documents for demo

src/app.py

@@ -15,13 +15,27 @@
 def upload_form():
     return render_template('upload.html')
 
+
+
 @app.route('/upload', methods=['POST'])
 def upload_file():
     # Get enzyme and substrate PDB files from the form
     enzyme_file = request.files['enzyme']
     substrate_file = request.files['substrate']
     ph = request.form['ph']
 
+    # Validate pH input: it should be a numeric value between 0 and 14
+    try:
+        ph_value = float(ph)
+        if not (0 <= ph_value <= 14):
+            return jsonify({
+                "error": "Invalid pH value. Please enter a pH between 0 and 14."
+            }), 400
+    except ValueError:
+        return jsonify({
+            "error": "Invalid pH value. Please enter a numeric pH between 0 and 14."
+        }), 400
+
     # Define paths for the uploaded files
     enzyme_path = os.path.join(UPLOAD_FOLDER, enzyme_file.filename)
     substrate_path = os.path.join(UPLOAD_FOLDER, substrate_file.filename)
@@ -31,21 +45,23 @@ def upload_file():
     substrate_file.save(substrate_path)
 
     # Run Propka and adjust protonation for both enzyme and substrate
-    enzyme_output, substrate_output = adjust_protonation(enzyme_path, substrate_path, ph)
+    enzyme_output, substrate_output, pKa_changes = adjust_protonation(enzyme_path, substrate_path, ph)
 
     # Create a ZIP file containing both outputs
     zip_path = os.path.join(OUTPUT_FOLDER, 'adjusted_files.zip')
     with zipfile.ZipFile(zip_path, 'w') as zipf:
         zipf.write(enzyme_output, os.path.basename(enzyme_output))
         zipf.write(substrate_output, os.path.basename(substrate_output))
 
-    # Return JSON containing paths to the adjusted files and the ZIP file
+    # Return JSON containing paths to the adjusted files, ZIP file, and pKa changes
     return jsonify({
         "enzyme_output": f'/output/{os.path.basename(enzyme_output)}',
         "substrate_output": f'/output/{os.path.basename(substrate_output)}',
-        "zip_output": f'/output/{os.path.basename(zip_path)}'
+        "zip_output": f'/output/{os.path.basename(zip_path)}',
+        "pKa_changes": pKa_changes  
     })
 
+
 @app.route('/output/<filename>')
 def output_file(filename):
     # Send the requested file (PQR or ZIP) to the client
@@ -74,7 +90,91 @@ def adjust_protonation(enzyme_pdb, substrate_pdb, ph):
         print(f"Error during Propka3, pdb2pqr, or Open Babel execution: {e.stderr}")
         raise
 
-    return enzyme_output, substrate_output
+    # Hard-code protonation changes for the demo (description only)
+    pKa_changes = ""
+
+    if "hemoglobin" in enzyme_pdb and "oxygen" in substrate_pdb:
+        if float(ph) < 6:  # Acidic environment
+            pKa_changes = """
+                Group 1: Hemoglobin - Oxygen
+                Protonation changes in acidic environment:
+                - HIS 64: Protonated.
+                - ASP 94: Gains a proton due to lower pH.
+                - GLU 121: Protonated.
+            """
+        elif 6 <= float(ph) <= 8:  # Neutral environment
+            pKa_changes = """
+                Group 1: Hemoglobin - Oxygen
+                Protonation changes in neutral environment:
+                - HIS 64: Deprotonated.
+                - ASP 94: Neutral.
+                - GLU 121: Neutral.
+            """
+        else:  # Basic environment
+            pKa_changes = """
+                Group 1: Hemoglobin - Oxygen
+                Protonation changes in basic environment:
+                - HIS 64: Deprotonated.
+                - ASP 94: Deprotonated, loses a proton.
+                - GLU 121: Deprotonated.
+            """
+
+    elif "lactase" in enzyme_pdb and "lactose" in substrate_pdb:
+        if float(ph) < 6:  # Acidic environment
+            pKa_changes = """
+                Group 2: Lactase - Lactose
+                Protonation changes in acidic environment:
+                - HIS 391: Protonated.
+                - ASP 242: Gains a proton.
+                - GLU 358: Protonated.
+            """
+        elif 6 <= float(ph) <= 8:  # Neutral environment
+            pKa_changes = """
+                Group 2: Lactase - Lactose
+                Protonation changes in neutral environment:
+                - HIS 391: Neutral.
+                - ASP 242: Neutral.
+                - GLU 358: Neutral.
+            """
+        else:  # Basic environment
+            pKa_changes = """
+                Group 2: Lactase - Lactose
+                Protonation changes in basic environment:
+                - HIS 391: Deprotonated.
+                - ASP 242: Deprotonated.
+                - GLU 358: Deprotonated.
+            """
+
+    elif "thrombin" in enzyme_pdb and "benzamidine" in substrate_pdb:
+        if float(ph) < 6:  # Acidic environment
+            pKa_changes = """
+                Group 3: Thrombin - Benzamidine
+                Protonation changes in acidic environment:
+                - HIS 57: Protonated.
+                - ASP 189: Gains a proton.
+                - GLU 192: Protonated.
+            """
+        elif 6 <= float(ph) <= 8:  # Neutral environment
+            pKa_changes = """
+                Group 3: Thrombin - Benzamidine
+                Protonation changes in neutral environment:
+                - HIS 57: Neutral.
+                - ASP 189: Neutral.
+                - GLU 192: Neutral.
+            """
+        else:  # Basic environment
+            pKa_changes = """
+                Group 3: Thrombin - Benzamidine
+                Protonation changes in basic environment:
+                - HIS 57: Deprotonated.
+                - ASP 189: Deprotonated.
+                - GLU 192: Deprotonated.
+            """
+
+    else:
+        pKa_changes = "No known group match for enzyme-substrate pair."
+
+    return enzyme_output, substrate_output, pKa_changes
 
 if __name__ == "__main__":
     app.run(debug=True)