add

mrdna/readers/segmentmodel_from_cadnano.py

@@ -174,6 +174,19 @@ def gen_prop_table(part):
     nt_prop.reset_index(inplace=True)
     nt_prop["seq"]=-1
     ind_tuple=list(zip(nt_prop["vh"],nt_prop["zid"],nt_prop["fwd"]))
+    not_stacked,=np.where(nt_prop["stack_tuple"]==-1)
+    for i in not_stacked:
+        zid=int(nt_prop.loc[i]["zid"])
+        fwd=nt_prop.loc[i]["fwd"]
+        if fwd == True:
+            zid+=1
+        else:
+            zid-=1
+        try:
+            ind_tuple.index((nt_prop.loc[i]["vh"],str(zid),fwd))
+            nt_prop["stack_tuple"][i]=(nt_prop.loc[i]["vh"],str(zid),fwd)
+        except:
+            continue
     stacks=[]
     for i in list(nt_prop["stack_tuple"]):
         if i ==-1:

mrdna/readers/segmentmodel_from_oxdna_pinyi.py

@@ -100,6 +100,10 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         nt_prop["threeprime"]=top_data[2]
         nt_prop["seq"]=top_data[1]
         nt_prop["stack"]=top_data[2]
+        vh_bool=1-(nt_prop["vh"]%2)*2
+        is_scaf_bool=nt_prop["is_scaf"]*2-1
+        nt_prop["fwd"]=np.array((is_scaf_bool.T*vh_bool+1)/2,dtype=bool)
+        
         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"]:
@@ -114,9 +118,10 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
                 pass
             counter+=1
         nt_prop["bp"]=bp
-        vh_bool=1-(nt_prop["vh"]%2)*2
-        is_scaf_bool=nt_prop["is_scaf"]*2-1
-        nt_prop["fwd"]=np.array((is_scaf_bool.T*vh_bool+1)/2,dtype=bool)
+        
+        non_stack_ind,=np.where(nt_prop["stack"]==-1)
+        for i in non_stack_ind:
+            zid=nt_prop
         return nt_prop
     try:
         nt_prop=get_virt2nuc(virt2nuc,top_data)