Update example in README

README.md

@@ -30,13 +30,26 @@ try {
         'UACGUAAGUA',              // Sequence
         2639                       // Author number of the first residue
     );
-    // NtC to apply on structural conformation
-    $ntcs = [
-        new \WebMMB\NtC('A', $rna->authToSeq(2639), $rna->authToSeq(2642), 'AA00', 1.5),
-        new \WebMMB\NtC('A', $rna->authToSeq(2642), $rna->authToSeq(2643), 'OP03', 1.5),
-        new \WebMMB\NtC('A', $rna->authToSeq(2643), $rna->authToSeq(2644), 'AA08', 1.5),
-        new \WebMMB\NtC('A', $rna->authToSeq(2644), $rna->authToSeq(2648), 'AA00', 1.5)
+    // Specify double helix pairing
+    $dh = new \WebMMB\DoubleHelix(
+        'A',
+        $rna->authToSeq(2639),
+        $rna->authToSeq(2641),
+        'A',
+        $rna->authToSeq(2648),
+        $rna->authToSeq(2646)
+    );
+    // NtCs to apply on structural conformation
+    $conformations = [
+        new \WebMMB\NtCConformation('A', $rna->authToSeq(2639), $rna->authToSeq(2642), 'AA00', 1.5),
+        new \WebMMB\NtCConformation('A', $rna->authToSeq(2642), $rna->authToSeq(2643), 'OP03', 1.5),
+        new \WebMMB\NtCConformation('A', $rna->authToSeq(2643), $rna->authToSeq(2644), 'AA08', 1.5),
+        new \WebMMB\NtCConformation('A', $rna->authToSeq(2644), $rna->authToSeq(2648), 'AA00', 1.5)
     ];
+    $ntcs = new \WebMMB\NtCs(
+        $conformations,  // List of NtC conformations to apply
+        3000             // NtC force scale factor - 3000 is the recommended default value
+    );
     // Create StandardCommands object
     $commands = new \WebMMB\StandardCommands(
         1, // First stage
@@ -46,6 +59,7 @@ try {
     );
     // Set up additional parameters
     $commands->compounds = [ $rna ]; // StandardCommands expects an array of compounds
+    $commands->double_helices = [ $dh ];
     $commands->ntcs = $ntcs;
 
     // Start the job