Release v0.4.0

0.4.0 - 2026-02-23

Summary

nvMolKit 0.4.0 adds GPU-accelerated substructure searching, optional stream control across Python APIs, and enhancements to Butina clustering.

Contributors

• Kevin Boyd (@scal444)
• Eva Xue (@evasnow1992)

Features

• GPU-accelerated substructure search with hasSubstructMatch, countSubstructMatches, and getSubstructMatches. Supports batch queries against batch targets with SMARTS-based query molecules.
• Optional stream parameter added to fingerprint generation, similarity, and Butina clustering APIs, enabling explicit CUDA stream control
• Butina clustering now supports optional centroid reporting via the return_centroids parameter (#82)
• Butina clustering performance improved by replacing CPU loops with CUDA Graph conditional nodes (#72)

Bug Fixes

• Fix data races when torch operations immediately followed nvMolKit calls on the default stream (Issue #84). Operations now correctly use the current stream or an explicit stream parameter (#36).
• Fix setup.py compatibility on some Python versions and rework CUDA target detection (#68)