Hello,
When trying to learn how to use nvMolKit, I noticed differences in similarity values when comparing RDKit-generated fingerprints with nvMolKit-generated fingerprints using the same fingerprint settings.
I then tried generating fingerprints with nvMolKit as batched and then one at a time. This produces different fingerprints for some molecules (using same mols, generator settings, and num_threads=1). Notably, the number of threads did not seem to make a difference.
I would have expected the fingerprints to be the same regardless of batch or one at a time.
RDKit (2026.03.1) and nVMolkit (0.5.0) were installed via conda-forge. Here is a minimal example below, thank you for providing this library and any clarification you can provide.
mols = []
suppl = Chem.SDMolSupplier('chembl_36.sdf')
for mol in suppl:
if mol is None:
continue
mols.append(mol)
if len(mols) >= 1_000:
break
# create nvmolkit fp generator
fpgen = MorganFingerprintGenerator(radius=3, fpSize=2048)
# batched
fps_batched = fpgen.GetFingerprints(mols, num_threads=1)
torch.cuda.synchronize()
# single
fps_single = [fpgen.GetFingerprints([mol], num_threads=1) for mol in mols]
torch.cuda.synchronize()
# convert to tensors
batched_tensor = fps_batched.torch()
single_tensors = [fp.torch() for fp in fps_single]
matches = [
torch.equal(batched_tensor[i].cpu(), single_tensors[i][0].cpu())
for i in range(len(mols))
]
print(f"Number of molecules: {len(mols)}")
print(f"Mismatched fingerprints: {matches.count(False)} / {len(mols)}")Output:
Number of molecules: 1000
Mismatched fingerprints: 101 / 1000
Hello,
When trying to learn how to use nvMolKit, I noticed differences in similarity values when comparing RDKit-generated fingerprints with nvMolKit-generated fingerprints using the same fingerprint settings.
I then tried generating fingerprints with nvMolKit as batched and then one at a time. This produces different fingerprints for some molecules (using same mols, generator settings, and num_threads=1). Notably, the number of threads did not seem to make a difference.
I would have expected the fingerprints to be the same regardless of batch or one at a time.
RDKit (2026.03.1) and nVMolkit (0.5.0) were installed via conda-forge. Here is a minimal example below, thank you for providing this library and any clarification you can provide.
Output: