nvMolKit APIs

Fingerprint Generation

fingerprints.MorganFingerprintGenerator(...)	Morgan fingerprint generator.
fingerprints.pack_fingerprint(fp)	Pack a 2D boolean tensor of shape (n_fps, fingerprint_size) into a 32-bit integer-encoded fingerprint.
fingerprints.unpack_fingerprint(fp)	Unpack a 32-bit integer-encoded fingerprint into a 2D boolean tensor of shape (len(fp), fingerprint_size).

Similarity Calculations

similarity.crossTanimotoSimilarity(...[, ...])	Returns the Tanimoto similarity within a set of fingerprints or between two sets of fingerprints.
similarity.crossTanimotoSimilarityMemoryConstrained(...)	Returns the Tanimoto similarity within a set of fingerprints or between two sets of fingerprints.
similarity.crossCosineSimilarity(...[, ...])	Returns the Cosine similarity between two sets of fingerprints.
similarity.crossCosineSimilarityMemoryConstrained(...)	Returns the Cosine similarity between two sets of fingerprints.

ETKDG Conformer Generation

embedMolecules.EmbedMolecules()

Embed multiple molecules with multiple conformers on GPUs.

MMFF Optimization

mmffOptimization.MMFFOptimizeMoleculesConfs()

Optimize conformers for multiple molecules using MMFF force field with BFGS minimization.

batchedForcefield.MMFFBatchedForcefield(...)	Evaluate MMFF energies and gradients, or run BFGS minimization, for a batch of molecules with all their conformers.
batchedForcefield.MMFFBatchElement(parent, idx)	Per-molecule view for configuring one molecule in an MMFF batch.

UFF Optimization

uffOptimization.UFFOptimizeMoleculesConfs()

Optimize conformers for multiple molecules using the UFF force field.

batchedForcefield.UFFBatchedForcefield(molecules)	Evaluate UFF energies and gradients, or run BFGS minimization, for a batch of molecules with all their conformers.
batchedForcefield.UFFBatchElement(parent, idx)	Per-molecule view for configuring one molecule in a UFF batch.

Butina Clustering

clustering.butina(distance_matrix, cutoff[, ...])

Perform Butina clustering on a distance matrix.

Substructure Search

substructure.hasSubstructMatch(targets, queries)	Check if targets contain query substructures (boolean results).
substructure.countSubstructMatches(targets, ...)	Count substructure matches per target/query pair.
substructure.getSubstructMatches(targets, ...)	Perform batch substructure matching on GPU, returning full atom-index mappings.

substructure.SubstructSearchConfig([...])	Configuration for GPU substructure search execution.
substructure.SubstructMatchResults(...)	Results of a batch substructure search.

Conformer RMSD

conformerRmsd.GetConformerRMSMatrix(mol[, ...])	Compute the pairwise RMSD matrix between all conformers of a molecule on GPU.
conformerRmsd.GetConformerRMSMatrixBatch(mols)	Compute pairwise RMSD matrices for a batch of molecules on GPU.

Torsion Fingerprint Deviation (TFD)

tfd.GetTFDMatrix(mol[, useWeights, maxDev, ...])	Calculate the TFD matrix for conformers of a molecule.
tfd.GetTFDMatrices(mols[, useWeights, ...])	Calculate TFD matrices for multiple molecules.

Types

types.AsyncGpuResult(obj[, gpu_id])	Handle to a GPU result.
types.HardwareOptions([...])	Configures GPU hardware settings for batch operations.

Hardware Autotuning (optional optuna extra)

autotune.is_available()	Return True if autotune dependencies are present (currently optuna).
autotune.tune_embed_molecules(molecules, ...)	Tune HardwareOptions for EmbedMolecules() on this hardware.
autotune.tune_mmff_optimize(molecules, *[, ...])	Tune HardwareOptions for MMFFOptimizeMoleculesConfs().
autotune.tune_uff_optimize(molecules, *[, ...])	Tune HardwareOptions for UFFOptimizeMoleculesConfs().
autotune.tune_batched_forcefield(molecules, ...)	Tune HardwareOptions for a batched-forcefield workflow.
autotune.tune_substructure(targets, queries, *)	Tune SubstructSearchConfig for a substructure-search workflow.
autotune.save(config, path)	Persist config to a JSON file at path.
autotune.load(path)	Load a configuration object previously saved with save().

autotune.TuneResult(best_config, ...)

Result returned by every tune_* wrapper.