Changelog#

v1.2.0#

Added:

Fixed:

  • Improved responsiveness of CLI calls

  • Fixed bug where openfe gather –report raw was only including first replicates.

v1.1.0#

Added:

  • Extended system solvation tooling, including support for; non-cubic boxes, explicitly defining the number of waters added, the box vectors, and box size as supported by Modeller.addSolvent in OpenMM 8.0 and above.

Changed:

  • Improved documentation of the OpenMMSolvationSettings.

  • The PersesAtomMapper now uses openff.units inline with the rest of the package.

  • Structural analysis data is no longer written to structural_analysis.json but rather a 32bit numpy compressed file named structural_analysis.npz (PR #937).

  • Structural analysis array data is no longer directly returned in the RelativeHybridTopologyProtocol result dictionary. Instead it should be accessed from the serialized NPZ file structural_analysis.npz. The structural_analysis key now contains a path to the NPZ file, if the structural analysis did not fail (the structural_analysis_error key will instead be present on failure) (PR #937).

  • Add duecredit citations for pymbar when calling openfe.protocols.openmm_utils.multistate_analysis.

Fixed:

  • 2D RMSD plotting now allows for fewer than 5 states (PR #896).

  • 2D RMSD plotting no longer draws empty axes when the number of states - 1 is not divisible by 4 (PR #896).

  • The RelativeHybridTopologyProtocol result unit is now much smaller, due to the removal of structural analysis data (PR #937).

v1.0.1#

Added:

  • Debug script in devtools to test OpenMM installation.

  • Use rever to manage changelog.

Changed:

  • Updated docs to reference miniforge instead of mambaforge since they are the same now, see conda-forge/miniforge.

  • The LomapAtomMapper defaults have now changed to better reflect real-life usage. Key kwarg changes include; max3d=1.0 and shift=False.

Fixed:

  • Calling get_forward_and_reverse_energy_analysis in the RFE and AFE protocols now results a warning if any results are None due to MBAR convergence issues.

  • Checkpoint interval default value has been set to 250 ps instead of 1 ps. This better matches the previous default for openfe versions < 1.0rc (See issue #772).