docs)
- Fix `ommanalyze top` subset mismatches between results in the app and `ommprotocol` itself.

Hotfix release!

- DCD output failed if `trajectory_atom_subset` was not set
- False warning about checkpoint key

Improvements in ommanalyze:

- NEW! `ommanalyze top` will inspect topologies and return selected atoms with `--subset`
- `ommanalyze rmsd` uses iterload now, streaming the trajectories instead of loading them at once. This allows to perform RMSD analysis in long trajectories with very little RAM requirements.

Anticipating the v0.2 release, which will be considered feature-stable. This version adds new defaults so the `input.yaml` files can be as simple as possible, as reflected in the new documentation. Beginning now, conda and pypi packages will be automatically built in Travis/AppVeyor and `constructor` installers will be available in the Releases section.

Check the [docs](http://ommprotocol.readthedocs.io/en/latest/install.html) for further details on the installation procedure.

- Use versioneer to identify version in use with reproducibility in mind
- Improved Python 2&3 compatibility
- New CLI commands: `state2pdb`, `exportframe`
- More robust handling of PRMTOP files
- More robust handling of box vectors