Snowball
v0.30.1 August 2025
General Notice
This package is built using
OpenEye-orionplatform=6.6.0,OpenEye-toolkits==2025.1.0,OpenEye-szmap==1.7.1.1, andOpenEye-szybki==2.8.0.1.
New Cubes
The new Docking Method Selector (Single Receptor) Cube has been added to select the docking method (FRED or Hybrid) based on similarity to the bound ligand and to emit the record to the corresponding port.
Cube Updates
OMEGA cubes now have the option to use Thompson sampling.
The Omega Conformation Cube now has an option to turn on Thompson sampling for OMEGA torsion driving.
A new OMEGA mode, ROCS-TS, generates conformers suitable for ROCS calculations using Thompson sampling.
The Generate 3D Cube now uses OEConformerBuilder, a Thompson sampling based method, to generate 3D structures for input molecules.
The Slice Ensemble Cube has the option to perform slice ensembles with or without RMS overlay.
The following cubes all use a protein mask from the receptor by default:
The following cubes have the option of whether or not to fail optimization for excessive bending of aromatic rings:
The Check clashes (Individual) Cube and Check clashes (Series) Cube have the option to choose the types of clashes to ignore: None, Hydrogen, or Any.
The Check Optimized Pose Cube emits a clashed status of each pose. It also emits a failure log if all poses are clashing or if they have deviated too far after optimization. By default, a hydrogen clash is allowed by this cube.
The Fixed-Protein Ligand Minimization Individual Cube and Fixed-Protein Ligand Minimization Series Cube emit the RMSD of optimized poses.
The Fixed-Protein Ligand Minimization Series Cube only sends the record to the failure port if none of the conformers of the molecule could be optimized.
The Brood DB Reader Cube can now handle tarballs created on macOS containing AppleDouble files (with the prefix ‘._’).
The Exhaustive Docking (Single Receptor) Cube has a new option to not fail when an apo receptor is passed for
HYBRIDmode, and switch to useFREDmode instead.