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Nvmolkit Usage

NVIDIAOfficialCreated by Kevin Boyd (@scal444)Distributed by NVIDIA

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  • Tool integration
  • Software development
  • Apache-2.0
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Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
— the description by Kevin Boyd (@scal444)

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Written by AutoGineer from the skill’s own files, not by the author

nvMolKit provides a Python API for high-throughput molecular operations by leveraging NVIDIA GPUs. It mirrors RDKit's API structure while enabling parallel processing of large batches of molecules. The library is designed for scenarios where throughput is prioritized over per-molecule latency, such as fingerprinting large libraries, bulk conformer embedding, or pairwise similarity calculations. It integrates with PyTorch for GPU-resident data handling, allowing for efficient chaining of operations without host-side round-trips.

What it does

  • Generates Morgan fingerprints in parallel on GPU.
  • Performs bulk Tanimoto and cosine similarity calculations.
  • Executes ETKDG conformer embedding and MMFF/UFF forcefield optimizations.
  • Calculates pairwise conformer RMSD and Torsion Fingerprint Deviation (TFD).
  • Provides GPU-accelerated Butina clustering and substructure searching.
  • Supports custom geometric constraints and forcefield configurations.

When to use it

  • When processing large batches of molecules (thousands or more).
  • When the same operation is repeated identically across a large dataset.
  • When you need to chain multiple molecular operations while keeping data on the GPU.
  • When optimizing for total wall-clock time across a batch.

Advantages

  • Significant throughput improvements for batch-oriented cheminformatics tasks.
  • Seamless integration with PyTorch for zero-copy GPU data exchange.
  • Supports asynchronous execution and custom CUDA stream control.
  • Provides flexible hardware tuning and autotuning capabilities.

Usage examples

“How do I calculate Morgan fingerprints for a list of SMILES strings using nvMolKit?”
The agent provides code to initialize a MorganFingerprintGenerator, process the list of RDKit Mol objects, and retrieve the results as a GPU-resident torch tensor.
“Can I perform MMFF94 minimization on a batch of conformers?”
The agent demonstrates using MMFFOptimizeMoleculesConfs to update conformer coordinates in-place on the GPU, returning optimized energies.
“How do I run a substructure search on a large library?”
The agent explains how to use the substructure module, including configuring batch sizes and worker threads for optimal GPU performance.
“How can I chain ETKDG embedding and similarity scoring without moving data to the CPU?”
The agent shows how to use CoordinateOutput.DEVICE to keep conformer coordinates on the GPU and pass them directly into downstream similarity or clustering functions.

Install

  1. Download the skill as a ZIP:

    https://autogineer.com/agent-skills/nvidia/nvmolkit-usage/download

  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip nvmolkit-usage.zip -d .agents/skills

Documentation by Kevin Boyd (@scal444)

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.

  • The same operation is repeated identically across the batch (fingerprinting a library, embedding/minimizing many conformers, bulk pairwise similarity), so the GPU stays saturated.

Requirements

  • An NVIDIA GPU with compute capability 7.0 (V100) or higher

  • A CUDA driver compatible with CUDA 12.6+.

  • A working torch install with CUDA support (nvMolKit returns GPU tensors via torch's CUDA array interface).

When helping with installation, make the user choose a PyTorch CUDA backend that the host driver supports before installing nvMolKit. nvMolKit's PyPI wheels are built with CUDA Toolkit 12.9 and depend on CUDA 12 runtime packages, but pip/uv can still select a CUDA 13 PyTorch wheel unless the install command says otherwise.

  • Conda: prefer conda-forge pytorch-gpu; pin cuda-version=12.6 or another CUDA version supported by the driver.

  • pip: send the user to the PyTorch install selector or previous-versions page to install torch for a CUDA 12.x backend before installing nvMolKit.

  • uv: install nvMolKit with an explicit backend, e.g. uv pip install --torch-backend=cu128 nvmolkit.

Inputs

  • Required: choose an operation and supply molecules or fingerprints from the user's code or molecular dataset. Parse SMILES with RDKit and reject failed parses (None).

  • Molecular operations use RDKit Mol objects. Add hydrogens for ETKDG; minimization and conformer comparisons need existing conformers.

  • Fingerprint similarity takes packed AsyncGpuResult, torch tensors, or NumPy arrays: one molecule per row, with int32 or uint32 words.

