Added convenience function to Segments and SegmentModel to select blunt DNA ends

mrdna/segmentmodel.py

@@ -909,6 +909,17 @@ class Segment(ConnectableElement, Group):
         ## TODO? ensure that data is consistent before _build_model calls
         return sorted(self.get_locations("5prime"),key=lambda x: x.address)
 
+    def get_blunt_DNA_ends(self):
+        if isinstance(self, SingleStrandedSegment): return []
+        ret = []
+        cl = self.get_connections_and_locations("intrahelical")
+        if not any([c[1].address == 0 for c in cl]):
+            ret.append((self.start5,self.start3,-1))
+        if not any([c[1].address == 1 for c in cl]):
+            ret.append((self.end5,self.end3,1))
+        # return [c for c in cl if c[1].address == 0 or c[1].address == 1]
+        return ret
+
     def iterate_connections_and_locations(self, reverse=False):
         ## connections to other segments
         cl = self.get_contour_sorted_connections_and_locations()
@@ -2270,6 +2281,9 @@ class SegmentModel(ArbdModel):
             else:
                 seg2.connect_start3(seg1.end5)
 
+    def get_blunt_DNA_ends(self):
+        return sum([s.get_blunt_DNA_ends for s in self.segments],[])
+
     def convert_crossovers_at_ends_beyond_cutoff_to_intrahelical(self,cutoff):
         if cutoff < 0:
             raise ValueError("Cutoff should be positive!")