Updated .js and HTML files to dynamically pass sequence to Hugging Face and display scores

.ipynb_checkpoints/app-checkpoint.py

@@ -116,16 +116,54 @@ def predict_protein_sequence(test_one_letter_sequence):
     
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(test_one_letter_sequence, normalized_scores)])
 
+    
     return result_str
 
 
+#interface = gr.Interface(
+#    fn=predict_protein_sequence,
+#    inputs=gr.Textbox(lines=2, placeholder="Enter protein sequence here..."),
+#    outputs=gr.Textbox(), #gr.JSON(),  # Use gr.JSON() for list or array-like outputs
+#    title="Protein sequence - Binding site prediction",
+#    description="Enter a protein sequence to predict its possible binding sites.",
+#)
+
+# Launch the app
+#interface.launch()
+
+# Function to fetch and visualize the PDB structure using py3Dmol
+def fetch_and_display_pdb(pdb_id):
+    # Fetch the PDB structure from the RCSB
+    pdb_url = f'https://files.rcsb.org/download/{pdb_id}.pdb'
+    response = requests.get(pdb_url)
+    
+    if response.status_code == 200:
+        pdb_structure = response.text
+    else:
+        return "Failed to load PDB structure. Please check the PDB ID."
+    
+    # Initialize the viewer
+    viewer = py3Dmol.view(width=800, height=400)
+    viewer.addModel(pdb_structure, "pdb")
+    viewer.setStyle({}, {"cartoon": {"color": "spectrum"}})
+    viewer.zoomTo()
+    
+    return viewer._make_html()
+
+# Define the Gradio interface
 interface = gr.Interface(
     fn=predict_protein_sequence,
-    inputs=gr.Textbox(lines=2, placeholder="Enter protein sequence here..."),
-    outputs=gr.Textbox(), #gr.JSON(),  # Use gr.JSON() for list or array-like outputs
-    title="Protein sequence - Binding site prediction",
-    description="Enter a protein sequence to predict its possible binding sites.",
+    inputs=[
+        gr.Textbox(lines=2, placeholder="Enter protein sequence here...", label="Protein Sequence"),
+        gr.Textbox(lines=1, placeholder="Enter PDB ID here...", label="PDB ID for 3D Visualization")
+    ],
+    outputs=[
+        gr.Textbox(label="Binding Site Predictions"),
+        gr.HTML(label="3Dmol Viewer")  # HTML output to render the 3Dmol viewer
+    ],
+    title="Protein Binding Site Prediction and 3D Structure Viewer",
+    description="Input a protein sequence to predict binding sites and view the protein structure in 3D using its PDB ID.",
 )
 
-# Launch the app
+# Launch the Gradio app
 interface.launch()

app.py

@@ -116,16 +116,54 @@ def predict_protein_sequence(test_one_letter_sequence):
     
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(test_one_letter_sequence, normalized_scores)])
 
+    
     return result_str
 
 
+#interface = gr.Interface(
+#    fn=predict_protein_sequence,
+#    inputs=gr.Textbox(lines=2, placeholder="Enter protein sequence here..."),
+#    outputs=gr.Textbox(), #gr.JSON(),  # Use gr.JSON() for list or array-like outputs
+#    title="Protein sequence - Binding site prediction",
+#    description="Enter a protein sequence to predict its possible binding sites.",
+#)
+
+# Launch the app
+#interface.launch()
+
+# Function to fetch and visualize the PDB structure using py3Dmol
+def fetch_and_display_pdb(pdb_id):
+    # Fetch the PDB structure from the RCSB
+    pdb_url = f'https://files.rcsb.org/download/{pdb_id}.pdb'
+    response = requests.get(pdb_url)
+    
+    if response.status_code == 200:
+        pdb_structure = response.text
+    else:
+        return "Failed to load PDB structure. Please check the PDB ID."
+    
+    # Initialize the viewer
+    viewer = py3Dmol.view(width=800, height=400)
+    viewer.addModel(pdb_structure, "pdb")
+    viewer.setStyle({}, {"cartoon": {"color": "spectrum"}})
+    viewer.zoomTo()
+    
+    return viewer._make_html()
+
+# Define the Gradio interface
 interface = gr.Interface(
     fn=predict_protein_sequence,
-    inputs=gr.Textbox(lines=2, placeholder="Enter protein sequence here..."),
-    outputs=gr.Textbox(), #gr.JSON(),  # Use gr.JSON() for list or array-like outputs
-    title="Protein sequence - Binding site prediction",
-    description="Enter a protein sequence to predict its possible binding sites.",
+    inputs=[
+        gr.Textbox(lines=2, placeholder="Enter protein sequence here...", label="Protein Sequence"),
+        gr.Textbox(lines=1, placeholder="Enter PDB ID here...", label="PDB ID for 3D Visualization")
+    ],
+    outputs=[
+        gr.Textbox(label="Binding Site Predictions"),
+        gr.HTML(label="3Dmol Viewer")  # HTML output to render the 3Dmol viewer
+    ],
+    title="Protein Binding Site Prediction and 3D Structure Viewer",
+    description="Input a protein sequence to predict binding sites and view the protein structure in 3D using its PDB ID.",
 )
 
-# Launch the app
+# Launch the Gradio app
 interface.launch()