Changelog#

0.3.0 - 2025-12-12#

Summary#

nvMolKit 0.3.0 adds Butina clustering support, improved performance to MMFF relaxation and conformer generation, and increased compatibility with libraries and compilers.

Contributors#

  • Kevin Boyd (@scal444)

  • Eva Xue (@evasnow1992)

  • Xuangui Huang (@stslxg-nv)

Features#

  • Butina clustering API enabled, using distance matrix input. On an H200 GPU, speedups of 400-1000x can be achieved on datasets up to 60k molecules

  • Improvements to BFGS minimizer. Up to 5x speedup compared to nvMolKit v0.2 on batches of small molecules (<20 atoms), with ~10-20% speedup in the general case. Applies to both MMFF relaxation and conformer generation.

  • Conda-forge releases now support RDKit versions 2024.9.6 to 2025.9.3

Bug Fixes#

  • Fixed a bug where synchronizations on the wrong stream could lead to data races in tests (Issue #28)

  • Fixed several areas where a memcpy could go out of scope before completing (Issue #28, Issue #29)

  • Fixed a bug where ETKDG would exit early with small CPU counts due to an incorrect identification of resource mis-configuration (Issue #31)

Miscellaneous#

  • (C++) Added support for CUB/CCCL > v2.8

  • (C++) Added support for externally specified CCCL

  • (C++) Added support for CUDA 13.0

0.2.0 - 2025-10-24#

Summary#

nvMolKit 0.2.0 comes with significant usability and feature-completeness improvements to existing functionality. It is also the first release to have a conda-forge release.

Contributors#

  • Kevin Boyd (@scal444)

  • Eva Xue (@evasnow1992)

  • Ignacio Pickering (@ignaciojpickering)

Features#

  • Add memory-segmented cross-similarity code, enabling larger datasets on systems with limited GPU memory (#13)

  • Support conformer deduplication in ETKDG conformer generation (#14)

  • Allow molecules > 256 atoms in conformer generation and MMFF optimization (#16)

  • Enable all combinations of (ET)(K)(DG) in conformer generator (#17)

Bug Fixes#

  • Fix compilation error on C++ build with target=native on Hopper architecture GPUs. (#6)

  • Fix lack of device-set cleanup in multi-GPU code (#8)

  • Fix bug in fingerprint bool->bitfield packing/unpacking code (#11)

  • Fix integer overflow leading to incorrect allocations in similarity calculation code. (#20)

  • Fix crash in most multithreaded APIs whenever exceptions are thrown inside of OpenMP loop. Exceptions now properly propagated to python (#18)

Miscellaneous#

  • Removed unsupported Bulk Similarity APIs (#12)

0.0.1 2025-09-09#

Summary#

Initial release of nvMolKit. Features include:

  • Morgan Fingerprints

  • Tanimoto and Cosine similarity

  • ETKDG conformer generation

  • MMFF optimization