Add explicitly_unstacked argument to oxDNA reader to ensure we get terminal_crossover connections

mrdna/readers/segmentmodel_from_lists.py

@@ -253,6 +253,15 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
     basepaired / stacked / phosphodiester-bonded nucleotide. If there
     is no such nucleotide, the value should be -1.
 
+    By default, where there is a 3'-to-5' connection between
+    double-straned helices, they will be connected by an intrahelical
+    connection that makes the helical domain continue across the
+    connection, even if they do not stack in the stacking
+    array. Instead, a "terminal_crossover" representing a relatively
+    free (e.g. kinked) junction can be placed by including the index
+    of one of the participating bases in the optional
+    :explicitly_unstacked: tuple.
+
     Args:
         basepair:  List of each nucleotide's basepair's index
         stack:  List containing index of the nucleotide stacked on the 3' of each nucleotide

mrdna/readers/segmentmodel_from_oxdna.py

@@ -143,7 +143,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
         orientation = [np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)]
         seq=nt_prop["seq"]
         bp=nt_prop["bp"]
-        stack=nt_prop["stack"]
+        stack=np.array((list(nt_prop["stack"])))
         three_prime=nt_prop["threeprime"]
         nt_prop["orientation"]=orientation
         nt_prop["r"]=list(r)
@@ -205,8 +205,9 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
     ## _debug_write_bonds()
 
     logger.info(f'mrdna_model_from_oxdna: num_bp, num_ss_nt, num_stacked: {np.sum(bp>=0)//2} {np.sum(bp<0)} {np.sum(stack >= 0)}')
-
-    model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+    model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation,
+                                              explicitly_unstacked = np.argwhere(stack == -1),
+                                              **model_parameters )
      
     """
     model.DEBUG = True