Create app.py

app.py

@@ -0,0 +1,48 @@
+import spaces
+import gradio as gr 
+
+from allmetal3d.utils.helpersNew import *
+from allmetal3d.utils.main import predict, predict_cli, update_mode
+
+from gradio_molecule3d import Molecule3D
+
+@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"])