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Python 2 Dropped, Solute Only Trajectories, and Trailblaze Bug fixes

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@Lnaden Lnaden released this 04 Oct 13:05
· 917 commits to master since this release

Dependency changes

  • Python 2.X Support officially removed - YANK now runs Python 3.5 and 3.6 only

Features Added by this Release

  • Added GAFF2 Torsion support based on YAML input files
  • Solute-only trajectories can now be stored every iteration, regardless of checkpoint interval

Improvements in this release

  • Added restraint selection flowchart to documentation
  • Use infinity instead of None to specify unlimited number of iterations (#772).
  • Parallelized setup of molecules and systems with MPI (#557)
  • Generalized restrained atoms selection during trailblaze scheme to include non-protein receptors (see also choderalab/openmmtools#290).

Notable Bugfixes

  • Fix loading of leap parameters from a local .dat files (allow us to use local versions of gaff parameters for validation)
  • Trailblaze protocol crashes with MPI (#762).
  • Fixed bug when computing reduced potentials of simulated energies during trailblaze scheme.
  • Automatic path is saved in YAML as a mix of python and numpy floats (#763)
  • Fixed the number of neutralizing counterions when receptor and ligand have opposite charges (we were adding too many in this case).
  • Fixed the log file name with lists of experiments that ended up being just .log.
  • Implemented workaround for fixing the net charge of cyclic multi-residue mol2 files.