renumbering portions of 3D structures with the index_chain

Former-commit-id: 10107a08

@@ -261,7 +261,8 @@ class Chain:
 
             # renumber this structure (portion of the original) with the index_chain and save it in a cif file
             t=pdb.Structure.Structure(new_s.get_id())
-            model=new_s[0]
+            #model=new_s[0]
+            for model in new_s:
                 new_model_t=pdb.Model.Model(model.get_id())
                 for chain in model:
                     nums=df[["index_chain", "old_nt_resnum", "nt_name"]]
@@ -283,7 +284,7 @@ class Chain:
                         resseq=int(resseq)
                         index_chain=nums.at[i, "index_chain"]
                         nt=nums.at[i, "nt_name"]
-                    if nt == 'A' or nt == 'G' or nt == 'C' or nt == 'U':
+                        if nt == 'A' or nt == 'G' or nt == 'C' or nt == 'U' or nt in ['DG', 'DU', 'DC', 'DA', 'DI', 'DT' ] or nt == 'N' or nt == 'I' :
                             res=chain[(' ', resseq, icode_res)]
                         else : #modified nucleotides (e.g. chain 5l4o_1_A)
                             het='H_' + nt

@@ -1710,480 +1710,25 @@
 6pmi_1_3
 6pmj_1_3
 5hjz_1_C
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