choderalab/yank: 0.22.0 RMSD the Casbah

Published May 12, 2018 | Version 0.22.0

Software Open

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

Files

Name	Size	Download all
choderalab/yank-0.22.0.zip md5:bd22f44d3f49695b671b19d2e0f71b41	8.6 MB	Preview Download