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Regions, Cerberus, and Errors
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@Lnaden Lnaden released this 22 Nov 00:37
· 824 commits to master since this release
0.19.0
bacbc48
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New Features

  • Added statistical inefficiency of replica state indices to the analysis (#819).
  • Improve automatically generate residue names for sdf and SMILES molecules (#819).
  • Improved automatic parameterization for FlatBottom restraint. An error is now raised if the restraint volume is greater than the periodic box volume (#797 ).
  • Added custom region selection to Topography, including compound regions
  • Custom regions can now be defined through YAML
  • Restraints atom selection in restraints can now use Topography Regions
  • Topography now can select from arbitrary string, either complex regions, DSL strings, and in the future SMARTS strings

Cerberus

  • Changed to Cerberus for data validation (was Schema), public facing validation schemas in the future

This requirement and package change modifies the way that YAML files are validated and returns a much more complete, and detailed description of the errors in your sections. This should drastically reduce the confusion around "What went wrong with my YAML file"

Critical Bugfixes

OpenMMTools 0.13.3 now required to fix bug in SamplerState

Minor Bugfixes

  • Fixed a bug where setup logs were saved in the wrong folder (#819).
  • Fixed a bug that caused FlatBottom/Harmonic restraints to crash when only a single atom was selected (#819).
  • Fixed a bug in extract-trajectory that was causing the trajectory to not be imaged properly (#819).
  • Implemented work-around that avoid tleap problems with numerical unit names (#819).
  • Added better error handling of known LEaP Errors
  • Fixed issue for start_frame and end_frame were ignored for trajectory extraction
  • Better MPI exception handling
  • Fixed bug where one MPI thread crashing did not stop other threads, resulting in them getting stuck in a blocking action, but not dying.
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