Update app.py

app.py

@@ -1,3 +1,5 @@
+import os
+
 import spaces
 import gradio as gr 
 
@@ -6,43 +8,36 @@ from allmetal3d.utils.main import predict, predict_cli, update_mode
 
 from gradio_molecule3d import Molecule3D
 
+os.system("pip install allmetal3d-0.4.0-py3-none-any.whl")
+
+
 @spaces.GPU
 def predict_zero_gpu(pdb, models, pthreshold, threshold, batch_size, mode, central_residue, radius):
     out, metal_pdb, metal_cube, water_pdb, water_cube, results_json, waters_json = predict(pdb, models, pthreshold, threshold, batch_size, mode, central_residue, radius)
 
 with gr.Blocks() as blocks: 
-        gr.Markdown("## AllMetal3D and Water3D")
-        pdb = Molecule3D(label="Input PDB", showviewer=False) #gr.File("2cba.pdb",label="Upload PDB file")
-    
-        gr.Markdown("Metals might bind anywhere in the protein, choose how to sample the residues in the protein. <br>Fast uses blocked sampling of residues to reduce required computational time, full uses all residues, site allows you to look around a specific site in the protein")
-        with gr.Row("Prediction mode"):
-            mode = gr.Dropdown(["fast", "all", "site"], value="fast", label="Mode")
-            central_residue = gr.Textbox(label="Central residue", info="add multiple residues with space e.g 101 203", visible=False)
-            radius = gr.Slider(value=8, minimum=4, maximum=50, label="Distance threshold", visible=False)
-        mode.change(update_mode, mode, [central_residue, radius])
-
-        models = gr.Radio(["AllMetal3D + Water3D", "Only AllMetal3D", "Only Water3D"], value="AllMetal3D + Water3D", label="Which models to run?")
-
-        with gr.Accordion("Settings"):
-            threshold = gr.Slider(value=7,minimum=0, maximum=10,  label="Threshold")
-            pthreshold = gr.Slider(value=0.25,minimum=0.1, maximum=1,  label="Probability Threshold")
-            batch_size = gr.Slider(value=50, minimum=0, maximum=100, label="Batch Size")
-
-        btn = gr.Button("Predict")
-
-        with gr.Row():
-            metal_pdb = gr.File(label="predicted metals (PDB)", visible=False)
-            metal_cube = gr.File(label="predicted metal density (CUBE)",visible=False)
-            water_pdb = gr.File(label="predicted waters (PDB)", visible=False)
-            water_cube = gr.File(label="predicted water density (CUBE)", visible=False)
-            
-        out = gr.HTML("")
-        results_json = gr.JSON(visible=False)
-        waters_json = gr.JSON(visible=False)
-
-
-        btn.click(predict_zero_gpu, inputs=[pdb, models, pthreshold, threshold, batch_size, mode, central_residue, radius], outputs=[out, metal_pdb, metal_cube, water_pdb, water_cube, results_json, waters_json])
-
-
-    # in order to get private link for the app for the viewer we need to disable thread lock and grab the link
-    blocks.launch(allowed_paths=["frontend"])
+    gr.Markdown("## AllMetal3D and Water3D")
+    pdb = Molecule3D(label="Input PDB", showviewer=False) #gr.File("2cba.pdb",label="Upload PDB file")
+    gr.Markdown("Metals might bind anywhere in the protein, choose how to sample the residues in the protein. <br>Fast uses blocked sampling of residues to reduce required computational time, full uses all residues, site allows you to look around a specific site in the protein")
+    with gr.Row("Prediction mode"):
+        mode = gr.Dropdown(["fast", "all", "site"], value="fast", label="Mode")
+        central_residue = gr.Textbox(label="Central residue", info="add multiple residues with space e.g 101 203", visible=False)
+        radius = gr.Slider(value=8, minimum=4, maximum=50, label="Distance threshold", visible=False)
+    mode.change(update_mode, mode, [central_residue, radius])
+    models = gr.Radio(["AllMetal3D + Water3D", "Only AllMetal3D", "Only Water3D"], value="AllMetal3D + Water3D", label="Which models to run?")
+    with gr.Accordion("Settings"):
+        threshold = gr.Slider(value=7,minimum=0, maximum=10,  label="Threshold")
+        pthreshold = gr.Slider(value=0.25,minimum=0.1, maximum=1,  label="Probability Threshold")
+        batch_size = gr.Slider(value=50, minimum=0, maximum=100, label="Batch Size")
+    btn = gr.Button("Predict")
+    with gr.Row():
+        metal_pdb = gr.File(label="predicted metals (PDB)", visible=False)
+        metal_cube = gr.File(label="predicted metal density (CUBE)",visible=False)
+        water_pdb = gr.File(label="predicted waters (PDB)", visible=False)
+        water_cube = gr.File(label="predicted water density (CUBE)", visible=False)
+    out = gr.HTML("")
+    results_json = gr.JSON(visible=False)
+    waters_json = gr.JSON(visible=False)
+    btn.click(predict_zero_gpu, inputs=[pdb, models, pthreshold, threshold, batch_size, mode, central_residue, radius], outputs=[out, metal_pdb, metal_cube, water_pdb, water_cube, results_json, waters_json])
+
+blocks.launch(allowed_paths=["frontend"])