swap H41 argument

amp_stats.py

@@ -46,6 +46,7 @@ argparser.add_argument("-rpf","--respair-file",type=str,metavar="RPF",help="Spec
 argparser.add_argument("-g","--gui",help="Open an ASE GUI.",action='store_true')
 argparser.add_argument("-s","--show",help="Show plots.",action='store_true')
 argparser.add_argument("-pa","--plot-alternate",help="Plot alternate h-bond definitions.",action='store_true')
+argparser.add_argument("-sh41","--swap-H41",help="Swap H41 and H42",action='store_true')
 
 args = argparser.parse_args()
 
@@ -191,7 +192,14 @@ if args.dna_hydrogen_bonds is not None:
             elif print_non_match:
               print(stripped_line)
           elif "DC" in stripped_line or "CTSN" in stripped_line:
-            if " H41 " in stripped_line:
+            if args.swap_H41:
+              search = " H42 "
+            else:
+              search = " H41 "
+
+            if search in stripped_line:
+              if args.swap_H41:
+                mout.warningOut("Using H42 instead of H41!")
             # if " H42 " in stripped_line:
               if len(split_line) == 11:
                 dc_reslist.append(split_line[3]+split_line[4])