Updated

.ipynb_checkpoints/app-checkpoint.py

@@ -7,7 +7,8 @@ from Bio.SeqUtils import seq1
 from typing import Optional, Tuple
 import numpy as np
 import os
-from gradio_molecule3d import Molecule3D
+# Remove the gradio_molecule3d import as it may be incompatible
+# from gradio_molecule3d import Molecule3D
 
 from model_loader import load_model
 
@@ -411,19 +412,7 @@ 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(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:
+with gr.Blocks() as demo:
     gr.Markdown("# Protein Binding Site Prediction")
     
     # Mode selection
@@ -437,23 +426,15 @@ with gr.Blocks(css="""
     # 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", elem_id="visualize-btn")
-
-    molecule_output2 = Molecule3D(label="Protein Structure", reps=[
-        {
-            "model": 0,
-            "style": "cartoon",
-            "color": "whiteCarbon",
-            "residue_range": "",
-            "around": 0,
-            #"byres": False,
-        }
-    ])
+    visualize_btn = gr.Button("Visualize Structure")
+
+    # Replace Molecule3D with HTML component
+    molecule_output2 = gr.HTML(label="Protein Structure")
 
     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", elem_id="predict-btn")
+        prediction_btn = gr.Button("Predict Binding Site")
 
     molecule_output = gr.HTML(label="Protein Structure")
     explanation_vis = gr.Markdown("""
@@ -472,29 +453,50 @@ with gr.Blocks(css="""
         if mode == "PDB ID":
             return process_pdb(pdb_id, chain_id)
         elif mode == "Upload File":
-            _, ext = os.path.splitext(pdb_file.name)
-            file_path = os.path.join('./', f"{_}{ext}")
+            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)
             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":
-            return fetch_pdb(pdb_id)
+            pdb_path = fetch_pdb(pdb_id)
+            if pdb_path:
+                mol_html = molecule(pdb_path)
+                return mol_html
+            return "Failed to fetch PDB"
         elif mode == "Upload File":
-            _, ext = os.path.splitext(pdb_file.name)
-            file_path = os.path.join('./', f"{_}{ext}")
-            #print(ext)
+            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)
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path= file_path
-            #print(pdb_path)
-            return pdb_path
+                pdb_path = file_path
+            mol_html = molecule(pdb_path)
+            return mol_html
         else:
             return "Error: Invalid mode selected"
 
@@ -533,4 +535,4 @@ with gr.Blocks(css="""
         outputs=[predictions_output, molecule_output, download_output]
     )
 
-demo.launch(share=True)
+demo.launch()

.ipynb_checkpoints/requirements-checkpoint.txt

@@ -9,6 +9,4 @@ scikit-learn>=0.24.0
 sentencepiece
 huggingface_hub>=0.15.0
 requests
-gradio>=4.0,<5.0
-gradio-molecule3d==0.0.1
 biopython>=1.81

app.py

@@ -7,7 +7,8 @@ from Bio.SeqUtils import seq1
 from typing import Optional, Tuple
 import numpy as np
 import os
-from gradio_molecule3d import Molecule3D
+# Remove the gradio_molecule3d import as it may be incompatible
+# from gradio_molecule3d import Molecule3D
 
 from model_loader import load_model
 
@@ -411,19 +412,7 @@ 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(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:
+with gr.Blocks() as demo:
     gr.Markdown("# Protein Binding Site Prediction")
     
     # Mode selection
@@ -437,23 +426,15 @@ with gr.Blocks(css="""
     # 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", elem_id="visualize-btn")
-
-    molecule_output2 = Molecule3D(label="Protein Structure", reps=[
-        {
-            "model": 0,
-            "style": "cartoon",
-            "color": "whiteCarbon",
-            "residue_range": "",
-            "around": 0,
-            #"byres": False,
-        }
-    ])
+    visualize_btn = gr.Button("Visualize Structure")
+
+    # Replace Molecule3D with HTML component
+    molecule_output2 = gr.HTML(label="Protein Structure")
 
     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", elem_id="predict-btn")
+        prediction_btn = gr.Button("Predict Binding Site")
 
     molecule_output = gr.HTML(label="Protein Structure")
     explanation_vis = gr.Markdown("""
@@ -472,29 +453,50 @@ with gr.Blocks(css="""
         if mode == "PDB ID":
             return process_pdb(pdb_id, chain_id)
         elif mode == "Upload File":
-            _, ext = os.path.splitext(pdb_file.name)
-            file_path = os.path.join('./', f"{_}{ext}")
+            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)
             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":
-            return fetch_pdb(pdb_id)
+            pdb_path = fetch_pdb(pdb_id)
+            if pdb_path:
+                mol_html = molecule(pdb_path)
+                return mol_html
+            return "Failed to fetch PDB"
         elif mode == "Upload File":
-            _, ext = os.path.splitext(pdb_file.name)
-            file_path = os.path.join('./', f"{_}{ext}")
-            #print(ext)
+            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)
             if ext == '.cif':
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
-                pdb_path= file_path
-            #print(pdb_path)
-            return pdb_path
+                pdb_path = file_path
+            mol_html = molecule(pdb_path)
+            return mol_html
         else:
             return "Error: Invalid mode selected"
 
@@ -533,4 +535,4 @@ with gr.Blocks(css="""
         outputs=[predictions_output, molecule_output, download_output]
     )
 
-demo.launch(share=True)
+demo.launch()

requirements.txt

@@ -9,6 +9,4 @@ scikit-learn>=0.24.0
 sentencepiece
 huggingface_hub>=0.15.0
 requests
-gradio>=4.0,<5.0
-gradio-molecule3d==0.0.1
 biopython>=1.81