environment.yaml

name: openff-env
channels:
    - conda-forge
dependencies:
    - python >=3.13 # For JupyterHub compatibility
    - jupyterlab
    - openff-toolkit-examples>=0.19.0 # Need at least 0.17.0 for NAGL compat.
    - openff-interchange>=0.5.4 # Need at least 0.4.7 for NAGL compat.
    # NOTE: packmol is not listed explicitly - ambertools >=23.6 bundles it and
    # declares a conflict with the standalone packmol package. Listing both pins
    # the solve back to ambertools 23.3, which has no Python 3.13 build.
    - rdkit==2024.09.6 # Newer versions hand on Topology.from_pdb in the protein-ligand notebook
    - ambertools >=23.6  # Needed for AM1-BCC charge assignment comparison, and provides packmol
    - MDAnalysis
    - prolif
    - py3dmol # For 3D visualization of of interactions in prolif
    - openbabel # For conversion of the pdbqt files to sdf (last exercise)