  • Optional: take conformer counts, fingerprint settings, cutoffs, output modes, and hardware options from the user's requested workflow; otherwise use the documented API defaults.

Limitations

  • CUDA is required; there is no CPU fallback. Use RDKit directly when CPU execution is needed.

  • Plain RDKit is usually preferable for single-molecule work or operations that cannot be batched.

  • ETKDG does not support custom bounds matrices, custom CPCI, coordinate maps, or separate-fragment embedding.

  • Substructure search does not support chirality-aware matching, enhanced stereochemistry, or other advanced RDKit SubstructMatchParameters options.

Instructions

  1. Run the smoke test below before writing nvMolKit code.

  2. Choose an API from the entry-point table and apply its input requirements.

  3. Handle its result as described below; synchronize asynchronous GPU results before host reads.

Verify the install before writing real code
import nvmolkit
import torch
from rdkit import Chem
from nvmolkit.fingerprints import MorganFingerprintGenerator

print("nvmolkit:", nvmolkit.__version__)
print("cuda available:", torch.cuda.is_available())
print("device count:", torch.cuda.device_count())

mols = [Chem.MolFromSmiles(smi) for smi in ["CCO", "c1ccccc1", "CC(=O)O"]]
fpgen = MorganFingerprintGenerator(radius=2, fpSize=1024)
result = fpgen.GetFingerprints(mols)
torch.cuda.synchronize()
fps = result.torch()
print("fps shape:", tuple(fps.shape), "dtype:", fps.dtype)
# Expected: shape (3, 32), dtype torch.int32  (1024 bits packed into 32 int32s per row)

If this fails, point the user at the installation guide rather than guessing.

Entry points

TaskModulePrimary entry point
Morgan fingerprintsnvmolkit.fingerprintsMorganFingerprintGenerator(radius, fpSize).GetFingerprints(mols)
Bulk Tanimoto / cosine similaritynvmolkit.similaritycrossTanimotoSimilarity(...), crossCosineSimilarity(...), plus *MemoryConstrained variants for results too large to fit in GPU memory
ETKDG conformer embeddingnvmolkit.embedMoleculesEmbedMolecules(molecules, params, confsPerMolecule, ...)
MMFF94 optimization (one-shot)nvmolkit.mmffOptimizationMMFFOptimizeMoleculesConfs(molecules, ..., minimizerKind=..., fireOptions=...)
UFF optimization (one-shot)nvmolkit.uffOptimizationUFFOptimizeMoleculesConfs(molecules, ..., minimizerKind=..., fireOptions=...)
Forcefield with custom options + constraintsnvmolkit.batchedForcefieldMMFFBatchedForcefield(mols, properties=..., nonBondedThreshold=..., ignoreInterfragInteractions=..., hardwareOptions=...), UFFBatchedForcefield(mols, vdwThreshold=..., ...). Per-molecule view ff[i] exposes add_distance_constraint, add_position_constraint, add_angle_constraint, add_torsion_constraint. Methods: .compute_energy(), .compute_gradients(), .minimize(maxIters, forceTol, minimizerKind=..., fireOptions=...)
Pairwise conformer RMSDnvmolkit.conformerRmsdGetConformerRMSMatrix(mol), GetConformerRMSMatrixBatch(mols)
Torsion Fingerprint Deviation (TFD)nvmolkit.tfdGetTFDMatrix(mol), GetTFDMatrices(mols)
Butina clusteringnvmolkit.clusteringbutina(distance_matrix, cutoff) (precomputed matrix), fused_butina(fingerprints, cutoff) (memory-efficient, on-the-fly); both support explicit RDKit and device output modes
Substructure searchnvmolkit.substructurehasSubstructMatch, countSubstructMatches, getSubstructMatches
Maximum common substructurenvmolkit.mcsfindMCS(mols, ...) for all pairs, explicit pairs, or two paired molecule lists
Hardware tuning (batch size, GPU IDs)nvmolkit.typesHardwareOptions(...) passed to ETKDG / MMFF / UFF
Optional autotuningnvmolkit.autotunetune_embed_molecules, tune_mmff_optimize, tune_uff_optimize, tune_batched_forcefield, tune_substructure, tune_mcs. Requires the optuna package

Result types and execution model

Two return shapes carry GPU-resident output, depending on what the operation produces.

