nvMolKit usage

What nvMolKit is

GPU-accelerated, batched implementations of common RDKit operations. APIs mirror RDKit where possible but are batch-oriented: they take lists of rdkit.Chem.Mol (or lists of fingerprints) and process them in parallel on one or more GPUs. nvMolKit links against RDKit at build time; inputs and outputs are real RDKit Mol objects.

Where nvMolKit does well

Reach for nvMolKit when:

• The workload is a large batch of molecules processed together (typically thousands or more).
• The metric is throughput / total wall time across the batch, not per-molecule latency.
• The same operation is repeated identically across the batch (fingerprinting a library, embedding/minimizing many conformers, bulk pairwise similarity), so the GPU stays saturated.

Plain RDKit is usually the better choice for single-molecule one-offs or workflows that can't be expressed as a batch. nvMolKit is not meant to replace RDKit for those cases.

Runtime requirements