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CHANGELOG.md

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Changes

4.0.3

  • Updated Gypsum-DL to version 1.1.7.
  • Revised $PATH/autogrow4/autogrow/user_vars.py to correct for error in handling the --conversion_choice. Obabel can now be run as the --conversion_choice without providing an MGLTools path (mgltools_directory).
  • Revised $PATH/autogrow4/autogrow/user_vars.py to enforce MGLToolsConversion as the only conversion option (--conversion_choice) when scoring with NN1/NN2 (--scoring_choice).
  • Minor code clean-up to $PATH/autogrow4/autogrow/user_vars.py.
  • Fixed user-reported bug in fragmenter_of_smi_mol.py.

4.0.2

  • Updated Gypsum-DL to version 1.1.5.
  • Updated Dimorphite-DL to version 1.2.4.
  • Fixed failure in $PATH/autogrow4/accessory_scripts/make_lineage_figures.py to detect source compounds when run had --use_docked_source_compounds set to False. This patched required the added user variable --use_docked_source_compounds. To maintain back-compatibility the default setting is to auto-detect from the vars.json file.
  • Added optional variable --purge_previous_pickled_files to $PATH/autogrow4/accessory_scripts/make_lineage_figures.py which automates removing all pickled files generated by the script. Useful for cleaning up files when done processing lineages and debugging. Default is False so it is backwards compatible.
  • Revised $PATH/autogrow4/autogrow/user_vars.py to correct minor typos with running custom filters.
  • Removed blank line in $PATH/autogrow4/source_compounds/naphthalene_smiles.smi.

4.0.1

  • Updated Gypsum-DL to version 1.1.4.
  • Updated Dimorphite-DL to version 1.2.3.
  • Revised $PATH/autogrow4/accessory_scripts/convert_vina_docked_pdbqt_to_pdbs.py to convert files that label atoms as HETATM. Previously, this script only converted atoms that were labeled as ATOM.
  • Revised $PATH/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py to remove None objects that could not be imported into RDKit. This prevents the None objects from causing errors in def convert_single_sdf_to_pdb.
  • Add raise Exception in $PATH/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py with debugging instructions if Gypsum-DL produces no SDF files. raise Exception added to def convert_sdf_to_pdbs.
  • Add raise Exception in $PATH/autogrow4/docker/autogrow_in_docker.py to check for sudo and administrator privileges.
  • Add --override_sudo_admin_privileges parameter to $PATH/autogrow4/docker/autogrow_in_docker.py. This parameter skips the check for sudo and administrator privileges for docker-compatible OS that do not have such permissions.
  • Fix dependency versions installed in $PATH/autogrow4/docker/Dockerfile. This ensures that AutoGrow4 continues to run in Docker even if future dependency updates cause compatibility issues.
  • Added an AutoGrow4 citation to the print statement in $PATH/autogrow4/RunAutogrow.py.
  • Revised ./docker/README.md to clarify docker use.
  • Updated the docker scripts. Bug fixes, added --rm to the docker command, etc.
  • Revised $PATH/autogrow4/autogrow/user_vars.py to correct minor typos with OS checks.
  • Updated $PATH/autogrow4/README.md with minor updates and developer notes.
  • Added Dependencies Notes to $PATH/autogrow4/README.md.
  • Added Developer Notes to $PATH/autogrow4/docker/README.md.
  • Added $PATH/autogrow4/CHANGELOG.md.

4.0.0

The original version described in:

Spiegel, J.O., Durrant, J.D. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 12, 25 (2020). [doi: 10.1186/s13321-020-00429-4]