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(molecules, params)

Embed multiple molecules with multiple conformers on GPUs.

MMFF Optimization

mmffOptimization.MMFFOptimizeMoleculesConfs(...)

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

Butina Clustering

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

Perform Butina clustering on a distance matrix.

Types

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