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Update transformer_fingerprints.py #23

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14 changes: 11 additions & 3 deletions rxnfp/transformer_fingerprints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,15 +131,23 @@ def get_default_model_and_tokenizer(model='bert_ft', force_no_cuda=False):
)
return model, tokenizer

def generate_fingerprints(rxns: List[str], fingerprint_generator:FingerprintGenerator, batch_size=1) -> np.array:
def generate_fingerprints(rxns: List[str], fingerprint_generator: FingerprintGenerator, batch_size=1) -> np.array:
fps = []

# Determine how many complete batches there are
n_batches = len(rxns) // batch_size
remaining = len(rxns) % batch_size # Check if there's a remaining partial batch
emb_iter = iter(rxns)

for i in tqdm(range(n_batches)):
batch = list(islice(emb_iter, batch_size))

fps_batch = fingerprint_generator.convert_batch(batch)
fps += fps_batch

# Handle the last remaining batch, if any
if remaining > 0:
batch = list(islice(emb_iter, remaining))
fps_batch = fingerprint_generator.convert_batch(batch)
fps += fps_batch
return np.array(fps)

return np.array(fps)