Added option to exclude interhelical bonds from atomic ENM

mrdna/segmentmodel.py

@@ -3449,7 +3449,7 @@ class SegmentModel(ArbdModel):
                             j = nt2._get_atomic_index(name=n2)
                             fh.write("bond %d %d %f %.2f\n" % (i,j,spring_constant,2.8))
 
-    def write_atomic_ENM(self, output_name, lattice_type=None):
+    def write_atomic_ENM(self, output_name, lattice_type=None, interhelical_bonds=True):
         ## TODO: ensure atomic model was generated already
         if lattice_type is None:
             try:
@@ -3600,20 +3600,20 @@ class SegmentModel(ArbdModel):
                                 ...
 
         # print("PUSH BONDS:", len(push_bonds))
-
-        if not self.useTclForces:
-            with open("%s.exb" % output_name, 'a') as fh:
-                for i,j in push_bonds:
-                    fh.write("bond %d %d %f %.2f\n" % (i,j,1.0,31))
-        else:
-            flat_push_bonds = list(sum(push_bonds))
-            atomList = list(set( flat_push_bonds ))
-            with open("%s.forces.tcl" % output_name,'w') as fh:
-                fh.write("set atomList {%s}\n\n" %
-                         " ".join([str(x-1) for x in  atomList]) )
-                fh.write("set bonds {%s}\n" %
-                         " ".join([str(x-1) for x in flat_push_bonds]) )
-                fh.write("""
+        if interhelical_bonds:
+            if not self.useTclForces:
+                with open("%s.exb" % output_name, 'a') as fh:
+                    for i,j in push_bonds:
+                        fh.write("bond %d %d %f %.2f\n" % (i,j,1.0,31))
+            else:
+                flat_push_bonds = list(sum(push_bonds))
+                atomList = list(set( flat_push_bonds ))
+                with open("%s.forces.tcl" % output_name,'w') as fh:
+                    fh.write("set atomList {%s}\n\n" %
+                             " ".join([str(x-1) for x in  atomList]) )
+                    fh.write("set bonds {%s}\n" %
+                             " ".join([str(x-1) for x in flat_push_bonds]) )
+                    fh.write("""
 foreach atom $atomList {
     addatom $atom
 }