Debbuging cadnanov2 export of paranemic crossovers when both segments…

… are in the 3' direction

.gitignore

@@ -26,3 +26,4 @@ tests_outputs/
 .vscode/
 dist/
 .mypy_cache/
+test_paranemic.py

scadnano/scadnano.py

@@ -6609,10 +6609,15 @@ def _cadnano_v2_place_crossover(helix_from_dct: Dict[str, Any], helix_to_dct: Di
             helix_to_dct[strand_type][start_to][:2] = [helix_from, start_from]
         elif forward_from and forward_to:
             helix_from_dct[strand_type][end_from - 1][2:] = [helix_to, start_to]
-            helix_to_dct[strand_type][end_to - 1][:2] = [helix_from, start_from]
+            helix_to_dct[strand_type][end_to-1][:2] = [helix_from, start_from]
+            if helix_from_dct["row"]%2 != helix_to_dct["row"]%2:
+                raise ValueError("Paranemic crossovers are only allowed between helices that have the same parity of row number, here helix num "+str(helix_from_dct['num'])+ " and helix num " + str(helix_to_dct['num']) + " have different parity of row number: respectively "+str(helix_from_dct["row"])+" and "+str( helix_to_dct["row"]))
+
         elif not forward_from and not forward_to:
             helix_from_dct[strand_type][start_from][2:] = [helix_to, end_to - 1]
-            helix_to_dct[strand_type][start_to][:2] = [helix_from, end_from - 1]
+            helix_to_dct[strand_type][end_to-1][:2] = [helix_from, start_from]
+            if helix_from_dct["row"]%2 != helix_to_dct["row"]%2:
+                raise ValueError("Paranemic crossovers are only allowed between helices that have the same parity of row number, here helix num "+str(helix_from_dct['num'])+ " and helix num " + str(helix_to_dct['num']) + " have different parity of row number: respectively "+str(helix_from_dct["row"])+" and "+str( helix_to_dct["row"]))
 
     @staticmethod
     def _cadnano_v2_color_of_stap(color: Color, domain: Domain) -> List[int]:
@@ -6650,6 +6655,9 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict,
                 next_helix = dct['vstrands'][next_helix_id]
                 self._cadnano_v2_place_crossover(which_helix, next_helix,
                                                  domain, next_domain, strand_type)
+
+
+
 
         # if the strand is circular, we need to close the loop
         if strand.circular:
@@ -6784,13 +6792,13 @@ def to_cadnano_v2_serializable(self, name: str = '') -> Dict[str, Any]:
                 if isinstance(domain, Loopout):
                     raise ValueError(
                         'We cannot handle designs with Loopouts as it is not a cadnano v2 concept')
-                right_direction: bool
+                cadnano_expected_direction: bool
                 if hasattr(strand, is_scaffold_key) and strand.is_scaffold:
-                    right_direction = (domain.helix % 2 == int(not domain.forward))
+                    cadnano_expected_direction = (domain.helix % 2 == int(not domain.forward))
                 else:
-                    right_direction = not (domain.helix % 2 == int(not domain.forward))
+                    cadnano_expected_direction = not (domain.helix % 2 == int(not domain.forward))
 
-                if not right_direction:
+                if not cadnano_expected_direction:
                     raise ValueError('We can only convert designs where even helices have the scaffold'
                                      'going forward and odd helices have the scaffold going backward see '
                                      f'the spec v2.txt Note 4. {domain}')
@@ -6803,6 +6811,7 @@ def to_cadnano_v2_serializable(self, name: str = '') -> Dict[str, Any]:
 
         for strand in self.strands:
             self._cadnano_v2_place_strand(strand, dct, helices_ids_reverse)
+
 
         return dct
 

tests/scadnano_tests.py

@@ -1629,6 +1629,19 @@ def test_paranemic_crossover(self) -> None:
         output_design = sc.Design.from_cadnano_v2(json_dict=json.loads(output_json))
         self.assertEqual(4, len(output_design.helices))
 
+    def test_paranemic_crossover_other_direction(self) -> None:
+        design = sc.Design.from_scadnano_file(
+            os.path.join(self.input_path, f'test_paranemic_crossover_other_direction.{self.ext}'))
+        # To help with debugging, uncomment these lines to write out the
+        # scadnano and/or cadnano file
+        #
+        # design.write_cadnano_v2_file(directory=self.output_path,
+        #                          filename='test_paranemic_crossover.json')
+        output_json = design.to_cadnano_v2_json()
+
+        output_design = sc.Design.from_cadnano_v2(json_dict=json.loads(output_json))
+        self.assertEqual(4, len(output_design.helices))
+
     def test_parity_issue(self) -> None:
         """ We do not design where the parity of the helix
         does not correspond to the direction.

tests_inputs/cadnano_v2_export/test_paranemic_crossover_other_direction.sc

@@ -0,0 +1,27 @@
+{
+  "version": "0.19.4",
+  "grid": "square",
+  "helices": [
+    {"grid_position": [19, 14], "idx": 1, "max_offset": 64},
+    {"grid_position": [19, 15], "idx": 0, "max_offset": 64},
+    {"grid_position": [19, 16], "idx": 3, "max_offset": 64},
+    {"grid_position": [19, 17], "idx": 2, "max_offset": 64}
+  ],
+  "strands": [
+    {
+      "color": "#0066cc",
+      "is_scaffold": true,
+      "domains": [
+        {"helix": 3, "forward": false, "start": 8, "end": 24},
+        {"helix": 1, "forward": false, "start": 8, "end": 24}
+      ]
+    },
+    {
+      "color": "#007200",
+      "domains": [
+        {"helix": 2, "forward": false, "start": 24, "end": 50},
+        {"helix": 0, "forward": false, "start": 24, "end": 50}
+      ]
+    }
+  ]
+}