Added an intrahelical angle potential between orientation beads

segmentmodel.py

@@ -1709,6 +1709,10 @@ class SegmentModel(ArbdModel):
                 if local_twist:
                     ## TODO optimize this paramter
                     k *= 0.5    # halve because orientation beads have similar springs
+                    angle = self.get_angle_potential(k,180)
+                    o1,o2,o3 = [b.orientation_bead for b in (b1,b2,b3)]
+                    parent.add_angle( o1, o2, o3, angle )
+
             else:
                 ## TODO: get correct number from ssDNA model
                 k = 1.5 * kT * (1.0 / (1-np.exp(-float(sep)/3))) * 0.00030461742; # kcal_mol/degree^2