Small Molecule Modeling Release Notes

v2.3.3 December 2025

General Notice

• This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.2.0, and OpenEye-Snowball==0.30.1.

Floe Updates

• Three new floes have been added in this release:

  • Clustering: 2D Scaffold (~25M compounds): This floe performs scaffold clustering on collections and files with inputs containing from 100K to millions of molecules.

  • Clustering: 2D Fingerprint, up to 100K compounds: This floe performs 2D-fingerprint-based DBSCAN, Hierarchical, and K-medoid clustering on inputs containing up to 100K molecules.

  • Clustering: 3D Shape/Color, ~10K compounds: This floe performs 3D ROCS based DBSCAN, Hierarchical, and K-medoid based clustering on inputs containing up to ~10K molecules.

• The OMEGA - Conformer Generation for Macrocycles floe now fails molecule early if molecule does not have stereo specified.

• The following floes have been deprecated:

  • DBSCAN 3D Similarity Clustering

  • DBSCAN 2D Similarity Clustering

  • Hierarchical 2D Similarity Clustering

  • Hierarchical 3D Similarity Clustering

  • K-Medoids 2D Similarity Clustering

  • K-Medoids 3D Similarity Clustering