Added support for circular structures in segmentmodel_from_lists

mrdna/readers/segmentmodel_from_lists.py

@@ -67,6 +67,46 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
             is_fwd[bp] = 0
             rank +=1
         hid += 1
+
+    ## Create "helix" for each circular segment
+    processed = set()
+    unclaimed_bases = np.where( (basepairs >= 0)*(helixmap == -1) )[0]
+    for nt0 in unclaimed_bases:
+        if nt0 in processed: continue
+        nt = nt0
+        all_nts = [nt]
+
+        counter = 0
+        while stacks_above[nt] >= 0:
+            nt = stacks_above[nt]
+            bp = basepairs[nt]
+            assert( bp >= 0 )
+            assert(helixmap[nt] == -1)
+            assert(helixmap[bp] == -1)
+
+            all_nts.append(nt)
+            if nt == nt0:
+                break
+
+            if counter > 1e6:
+                raise Exception("DNA is apparently too long; probably there is something wrong with the structure")
+            counter += 1
+
+        ## Split circular helix into two groups (TODO: fix segmentmodel so that circular helices work and this is not needed)
+        for group in (all_nts[:len(all_nts)//2], all_nts[len(all_nts)//2:]):
+            rank = 0
+            for nt in group:
+                bp = basepairs[nt]
+                is_fwd[bp] = 0
+                rank +=1
+                helixmap[nt] = helixmap[bp] = hid
+                helixrank[nt] = helixrank[bp] = rank
+                processed.add(nt)
+                processed.add(bp)
+                rank +=1
+            hid += 1
+
+
     return helixmap, helixrank, is_fwd