AsyncGpuResult

Used by operations that return a single flat tensor (fingerprints, similarity matrices, RMSD/TFD vectors, Butina inputs). Key behaviors:

  • Asynchronous. The kernel may not have completed when the call returns.

  • result.torch() returns a zero-copy torch.Tensor on the GPU. Caller is responsible for synchronizing before reading values on the host.

  • result.numpy() synchronizes and returns a CPU numpy array.

  • Exposes __cuda_array_interface__, so it can be passed directly into other nvMolKit functions (e.g. fingerprints → similarity) with no host round-trip.

CUDA stream control

A subset of the AsyncGpuResult-returning APIs accept an optional stream: torch.cuda.Stream | None = None argument so callers can submit nvMolKit work to a non-default stream and overlap it with their own kernels. When omitted, the call uses the current torch stream.

APIs that take a stream argument:

  • MorganFingerprintGenerator.GetFingerprints

  • crossTanimotoSimilarity, crossCosineSimilarity, and their *MemoryConstrained variants

  • butina, fused_butina

  • GetConformerRMSMatrix, GetConformerRMSMatrixBatch

Other APIs (ETKDG, MMFF/UFF optimization, TFD, substructure search, MCS) are synchronous to the caller — no stream plumbing needed.

Typical pattern:

import torch
from rdkit import Chem
from nvmolkit.fingerprints import MorganFingerprintGenerator
from nvmolkit.similarity import crossTanimotoSimilarity

stream = torch.cuda.Stream()
fpgen = MorganFingerprintGenerator(radius=2, fpSize=1024)
mols = [Chem.MolFromSmiles(smi) for smi in ["CCO", "c1ccccc1", "CC(=O)O"]]

with torch.cuda.stream(stream):
    fps = fpgen.GetFingerprints(mols, stream=stream)
    sim = crossTanimotoSimilarity(fps, stream=stream)
stream.synchronize()
print(sim.torch())
Device3DResult

Used by ETKDG embedding and MMFF/UFF optimization (one-shot and BatchedForcefield) when called with output=CoordinateOutput.DEVICE. The GPU-resident equivalent of writing conformers back to Mol objects. Fields:

  • values: AsyncGpuResult of shape (total_atoms, 3) float64. Concatenated conformer coordinates in CSR-style layout.

  • atom_starts, mol_indices, conf_indices: AsyncGpuResult int32 buffers describing the layout (values[atom_starts[i]:atom_starts[i+1]] is conformer i's atoms).

  • energies, converged: AsyncGpuResult buffers populated only for MMFF/UFF minimization (not for plain ETKDG).

  • gpu_id: device the buffers live on. The targetGpu argument on each API picks this; targetGpu=-1 uses the default consolidation device.

  • .per_molecule() returns nested list[list[torch.Tensor]] of per-conformer views; .dense(pad_value=nan) materializes a padded (n_mols, max_confs, max_atoms, 3) tensor.

The default mode (CoordinateOutput.RDKIT_CONFORMERS) still writes optimized coordinates back into each Mol and returns Python lists of energies/convergence flags. Reach for CoordinateOutput.DEVICE when chaining downstream GPU work (e.g. ETKDG → MMFF → similarity scoring) without host round-trips.

MCSBatchResult

findMCS is synchronous and returns an MCSBatchResult backed by CPU NumPy arrays. Results are always flat: result[k] (or result.get_result(k)) materializes the result at pair position k, not generally the result for molecule k. Use result.pairs[k] to identify that pair. In all_pairs mode these are the generated pairs over mols; in pairs mode they exactly preserve the supplied pair sequence; in paired_lists mode item k compares mols[k] with mols_b[k], while result.pairs[k] uses the combined-table indices (k, len(mols) + k). Each MCSResult has pair, num_atoms, num_bonds, canceled, atom_mapping, and bond_mapping; the two columns of each mapping index the first and second molecule of that result pair, respectively.

Configuration

For ETKDG, forcefield, substructure, or MCS tuning, read the advanced configuration reference. It lists configuration fields, defaults, GPU selection, and autotuning APIs.

