Updated

.ipynb_checkpoints/app-checkpoint.py

@@ -7,8 +7,7 @@ from Bio.SeqUtils import seq1
 from typing import Optional, Tuple
 import numpy as np
 import os
-# Remove the gradio_molecule3d import as it may be incompatible
-# from gradio_molecule3d import Molecule3D
+from gradio_molecule3d import Molecule3D
 
 from model_loader import load_model
 
@@ -412,7 +411,19 @@ def molecule(input_pdb, residue_scores=None, segment='A'):
     return f'<iframe width="100%" height="700" srcdoc="{html_content.replace(chr(34), "&quot;").replace(chr(39), "&#39;")}"></iframe>'
 
 # Gradio UI
-with gr.Blocks() as demo:
+with gr.Blocks(css="""
+    /* Customize Gradio button colors */
+    #visualize-btn, #predict-btn {
+        background-color: #FF7300; /* Deep orange */
+        color: white;
+        border-radius: 5px;
+        padding: 10px;
+        font-weight: bold;
+    }
+    #visualize-btn:hover, #predict-btn:hover {
+        background-color: #CC5C00; /* Darkened orange on hover */
+    }
+""") as demo:
     gr.Markdown("# Protein Binding Site Prediction")
     
     # Mode selection
@@ -426,15 +437,23 @@ with gr.Blocks() as demo:
     # Input components based on mode
     pdb_input = gr.Textbox(value="2F6V", label="PDB ID", placeholder="Enter PDB ID here...")
     pdb_file = gr.File(label="Upload PDB/CIF File", visible=False)
-    visualize_btn = gr.Button("Visualize Structure")
-
-    # Replace Molecule3D with HTML component
-    molecule_output2 = gr.HTML(label="Protein Structure")
+    visualize_btn = gr.Button("Visualize Structure", elem_id="visualize-btn")
+
+    molecule_output2 = Molecule3D(label="Protein Structure", reps=[
+        {
+            "model": 0,
+            "style": "cartoon",
+            "color": "whiteCarbon",
+            "residue_range": "",
+            "around": 0,
+            "byres": False,
+        }
+    ])
 
     with gr.Row():
         segment_input = gr.Textbox(value="A", label="Chain ID (protein)", placeholder="Enter Chain ID here...",
         info="Choose in which chain to predict binding sites.")
-        prediction_btn = gr.Button("Predict Binding Site")
+        prediction_btn = gr.Button("Predict Binding Site", elem_id="predict-btn")
 
     molecule_output = gr.HTML(label="Protein Structure")
     explanation_vis = gr.Markdown("""
@@ -453,50 +472,29 @@ with gr.Blocks() as demo:
         if mode == "PDB ID":
             return process_pdb(pdb_id, chain_id)
         elif mode == "Upload File":
-            try:
-                # Handle new Gradio file format
-                file_path = pdb_file.name
-            except AttributeError:
-                # For older Gradio versions that provided a tuple
-                if isinstance(pdb_file, tuple):
-                    file_path = pdb_file[0]
-                else:
-                    file_path = pdb_file
-                    
-            _, ext = os.path.splitext(file_path)
+            _, ext = os.path.splitext(pdb_file.name)
+            file_path = os.path.join('./', f"{_}{ext}")
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path = file_path
+                pdb_path= file_path
             return process_pdb(pdb_path, chain_id)
         else:
             return "Error: Invalid mode selected", None, None
 
     def fetch_interface(mode, pdb_id, pdb_file):
         if mode == "PDB ID":
-            pdb_path = fetch_pdb(pdb_id)
-            if pdb_path:
-                mol_html = molecule(pdb_path)
-                return mol_html
-            return "Failed to fetch PDB"
+            return fetch_pdb(pdb_id)
         elif mode == "Upload File":
-            try:
-                # Handle new Gradio file format
-                file_path = pdb_file.name
-            except AttributeError:
-                # For older Gradio versions that provided a tuple
-                if isinstance(pdb_file, tuple):
-                    file_path = pdb_file[0]
-                else:
-                    file_path = pdb_file
-                    
-            _, ext = os.path.splitext(file_path)
+            _, ext = os.path.splitext(pdb_file.name)
+            file_path = os.path.join('./', f"{_}{ext}")
+            #print(ext)
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path = file_path
-            mol_html = molecule(pdb_path)
-            return mol_html
+                pdb_path= file_path
+            #print(pdb_path)
+            return pdb_path
         else:
             return "Error: Invalid mode selected"
 
@@ -535,4 +533,5 @@ with gr.Blocks() as demo:
         outputs=[predictions_output, molecule_output, download_output]
     )
 
-demo.launch()
+#demo.launch(share=True)
+demo.launch()

