fix interface of Molecule3D after testing

app.py

@@ -54,57 +54,70 @@ with gr.Blocks(title="RFD3 Test") as demo:
     gen_directory = gr.State(None)
     gen_results = gr.State(None)
     gen_btn = gr.Button("Run Unconditional Generation")
-    #gen_output = gr.Textbox(label="Generation Result")
-    gen_btn.click(unconditional_generation, inputs=[num_batches, num_designs_per_batch, length], outputs=[gen_directory, gen_results])
+
+
 
 
     # New visualize section
     with gr.Row():
-        viz_btn = gr.Button("Visualize", visible=True)
         batch_dropdown = gr.Dropdown(
             choices=[], 
             label="Select Batch",
-            visible=False
+            visible=True
         )
         design_dropdown = gr.Dropdown(
             choices=[], 
             label="Select Design",
-            visible=False
+            visible=True
         )
-        viewer = Molecule3D(visible=False)
+        visualize_btn = gr.Button("Visualize", visible=True)
+        
+    display_state = gr.Textbox(label="Selected Batch and Design", visible=True)
+    display_state.value = "Please Select a Batch and Design number to visualize."
+    viewer = Molecule3D(visible=True)
 
-    def toggle_visualize(result):
+    def update_batch_choices(result):
         if result is None:
-            return gr.Dropdown(visible=False), gr.Dropdown(visible=False), Molecule3D(visible=False)
+            return gr.Dropdown(choices = [])
         batches = sorted(list({d["batch"] for d in result}))
-        return (
-            gr.update(choices=batches, visible=True),  # Batch dropdown
-            gr.update(choices=[], visible=True),       # Design empty initially
-            gr.update(visible=False)
-        )
+        return gr.update(choices=batches, visible=True)
+        
+    gen_btn.click(unconditional_generation, inputs=[num_batches, num_designs_per_batch, length], outputs=[gen_directory, gen_results]).then(
+        update_batch_choices,
+        inputs=gen_results,
+        outputs=batch_dropdown)
+
+
+
 
     def update_designs(batch, result):
         if batch is None:
             return gr.update(choices=[])
         designs = sorted(list({d["design"] for d in result if d["batch"] == batch}))
         return gr.update(choices=designs)
+    
+
+    
+    batch_dropdown.change(update_designs, inputs=[batch_dropdown, gen_results], outputs=[design_dropdown])
+    design_dropdown.change()
+
+    def visualize_selection(batch, design):
+        if batch is None or design is None:
+            return gr.update(value="**Please select both batch and design.**", visible=True)
+        return gr.update(value=f"**Selected Batch: {batch}, Design: {design}**", visible=True)
+
+        
+
+    visualize_btn.click(visualize_selection, inputs=[batch_dropdown, design_dropdown], outputs=display_state)
+
 
     def load_viewer(batch, design, result):
         if batch is None or design is None:
-            return gr.update(visible=False)
+            return gr.update()
         pdb_data = next(d["pdb"] for d in result if d["batch"] == int(batch) and d["design"] == int(design))
         return gr.update(value=pdb_data, visible=True, reps=[{"style": "cartoon"}])  # Customize style
 
-    # Events
-    viz_btn.click(toggle_visualize, inputs=gen_directory, outputs=[batch_dropdown, design_dropdown, viewer])
-    batch_dropdown.change(update_designs, inputs=[batch_dropdown, gen_directory], outputs=design_dropdown)
-    batch_dropdown.select(fn=update_designs, inputs=[batch_dropdown, gen_directory], outputs=design_dropdown)  # For selection
-    gr.Dropdown.select(update_designs, batch_dropdown, design_dropdown).then(  # Chain
-        lambda b, d, r: load_viewer(b, d, r),
-        inputs=[batch_dropdown, design_dropdown, gen_directory],
-        outputs=viewer
-    )
-
+    visualize_btn.click(load_viewer, inputs=[batch_dropdown, design_dropdown, gen_results], outputs=viewer)
 
 if __name__ == "__main__":
     demo.launch()

utils/pipelines.py

@@ -104,4 +104,6 @@ def mcif_gz_to_pdb_string_gemmi(file_path: str) -> str:
     """
     st = gemmi.read_structure(file_path)
     st.setup_entities()  # Recommended for consistent entity handling [web:18]
-    return st.make_pdb_string(gemmi.PdbWriteOptions(minimal=True))
+    pdb_path = file_path.replace(".cif.gz", ".pdb")
+    st.write_minimal_pdb(pdb_path)
+    return pdb_path