Examples

Morgan fingerprints + bulk Tanimoto similarity
import torch
from rdkit import Chem
from nvmolkit.fingerprints import MorganFingerprintGenerator
from nvmolkit.similarity import crossTanimotoSimilarity

smiles = ["CCO", "CCN", "c1ccccc1", "CC(=O)O", "CCOCC"]
mols = [Chem.MolFromSmiles(smi) for smi in smiles]

fpgen = MorganFingerprintGenerator(radius=2, fpSize=1024)
fps = fpgen.GetFingerprints(mols)

sim = crossTanimotoSimilarity(fps)
torch.cuda.synchronize()
print(sim.torch())

Inputs are list[Mol]. Output of GetFingerprints is an AsyncGpuResult wrapping an (n_mols, fpSize / 32) int32 tensor of packed bits. Pass it straight into crossTanimotoSimilarity for an (n, n) similarity matrix; pass two fingerprint sets for an (n, m) cross-matrix. For sets too large to materialize on the GPU, use crossTanimotoSimilarityMemoryConstrained (chunked compute, returns numpy on CPU).

ETKDG conformer embedding
from rdkit.Chem import AddHs, MolFromSmiles
from rdkit.Chem.rdDistGeom import ETKDGv3
from nvmolkit.embedMolecules import EmbedMolecules

mols = [AddHs(MolFromSmiles(smi)) for smi in ["C1CCCCC1", "C1CCCCC2CCCCC12", "COO"]]
params = ETKDGv3()

EmbedMolecules(mols, params, confsPerMolecule=10, maxIterations=-1)

for mol in mols:
    print(mol.GetNumConformers())

Inputs are sanitized list[Mol] with hydrogens added (AddHs). Conformers are added in-place; see Limitations for unsupported embedding options.

MMFF94 minimization of a batch of conformers
from rdkit.Chem import AddHs, MolFromSmiles
from rdkit.Chem.rdDistGeom import ETKDGv3
from nvmolkit.embedMolecules import EmbedMolecules
from nvmolkit.mmffOptimization import MMFFOptimizeMoleculesConfs

mols = [AddHs(MolFromSmiles(smi)) for smi in ["CCO", "CCN", "c1ccccc1"]]
params = ETKDGv3()
EmbedMolecules(mols, params, confsPerMolecule=5)

energies = MMFFOptimizeMoleculesConfs(mols, maxIters=500)
for mol, mol_energies in zip(mols, energies):
    print(mol.GetNumConformers(), mol_energies)

Inputs are list[Mol] with conformers already populated (typically by ETKDG, RDKit's EmbedMultipleConfs, or a prior nvMolKit call). Coordinates are updated in place; the return is list[list[float]] of optimized energies aligned with the input molecule order and conformer index. UFF is identical in shape: swap in from nvmolkit.uffOptimization import UFFOptimizeMoleculesConfs.

BFGS is the default minimizer. To use FIRE, pass minimizerKind="FIRE"; optionally customize it with a nvmolkit.types.FireOptions instance through fireOptions=. The one-shot MMFF and UFF functions and both batched-forcefield .minimize() methods accept the same selector.

If any input molecule is None or lacks MMFF/UFF atom types, the call raises ValueError. The exception's args[1] is a dict with keys "none" and "no_params" listing the offending indices - useful for filtering a noisy input set.

Conformer RMSD and Butina clustering
import torch
from rdkit import Chem
from rdkit.Chem.rdDistGeom import EmbedMultipleConfs
from nvmolkit.clustering import ButinaOutputMode, butina
from nvmolkit.conformerRmsd import GetConformerRMSMatrixBatch

mols = [Chem.AddHs(Chem.MolFromSmiles(smi)) for smi in ["CCCCCC", "c1ccccc1"]]
for mol in mols:
    EmbedMultipleConfs(mol, numConfs=10)

# Remove hydrogens after embedding for heavy-atom RMSD.
heavy_mols = [Chem.RemoveHs(mol) for mol in mols]

# Default RMSD output is RDKit-compatible condensed lower-triangle form.
condensed = GetConformerRMSMatrixBatch(heavy_mols)

# Butina expects a square distance matrix, so request square GPU tensors.
square = GetConformerRMSMatrixBatch(heavy_mols, output_format="square")
results = [
    butina(distance_matrix, cutoff=0.5, output=ButinaOutputMode.DEVICE)
    for distance_matrix in square
]

torch.cuda.synchronize()
for result in results:
    print(result.cluster_ids.torch().cpu().tolist())

Both Butina functions return GPU-resident results by default:

  • The default, output=ButinaOutputMode.DEVICE, returns cluster IDs, centroids, and sizes.

