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CHANGELOG.md

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Update log

Version 1.9.0 | 2022-03-24

Features

  • Added Kallisto step (fast atomic featurizer).
  • Added Jazzy step.
  • Added validator entry point that allows to check configuration JSONs against a JSON Schema.

Internal

  • Added version check between configuration files and installation.
  • Add internal mechanism for handling gromacs simulation state.
  • Various fixes for pmx steps + SLURM interface.

Version 1.8.0 | 2022-02-23

Features

  • Improved DNA support for GROMACS simulations.

Internal

  • GROMACS unit test update.

Version 1.7.1 | 2022-02-23

Features

  • Added version logging.

Internal

  • Update of environment specification.
  • Improvements to ESPsim integration.

Version 1.7.0 | 2022-02-16

Features

  • Added Gold docking backend.
  • Added OpenFF parametrisation for GROMACS simulations.

Internal

  • Refactor MD system parametrisation and GROMACS topology handling.
  • Refactor step dispatching to allow for cleaner parallelization.
  • Various bug fixes and stability improvements.

Version 1.6.0 | 2022-02-04

Internal

  • Unit tests fixed.
  • Improved stability for AutoDock Vina and RDkit embedding steps.
  • Change nomenclature for parallel step dispatch and Slurm interface
  • Improve error handling for PMX steps

Version 1.5.0 | 2022-02-01

Internal

  • Refactored gromacs + free energy tools to use ambertools installed in the conda env.
  • Restructured repository to make the package pip installable.
  • Improved unit test coverage for pmx steps.

Version 1.4.0 | 2022-01-19

Features

  • Added support for non-equilibrium relative binding free energy calculation with PMX.
  • Added Glide support for feeding in "in" files from Maestro directly.
  • Added AutoDock Vina as docking backend.

Internal

  • Limited refactoring of support functions.

Version 1.3.0 | 2021-11-18

Features

  • Added Iterator mechanism for parallel step execution.
  • Pose rescoring my RMSD workflow.
  • MMGBSA workflow with GROMACS.

Internal

  • Improved error logging from subprocesses.
  • Improvements to MDpocket workflows.
  • Refactored example workflows + added new examples.

Version 1.2.0 | 2021-09-15

Features

  • Added MDpocket workflow for pocket identification.
  • Expanded scope of GROMACS workflow for improved ligand/cofactor parametrisation.
  • Improved FEP+ workflow map construction and analysis.
  • Performance optimisation for Turbomole and Prime.
  • Added PDBFixer step.
  • Added ensemble docking.

Internal

  • Improved temporary file handling.

Version 1.1.0 | 2021-06-30

Features

  • Added Ligprep workflow step.
  • Added Glide workflow step.
  • Added run-time global variables.
  • Added JSON input type (REINVENT-compatible).
  • Additional GROMACS binaries, and automated ligand parametrisation.
  • Added support for Schrodinger's FEP+ workflow.
  • Added support for OptunaAZ model building.

Bug fixes

  • Fixed problems in tabular write-out (no compound names and sometimes lost column order).
  • Fixed bug in aggregation (highest_is_best parameter was not working properly).
  • Fixed instability with step write-out (occurred when no conformers were associated with a compound).
  • Fixed bug in the parallelization of Ligprep.

Internal

  • Refactored structure for Schrodinger binaries.
  • Reworked the write-out functionality.
  • Reworked internal file handling.
  • Reworked generic data handling.

Version 1.0.0 | 2021-05-21

Features

  • Basic functionality (data handling, backend wrapping).
  • Various steps implemented (Turbomole, Cosmo, OMEGA, GROMACS, ...).

Bug fixes

  • Fixed issues with Turbomole execution.
  • Enforced GROMACS execution in tmp_dir.

Internal

  • Adapted pydantic interface.