Fixed ENM so it produces bonds across intrahelical connections

mrdna/model/CanonicalNucleotideAtoms.py

@@ -39,10 +39,7 @@ class Nucleotide(Group):
         return self.get_intrahelical_nucleotide(-1)
 
     def get_intrahelical_nucleotide(self,offset=1):
-        """ Returns nucleotide in same strand-side of helix with some offset along 5'-to-3'
-
-        TODO: Does not yet cross intrahelical connections
-        """
+        """ Returns nucleotide in same strand-side of helix with some offset along 5'-to-3' """
 
         strand_piece = self.parent
         is_fwd = strand_piece.is_fwd
@@ -53,9 +50,17 @@ class Nucleotide(Group):
         else:
             nt_idx = hi-strand_piece.children.index(self) - offset
 
+
         seg = strand_piece.segment
         if nt_idx < 0 or nt_idx >= seg.num_nt:
-            return None
+            """ Cross intrahelical connections if possible """
+            ret = seg._ntpos_to_seg_and_ntpos(nt_idx, is_fwd)
+            if ret is None:
+                ret = seg._ntpos_to_seg_and_ntpos(nt_idx, is_fwd)
+                return None
+            else:
+                seg, nt_idx, is_fwd = ret
+                return seg._get_atomic_nucleotide(nt_idx, is_fwd)
         else:
             return seg._get_atomic_nucleotide(nt_idx, is_fwd)
 

mrdna/segmentmodel.py

@@ -718,6 +718,36 @@ class Segment(ConnectableElement, Group):
 
         return orientation
 
+    def _ntpos_to_seg_and_ntpos(self, nt_pos, is_fwd=True, visited_segs=tuple()):
+        """ Cross intrahelical to obtain a tuple of the segment nucleotide position """
+        """ TODO: This function could perhaps replace parts of SegmentParticle.get_contour_position """
+
+        if nt_pos >= 0 and nt_pos < self.num_nt:
+            return (self,nt_pos,is_fwd)
+        else:
+            c,A,B = self.get_contour_sorted_connections_and_locations(type_='intrahelical')[0 if nt_pos < 0 else -1]
+            ## Special logic for circular segments
+            assert(A.container == self)
+            if A.container == B.container:
+                if (nt_pos < 0 and A.address > B.address) or (nt_pos >= self.num_nt and A.address < B.address):
+                    A,B = (B,A)
+
+            other_seg = B.container
+            if A.address == (0 if nt_pos < 0 else 1) and other_seg not in visited_segs:
+                ## Cross the crossover
+                other_pos = (nt_pos-self.num_nt) if nt_pos >= self.num_nt else -nt_pos-1
+                if B.address > 0.5:
+                    other_pos = (other_seg.num_nt-1) - other_pos
+                other_fwd = not is_fwd if A.address == B.address else is_fwd
+                return other_seg._ntpos_to_seg_and_ntpos(other_pos, other_fwd,
+                                                         list(visited_segs)+[self])
+
+            else:
+                ## Could not find a path to nt_pos
+                return None
+        assert(False)
+
+
     def get_contour_sorted_connections_and_locations(self,type_):
         sort_fn = lambda c: c[1].address
         cl = self.get_connections_and_locations(type_)