query -> promps

app.py

@@ -23,14 +23,14 @@ protein_calmodulin = "MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMISELDQ
 protein_calcineurin = "MSSKLLLAGLDIERVLAEKNFYKEWDTWIIEAMNVGDEEVDRIKEFKEDEIFEEAKTLGTAEMQEYKKQKLEEAIEGAFDIFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIRQMWDQNGDWDRIKELKFGEIKKLSAKDTRGTIFIKVFENLGTGVDSEYEDVSKYMLKHQ"
 
 
-def format_query(prot1,prot2):
+def format_prompt(prot1,prot2):
     # Formatting prompt to match pre-training syntax
     return f"<@TOKENIZER-TYPE=AA><BINDING_AFFINITY_CLASS><SENTINEL_ID_0><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{prot1}<SEQUENCE_NATURAL_END><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{prot2}<SEQUENCE_NATURAL_END><EOS>"
 
-def run_query(query):
+def run_prompt(prompt):
     # Create and load sample
     sample_dict = dict()
-    sample_dict[ENCODER_INPUTS_STR] = query
+    sample_dict[ENCODER_INPUTS_STR] = prompt
 
     # Tokenize
     sample_dict=tokenizer_op(
@@ -58,9 +58,9 @@ def run_query(query):
     
     return generated_output,score
 
-def create_and_run_query(prot1, prot2):
-    query = format_query(prot1, prot2)
-    res=query, *run_query(query=query)
+def create_and_run_prompt(prot1, prot2):
+    prompt = format_prompt(prot1, prot2)
+    res=prompt, *run_prompt(prompt=prompt)
     return res
 
 def create_application():
@@ -92,16 +92,16 @@ Given two protein sequences, estimate if the proteins interact or not.
                 value=protein_calcineurin,
             )
         with gr.Row():
-            run_mammal = gr.Button("Run Mammal query for Protein-Protein Interaction",variant='primary')
+            run_mammal = gr.Button("Run Mammal prompt for Protein-Protein Interaction",variant='primary')
         with gr.Row():
-            query_box = gr.Textbox(label="Mammal query",lines=5)
+            prompt_box = gr.Textbox(label="Mammal prompt",lines=5)
         
         with gr.Row():
             decoded = gr.Textbox(label="Mammal output")
             run_mammal.click(
-                fn=create_and_run_query,
+                fn=create_and_run_prompt,
                 inputs=[prot1,prot2],
-                outputs=[query_box,decoded,gr.Number(label='PPI score')]
+                outputs=[prompt_box,decoded,gr.Number(label='PPI score')]
             )
         with gr.Row():
             gr.Markdown("```<SENTINEL_ID_0>``` contains the binding affinity class, which is ```<1>``` for interating and ```<0>``` for non-interating")