🗒️ Changelog

🗒️ 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.

unreleased#

0.2.1-2025.09.26#

Added#

  • Make it available on conda-forge.

Changed#

  • Handle installation of ParmED at conda level.

  • Update versioning.

0.2.0-2025.06.19#

Added#

  • pytest.ini for better handling of warning during test.

Changed#

  • Updating docs, installation instructions and improving readability.

Fixed#

  • Espaloma force field is available on MacOS.

  • Espaloma force field generation is handling directly and not through openmmforcefields.generators.

  • Easy installation and dependencies handling. micromamba is now the preferred environment manager.

  • Improve code covering and code grading.

  • CI for upload to PyPi.

0.1.0-2023.07.27#

Added#

  • toff.utils.generate_structure(). this function can now be used to also take parameters from GAFF and/or Espaloma. For that openmmforcefields must be installed. In the case of Espaloma, this module has to be installed as well.

Changed#

  • Now the default force field in the class toff.utils.Parameterize is selected base on the keyword force_field_type. They are:

    • openff -> openff_unconstrained-2.0.0.offxml

    • gaff -> gaff-2.11

    • espaloma -> espaloma-0.2.2

0.0.2-2023.03.27#

Added#

  • toff.utils.get_rdkit_mol() accept sdf molecules too. Only the first molecule/conformer will be used.

  • Example using the safe_naming_prefix on toff.utils.Parameterize.

0.0.1-2023.01.08#

Changed#

  • toff.utils.confgen now check if it is needed to generate a conformation and add hydrogens.

Removed#

  • Parameter gen_conformer from toff.utils.get_rdkit_mol() and toff.utils.parameterize.__call__().

Added#

  • toff.utils.safe_naming(). Add a prefix to the atom types.

  • safe_naming_prefix keyword on toff.utils.Parameterize. It uses the previous function if some string is provided.

  • max_iter to toff.utils.charge_sanitizer(). Maximum number of iteration in case of charge correction.

Fixed#

  • Improve documentation

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