fix bug in bio_embedding usage

app.py

@@ -99,8 +99,10 @@ def display_dti():
             if selected_encoder == 'SeqVec':
                 from bio_embeddings.embed import SeqVecEmbedder
                 encoder = SeqVecEmbedder()
-                embedding = encoder([sequence])
-                embedding = encoder.reduce_per_protein(embedding)
+                embeddings = encoder.embed_batch([sequence])
+                for emb in embeddings:
+                    embedding = encoder.reduce_per_protein(emb)
+                    break
                 #from huggingface_hub import hf_hub_download
                 #precomputed_embs = f'{selected_encoder}_encoding.csv'
                 #REPO_ID = "emmas96/Lenselink"
@@ -116,13 +118,17 @@ def display_dti():
             elif selected_encoder == 'ESM-1b':
                 from bio_embeddings.embed import ESM1bEmbedder
                 encoder = ESM1bEmbedder()
-                embedding = encoder([sequence])
-                embedding = encoder.reduce_per_protein(embedding)
+                embeddings = encoder.embed_batch([sequence])
+                for emb in embeddings:
+                    embedding = encoder.reduce_per_protein(emb)
+                    break
             elif selected_encoder == 'ProtT5':
                 from bio_embeddings.embed import ProtTransT5XLU50Embedder
                 encoder = ProtTransT5XLU50Embedder()
-                embedding = encoder([sequence])
-                embedding = encoder.reduce_per_protein(embedding)
+                embeddings = encoder.embed_batch([sequence])
+                for emb in embeddings:
+                    embedding = encoder.reduce_per_protein(emb)
+                    break
             else: 
                 st.write('No pre-trained version of HyperPCM is available for the chosen encoder.')
                 embedding = None