Biocentral Tour

Python Example: Embedding (1)

1. Create the biocentral_api object:


                    from biocentral_api import BiocentralAPI

                    biocentral_api = BiocentralAPI().wait_until_healthy()

Python Example: Embedding (2)

2. Load data and set parameters:


                    from biocentral_api import CommonEmbedder

                    reduce = True  # per-sequence embeddings
                    sequence_data = {"Seq1": "MMALSLALM",
                     "Seq2": "PRTEIN",
                    "Seq3": "PRT",
                    "Seq4": "SEQWENCE",
                    "Seq5": "MMPRTEINSEQWENCE",
                    }
                    embedder_name = CommonEmbedder.ProtT5

Python Example: Embedding (3)

3. Run the embedding task:


                    embeddings = biocentral_api.embed(
                        embedder_name=embedder_name, 
                        reduce=reduce,
                        sequence_data=sequence_data,
                        use_half_precision=False).run_with_progress()

Python Example: Embedding (4)

4. Use the embedding result directly in your code:


                    print(embeddings["Seq1"])
                    embeddings.save("local_path.h5")
                    print(embeddings.to_dict())