Classic Lead Optimization Release Notes

v0.15.1 February 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.2.0, and OpenEye-Snowball==0.29.1.

Floe Updates

  • The CHOMP - Generate BROOD Fragment Database Floe has been improved as follows to improve usability and robustness:

    • A Report Only parameter has been added that would produce a quick report of fragments without attempting to generate the database.

    • The memory requirement per fragment has been reduced by keeping track of just a single source molecule instead of five.

    • Instead of failing due to lack of required memory, the floe now attempts to complete the task with the amount of fragments that it could process.

    • An Input Existing Brood Database parameter has been added to enable passing in an existing database, fragments from which should not be included in the newly created database.

    • The default setting has been adjusted for fragments larger than nine heavy atoms to be included in the database if the fragment is contained in at least two of the source molecules.

    • The zipped database, in .TAR.GZ format, is saved by default.

    • The floe no longer fails to write fragments when input molecules are missing titles.

  • The BROOD - 3D Fragment Replacement Floe has gone through the following changes:

    • The Floe Report now provides comprehensive information on the hit list generation along with the details of the clustering and the hit molecules.

    • The default memory for the hit list generation cube has been increased to 48*1.8*1024

  • The FreeForm - Bound Ligand Configurational Free Energies with SZYBKI Floe now properly uses the bound ligand from the primary molecule field when an input ensemble is provided by the user through a separate field.

  • The BROOD - DB File to Collection Floe now generates a report if it fails to complete successfully for some reason.

  • The BROOD - Query Builder Floe now generates a report if it fails to complete successfully for some reason.

  • The POSIT - Ligand Guided Small Molecule Posing Floe now properly respects user choice for the Relaxation Mode parameter. The default for the Relaxation Mode has also been changed to Clashed, to ensure that generated poses are clash free by default.

  • The Calculate Atropisomerism Floe now assigns AM1BCCELF10 charges by default and provides an option to change the default behavior.