add

mrdna/readers/segmentmodel_from_oxdna_pinyi.py

@@ -107,13 +107,8 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
 
         for i in nt_prop.index:
             if nt_prop.loc[i]["threeprime"] in nt_prop.index:
-                if nt_prop.loc[nt_prop.loc[i]["threeprime"]]["vh"]!=nt_prop.loc[i]["vh"]:
-                    vh=nt_prop.loc[i]["vh"]
-                    zid=int(nt_prop.loc[i]["zid"])+int(nt_prop.loc[i]["fwd"])*2-1
-                    if (vh,str(zid),nt_prop.loc[i]["fwd"]) in bp_map.keys():
-                        nt_prop["stack"][i]=bp_map[ (vh,str(zid),nt_prop.loc[i]["fwd"])]
-                    else:   
-                        nt_prop["stack"][i]=-1
+                if nt_prop.loc[nt_prop.loc[i]["threeprime"]]["vh"]!=nt_prop.loc[i]["vh"]:   
+                    nt_prop["stack"][i]=-1
         
         bp=-np.ones(len(nt_prop.index),dtype=int)
         counter=0