Ommprotocol Versions Save

Fixes issue #16 (box vectors are ignored in CHARMM)

This release fixes issue #13. Basically, you can now use this input:

# input
topology: sys.prmtop
velocities: null
checkpoint: simulation.state.xml

The checkpoint file will provide all the data needed for restart the simulation, but with velocities=None, these will be reassigned to match temperature. Useful for running replicas!

• 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 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