Fixed error in list reader that would create intrahelical connections between...

Fixed error in list reader that would create intrahelical connections between double- and single-stranded segments; now using sscrossover connections

mrdna/RELEASE-VERSION

-1.0a.dev180
+1.0a.dev187

mrdna/readers/segmentmodel_from_lists.py

@@ -332,7 +332,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
     _has_bp =  (bps >= 0)
     _has_stack = (stack >= 0)
     _stack_has_basepair = (bps[stack] >= 0) * _has_stack
-    stack = np.where( (stack[bps[stack]] == bps) * _has_bp * _has_stack * _has_bp,
+    stack = np.where( (stack[bps[stack]] == bps) * _has_bp * _has_stack * _stack_has_basepair,
                       stack, -np.ones(len(stack),dtype=int) )
 
     five_prime = _three_prime_list_to_five_prime(three_prime)
@@ -421,7 +421,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
         is_terminal1 = (nt1,f1) in ((0,0),(seg1.num_nt-1,1))
         is_terminal2 = (nt2,f2) in ((0,1),(seg2.num_nt-1,0))
 
-        # devlogger.info(seg1,seg2, r1, r2, is_terminal1, is_terminal2)
+        # devlogger.info(f'{(hmap[r1],hmap[r2], r1, r2, is_terminal1, is_terminal2)}')
         if is_terminal1 or is_terminal2:
             """ Ensure that we don't have three-way dsDNA junctions """
             if is_terminal1 and (bps[r1] >= 0) and (five_prime[bps[r1]] >= 0) and (three_prime[r1] >= 0):
@@ -437,7 +437,8 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
             if is_terminal1 and is_terminal2 and (r1 not in explicitly_unstacked) and (r2 not in explicitly_unstacked):
                 end1 = seg1.end3 if f1 else seg1.start3
                 end2 = seg2.start5 if f2 else seg2.end5
-                seg1._connect_ends( end1, end2, type_='intrahelical')
+                _type = 'intrahelical' if type(seg1) == type(seg2) else 'sscrossover'
+                seg1._connect_ends( end1, end2, type_=_type)
             else:
                 seg1.add_crossover(nt1,seg2,nt2,[f1,f2],type_="terminal_crossover")
         else: