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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Version X.X.X

Authors

talagayev, MarvinTaterra

Added

  • Added native glycoprotein support in OpenMMDL Setup AMBER path (2026-05-20, PR#210)
  • Added glycan-aware PBC imaging in OpenMMDL Simulation postprocessing (2026-05-20, PR#210)
  • Added openmmdl check for testing correct installation (2026-05-03, PR#207)

Fixed

  • Fixed peptide pharmacophore error (2026-05-18, PR#209)
  • Fixed remaining water type recognition errors (2026-04-29, PR#205)
  • Fixed OPC water recognition error (2026-04-28, PR#204)

Changed

  • Changed -n to optional to fix peptide issues in OpenMMDL Analysis (2026-05-13, PR#208)
  • Changed imports to lightweight imports in OpenMMDL Analysis (2026-05-03, PR#206)

Version 1.3.0

Authors

talagayev, NDoering99

Added

  • Added additional values for boolean flags in OpenMMDL Analysis (2026-04-09, PR#200)
  • Added equilibration protocol to OpenMMDL Simulation (2026-04-07, PR#194)
  • Added multiple ligand support in OpenMMDL Simulation (2026-04-05, PR#198)
  • Added flag for OpenMMDL Simulation restart when encoutering Nan error (2026-04-04, PR#197)
  • Added high throughput simulation option in OpenMMDL Setup (2026-04-01, PR#196)
  • Added write out of ligand in mol2 with partial charges during OpenMMDL Simulation (2026-03-14, PR#191)
  • Added extensions in OpenMMDL Setup (2026-03-01, PR#189)
  • Added Back button in OpenMMDL Setup (2026-02-28, PR#188)
  • Added Drag & Drop option for file upload in OpenMMDL Setup (2026-02-28, PR#187)

Fixed

  • Fixed double click bug in OpenMMDL Setup (2026-03-01, PR#190)

Changed

  • Adjusted Cleanup option to remove all intermediate files in OpenMMDL Simulation (2026-04-12, PR#201)
  • Removed the saving of the original uploaded PDB file in OpenMMDL Setup (2026-04-05, PR#199)
  • Transition to logging in OpenMMDL Analysis (2026-03-31, PR#195)

Version 1.2.0

Authors

talagayev, NDoering99

Added

  • Addition of ProLIF option for interaction calculation (2026-01-26, PR#179)
  • Addition of two protein and residue interaction in binding modes (2026-01-19, PR#170)
  • Addition of force field version selection for GAFF & SMINROFF (2025-12-15, PR #169)
  • Addition of CHARM2024 forcefield (2025-11-03, PR #163)

Fixed

  • Fixed errors during only protein simulation (2026-01-22, PR #177)
  • Fixed errors during postprocessing in post_md_conversion.py (2026-01-21, PR #176)
  • Fixed 'warinings' import error for 'openmmdlsetup.py' (2026-01-18, PR #173)
  • Adjusted the water selection for Amber19 (2025-12-08, PR #166)
  • Fixes import error in visualization.ipynb (2025-10-14, PR #159)
  • Fixes numpy error in due current incompatbility with parmed (2025-10-19, PR #160)

Changed

  • Changed the layout of OpenMMDL Setup (2026-01-19, PR #175)
  • Changed the entry points to be bundled in cli.py (2026-01-19, PR #174)
  • Transition to Ruff linting with Black style (2025-10-20, PR #161)

Version 1.1.1

Authors

talagayev

Added

  • Implementation of Amber19 forcefield (2025-07-07, PR #157)
  • Implementation of OPC and OPC3 water models (2025-06-17, PR #156)

Fixed

  • Update of OpenFF forcefield version and fixed GAFF type error (2025-06-17, PR #155)

Changed

Version 1.1.0

Authors

talagayev, NDoering99

Added

  • Addition of option to select final frame in OpenMMDL Analysis (2025-04-23, Issue #136, PR #140)
  • Addition of MDontallo Visualization (2025-04-11)
  • Addition of SMIRNOFF small molecule force field (2025-04-10, Issue #76)
  • Addition of PyMOL support for visualization (2025-04-10)
  • Added Dockerfile for image creation (2025-04-10)
  • Addition of citation page in documentation (2025-04-10)

Fixed

  • Fixed error cases, where ligand name was not specified (2025-04-22, Issue #138, PR #139)
  • Fixed wrong color of the positive and negative ionizable interactions (2025-04-21, PR #137)
  • Fixed the XMLSerializer error appearing during simulation (2025-04-10, Issue #122)
  • Fixed the sanitization implementation in OpenMMDL Setup (2025-04-09)

Changed

  • Scripts moved into analysis, core and visualization` sections (PR #149)
  • Functions update_dict, combine_subdict_values, update_values, remove_duplicate_values, read_pdb_as_dataframe and filter_and_parse_pdbwere moved to utils.py (PR #149)
  • Classes ImageMerger and FigureArranger were moved to image_handler.py (2025-04-30, Issue #141, PR #142)
  • The class TrajectorySaver was moved to trajectory_saving.py (2025-04-24, Issue #141, PR #142)
  • Changed to the use of RDKitConverter for Ligand recognition without -l flag in OpenMMDL Analysis (2025-04-10)

Deprecated

Removed