0.22.0 RMSD the Casbah

Enhancements and features

• Added RMSD Type restraint, requires OpenMM 7.3 or greater to access. You can have older versions of OpenMM, but this feature is unavailable and will raise a graceful error should you attempt to use it.
• Added more robust last good iteration saving
• Added more robust restore from checkpoint access
• Exposed checkpoint interval iterations in MultiStateReporter
• Generalized the Boresch restraints to a BoreschLike restraint to support new energy functions.
• Boresch restraint automatic atom selection now picks bonded heavy atoms
• Boresch restraints no longer accept standard_state_correction_method as an option
• Added new Haversined Torsion Boresch Torsion (PeriodicTorsionBoresch) Boresch-like restraint where functional form of torsion is periodic support more numerically stable energy functions
• Changed the timeseries analysis to only consider a maximum number of points on which to evaluate "is this equilibrium" to speed up process.
• Implement #848 Use MDTraj Trajectory.save() method instead of inferring function from extension.
• Implement #635 Allow extract-trajectory to handle trajectories with 1 frame.

Bugfixes

• Fix bug #941 where unbiasing the restraint would crash the analysis if using a 32-bit OpenCL platform.
• Fix bug #945 where relative imports of OpenEye tools would cause problems on some systems.
• Temporarily pinned NetCDF4 to 1.3.1 until we can fix the bug introduced in 1.4.0 where masked arrays are always returned. This pin will be lifted in future releases.
• Fix a bug where max_n_iterations was ignored when computing the mixing statistics of the calculation (PR #963).
• Fix bug #944 where ReplicaExchange.create() did not accept a single SamplerState anymore.
• Fix a bug where the box vectors of SamplerStates were initialized incorrectly in MultiStateSampler.create() for NVT calculations (PR #969).
• Fix bug #964 where using the state index argument in extract_trajectory with SAMS calculations would cause a crash.

Backwards compatibility breaks

• Boresch Standard State Correction no longer has an analytical correction