  • output=ButinaOutputMode.RDKIT returns RDKit cluster tuples on the host. The first element of each cluster is its centroid.

The device output fields are AsyncGpuResult objects. Use .torch() to access their CUDA tensors without a host copy or .numpy() to synchronize and copy a field to the host.

GetConformerRMSMatrix(mol) and GetConformerRMSMatrixBatch(mols) default to output_format="condensed", returning AsyncGpuResult objects that wrap RDKit-style flat vectors of length N * (N - 1) // 2. Use output_format="square" when chaining into butina() or any other API that expects an N x N distance matrix. Both forms live on the GPU; call .numpy() on condensed results or synchronize before moving square tensors to the CPU.

Atom-Atom Path similarity and directed sphere exclusion clustering

Atom-Atom Path (AAP) similarity with directed sphere exclusion (DISE) clustering provides device and RDKit-style output modes:

from rdkit import Chem
from nvmolkit.clustering import DISEOutputMode, aap_dise

molecules = [Chem.MolFromSmiles(smiles) for smiles in ["CCCC", "CCCO", "CCOC"]]
device_result = aap_dise(molecules)
rdkit_clusters = aap_dise(molecules, output=DISEOutputMode.RDKIT)

device_result has cluster_ids, centroids, and cluster_sizes fields; cluster IDs are zero-based and contiguous. DISEOutputMode.RDKIT describes the centroid-first RDKit cluster representation, not an RDKit implementation of the AAP+DISE algorithm. The current DISE control loop synchronizes before returning either mode; DEVICE describes the stable schema and where the result resides, not asynchronous execution of the overall call.

Maximum common substructure search
from rdkit import Chem
from nvmolkit.mcs import findMCS

mols = [Chem.MolFromSmiles(smi) for smi in ["CCO", "CCN", "c1ccccc1O"]]
result = findMCS(mols, mode="pairs", pairs=[(0, 1), (0, 2)])

for pair_idx, pair in enumerate(result.pairs):
    item = result[pair_idx]
    print(pair, item.num_atoms, item.num_bonds, item.atom_mapping)

The default mode="all_pairs" generates the upper triangle including the diagonal. mode="pairs" preserves an explicit pair list exactly, including duplicates and reversed pairs. mode="paired_lists" zips mols with an equally sized mols_b. Timeouts are per pair; inspect item.canceled because a timed-out result can contain the best partial MCS found.

Matching options include atom_compare, bond_compare, valence/formal-charge matching, and atom/bond ring-only matching. Unsupported RDKit fMCS options raise instead of silently changing semantics. For repeated representative explicit-pair workloads, nvmolkit.autotune.tune_mcs returns a TuneResult. Its best_config is the tuned MCSConfig to pass to findMCS(..., config=result.best_config).

Custom forcefield options + constraints (BatchedForcefield)

For per-molecule forcefield settings, geometric constraints, or separate energy and gradient calls, read the advanced forcefield recipe.

Troubleshooting

SymptomLikely causeAction
torch.cuda.is_available() is falseGPU access, driver compatibility, or the torch CUDA build is missingCheck the GPU and driver, then follow the installation guidance above to select a compatible torch build.
RuntimeError: invalid device ordinalA requested gpuIds entry is not visibleUse device indices below torch.cuda.device_count() or the API's documented GPU defaults.
An RDKit option is rejectedThe option is unsupported by that nvMolKit APIUse supported options only if they preserve the requested behavior; otherwise use RDKit for that operation.

Going deeper

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Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs Python

Security

What our scanner noticed· Medium risk

  • Large base64-encoded blobs
  • Instructions that use the network

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Attribution and licence

Created by
Kevin Boyd (@scal444)
Publisher
NVIDIA (Official)
Distributed by
NVIDIA
Source
NVIDIA/skills · skills/bionemo-nvmolkit-usage · commit fce3cca
Licence
Apache License 2.0 (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE-APACHE)
  • ATTRIBUTION.md (written by AutoGineer)
Synced

AutoGineer is not affiliated with or endorsed by Kevin Boyd (@scal444) or NVIDIA.

Download ZIP

The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download nvmolkit-usage.zip