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nvmolkit-usage

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Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.

skills/bionemo-nvmolkit-usage/SKILL.md

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# nvMolKit usage

## Purpose

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.

This skill covers the installed Python API. Building nvMolKit from source is out of scope.

## 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.