Snowball Release Notes

v0.29.1 February 2025

General Notice

• This package is built using the following dependencies:

  • openeye-orionplatform>=6.2.0,<7.0.0.

  • OpenEye-Toolkits>=2024.2.0.

  • OpenEye-szmap>=1.7.1,<2.0.0.

  • OpenEye-szybki>=2.8.0,<3.0.0.

New Cubes

• New Check clashes (Individual) and Check clashes (Series) Cubes have been added that enable checking if there are clashes between a ligand and the target protein.

• A new Check Optimized Pose Cube has been added that enables checking if a ligand pose has moved too far out due to optimization.

• A new Dock Output Quality preference Cube has been added that enables selection of the quality desired in docking output.

• New EON Overlay, EON Overlay (Multi Query), and Combine EON Queries Cubes have been added that enable electrostatic overlays using the new Eon toolkit.

Cube Updates

• The following issues have been fixed in the Generate Chomp 2D Fragments Cube:

  • Input molecules without a title are given a title of Molecule.

  • The cube now properly uses the text contents from the file coming through the smarts_port.

• The following features have been added to the Build 2D BROOD Database Cube:

  • A new Report Only parameter produces a quick report of fragments without attempting to emit the database fragments.

  • A new init port accepts existing database collections, fragments of which are ignored in the newly built library.

  • A new info port emits information about fragments accumulated during library building.

• Behavior of the following cubes related to CHOMP has been improved to track memory usage and process the maximum amount it can handle instead of failing due to lack of memory.

  • Build 2D BROOD Database

  • Generate BROOD Database

• The Chomp Report Cube has been improved to provide more comprehensive information.

• The Brood Hit list Cube now emits comprehensive information on hit list building through a summary port.

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

• The Sage force field in the following cubes now points to the latest supported Sage version (2.1.0) in the associated toolkit:

  • Ligand Entropy

  • Torsion Scan

  • Ligand Minimization

  • Ligand Energy

  • Ligand Restrained Minimization

  • Atropisomerism

  • Ligand Torsions Minimization

  • Ligand Hydrogen Optimization

  • Freeform Conf Initial Optimization

  • Freeform Conf Optimization

  • Freeform Conf Energy Calculation

  • Freeform Conf Restriction Energies

  • Freeform Conf Energies

  • Freeform Ligand Strain

• The constant for conversion from KT to kcal has been updated from 0.59 to 0.592 in both the MMPBSA (Series) and MMPBSA (Individual) Cubes.

• The Freeform Conf Prepare Ensemble Cube now properly uses the bound conformer when an input ensemble of given molecules is passed through a field other than the primary molecule field.

• The following cubes now accept molecules with up to 40 heavy atoms as query molecules:

  • Find ShapeQuery

  • ROCS for EON

  • EON Score

  • EON Score (Multi Query)

• The Spruce DU to Mol Cube now fails if it does not find the specified components.

• The Loop Builder Cube now adds a conformer ID for each generated conformer.

• The Spruce Minimize Design Unit Cube Cube now recalculates interactions after minimization.