.ipynb_checkpoints/requirements-checkpoint.txt

@@ -9,4 +9,5 @@ scikit-learn>=0.24.0
 sentencepiece
 huggingface_hub>=0.15.0
 requests
+gradio_molecule3d
 biopython>=1.81

app.py

@@ -7,8 +7,7 @@ from Bio.SeqUtils import seq1
 from typing import Optional, Tuple
 import numpy as np
 import os
-# Remove the gradio_molecule3d import as it may be incompatible
-# from gradio_molecule3d import Molecule3D
+from gradio_molecule3d import Molecule3D
 
 from model_loader import load_model
 
@@ -412,7 +411,19 @@ def molecule(input_pdb, residue_scores=None, segment='A'):
     return f'<iframe width="100%" height="700" srcdoc="{html_content.replace(chr(34), "&quot;").replace(chr(39), "&#39;")}"></iframe>'
 
 # Gradio UI
-with gr.Blocks() as demo:
+with gr.Blocks(css="""
+    /* Customize Gradio button colors */
+    #visualize-btn, #predict-btn {
+        background-color: #FF7300; /* Deep orange */
+        color: white;
+        border-radius: 5px;
+        padding: 10px;
+        font-weight: bold;
+    }
+    #visualize-btn:hover, #predict-btn:hover {
+        background-color: #CC5C00; /* Darkened orange on hover */
+    }
+""") as demo:
     gr.Markdown("# Protein Binding Site Prediction")
     
     # Mode selection
@@ -426,15 +437,23 @@ with gr.Blocks() as demo:
     # Input components based on mode
     pdb_input = gr.Textbox(value="2F6V", label="PDB ID", placeholder="Enter PDB ID here...")
     pdb_file = gr.File(label="Upload PDB/CIF File", visible=False)
-    visualize_btn = gr.Button("Visualize Structure")
-
-    # Replace Molecule3D with HTML component
-    molecule_output2 = gr.HTML(label="Protein Structure")
+    visualize_btn = gr.Button("Visualize Structure", elem_id="visualize-btn")
+
+    molecule_output2 = Molecule3D(label="Protein Structure", reps=[
+        {
+            "model": 0,
+            "style": "cartoon",
+            "color": "whiteCarbon",
+            "residue_range": "",
+            "around": 0,
+            "byres": False,
+        }
+    ])
 
     with gr.Row():
         segment_input = gr.Textbox(value="A", label="Chain ID (protein)", placeholder="Enter Chain ID here...",
         info="Choose in which chain to predict binding sites.")
-        prediction_btn = gr.Button("Predict Binding Site")
+        prediction_btn = gr.Button("Predict Binding Site", elem_id="predict-btn")
 
     molecule_output = gr.HTML(label="Protein Structure")
     explanation_vis = gr.Markdown("""
@@ -453,50 +472,29 @@ with gr.Blocks() as demo:
         if mode == "PDB ID":
             return process_pdb(pdb_id, chain_id)
         elif mode == "Upload File":
-            try:
-                # Handle new Gradio file format
-                file_path = pdb_file.name
-            except AttributeError:
-                # For older Gradio versions that provided a tuple
-                if isinstance(pdb_file, tuple):
-                    file_path = pdb_file[0]
-                else:
-                    file_path = pdb_file
-                    
-            _, ext = os.path.splitext(file_path)
+            _, ext = os.path.splitext(pdb_file.name)
+            file_path = os.path.join('./', f"{_}{ext}")
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path = file_path
+                pdb_path= file_path
             return process_pdb(pdb_path, chain_id)
         else:
             return "Error: Invalid mode selected", None, None
 
     def fetch_interface(mode, pdb_id, pdb_file):
         if mode == "PDB ID":
-            pdb_path = fetch_pdb(pdb_id)
-            if pdb_path:
-                mol_html = molecule(pdb_path)
-                return mol_html
-            return "Failed to fetch PDB"
+            return fetch_pdb(pdb_id)
         elif mode == "Upload File":
-            try:
-                # Handle new Gradio file format
-                file_path = pdb_file.name
-            except AttributeError:
-                # For older Gradio versions that provided a tuple
-                if isinstance(pdb_file, tuple):
-                    file_path = pdb_file[0]
-                else:
-                    file_path = pdb_file
-                    
-            _, ext = os.path.splitext(file_path)
+            _, ext = os.path.splitext(pdb_file.name)
+            file_path = os.path.join('./', f"{_}{ext}")
+            #print(ext)
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path = file_path
-            mol_html = molecule(pdb_path)
-            return mol_html
+                pdb_path= file_path
+            #print(pdb_path)
+            return pdb_path
         else:
             return "Error: Invalid mode selected"
 
@@ -535,4 +533,5 @@ with gr.Blocks() as demo:
         outputs=[predictions_output, molecule_output, download_output]
     )
 
-demo.launch()
+#demo.launch(share=True)
+demo.launch()

requirements.txt

@@ -9,4 +9,5 @@ scikit-learn>=0.24.0
 sentencepiece
 huggingface_hub>=0.15.0
 requests
+gradio_molecule3d
 biopython>=1.81