Add Analysis Settings section with reproduction info

Author: AmirMohammad Cheraghali

src/utils/pdfGenerator.ts

@@ -528,7 +528,55 @@ const addInstructionPage = (
 
     y += 10;
 
-    // 4. Interaction Legend (Bottom)
+    // 4. Analysis Settings Box
+    doc.setFont("helvetica", "bold");
+    doc.setFontSize(11);
+    doc.setTextColor(0);
+    doc.text("Analysis Settings", margin, y);
+    y += 8;
+
+    doc.setDrawColor(200);
+    doc.setFillColor(250, 250, 250);
+    const settingsBoxHeight = 35;
+    doc.roundedRect(margin, y, 170, settingsBoxHeight, 2, 2, 'FD');
+
+    let settingsY = y + 8;
+    const settingsLeftPad = margin + 8;
+
+    doc.setFont("helvetica", "normal");
+    doc.setFontSize(9);
+    doc.setTextColor(50);
+
+    // Distance Thresholds
+    doc.setFont("helvetica", "bold");
+    doc.text("Distance Cutoffs:", settingsLeftPad, settingsY);
+    doc.setFont("helvetica", "normal");
+    doc.text("Close Contact < 5.0 A  |  Proximal 5.0-8.0 A", settingsLeftPad + 42, settingsY);
+    settingsY += 6;
+
+    // Analysis Type
+    doc.setFont("helvetica", "bold");
+    doc.text("Method:", settingsLeftPad, settingsY);
+    doc.setFont("helvetica", "normal");
+    doc.text("Euclidean distance between Ca atoms", settingsLeftPad + 42, settingsY);
+    settingsY += 6;
+
+    // Interaction Types Detected
+    doc.setFont("helvetica", "bold");
+    doc.text("Interaction Types:", settingsLeftPad, settingsY);
+    doc.setFont("helvetica", "normal");
+    doc.text("Salt Bridges, Disulfide Bonds, Hydrophobic, Pi-Stacking", settingsLeftPad + 42, settingsY);
+    settingsY += 6;
+
+    // Note about reproducibility
+    doc.setFont("helvetica", "italic");
+    doc.setFontSize(8);
+    doc.setTextColor(100);
+    doc.text("Settings ensure reproducible analysis. Scan QR for interactive view.", settingsLeftPad, settingsY);
+
+    y += settingsBoxHeight + 10;
+
+    // 5. Interaction Legend (Bottom)
     // Check space
     if (y > doc.internal.pageSize.getHeight() - 60) {
         doc.addPage();