Debugging cadnanov2 export of paranemic crossovers when both segments…

.gitignore

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

doc/index.rst

@@ -31,10 +31,11 @@ Scadnano provides function to convert design to and from cadnano v2:
 **Important**
 
 All ``cadnanov2`` designs can be imported to scadnano. However **not all scadnano designs can be imported 
-to cadnanov2**, to be importable to ``cadnanov2`` a scadnano design need to comply with the following points:
+to cadnanov2**, to be exportable to ``cadnanov2`` a scadnano design need to comply with the following points:
 
 * The design cannot feature any :py:class:`Loopout` as it is not a concept that exists in ``cadnanov2``.
 * Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and helices with **odd** number **backward**.
+* If you use paranemic crossovers (i.e. crossovers where the domains before and after the crossover are in the same direction), the helices' row number (i.e. not the helices' indexes but their y coordinate) of the domains must have the same parity e.g. rows 0 and 2, or 1 and 3, but not 0 and 1.
 
 Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2`` needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid.
 The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design.

scadnano/scadnano.py

@@ -6610,9 +6610,20 @@ def _cadnano_v2_place_crossover(helix_from_dct: Dict[str, Any], helix_to_dct: Di
         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]
+            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 "
+                                 f"row number, here helix num {helix_from_dct['num']} and helix num "
+                                 f"{helix_to_dct['num']} have different parity of row number: respectively "
+                                 f"{helix_from_dct['row']}  and {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 "
+                                 f"row number, here helix num {helix_from_dct['num']} and helix num "
+                                 f"{helix_to_dct['num']} have different parity of row number: respectively "
+                                 f"{helix_from_dct['row']} and {helix_to_dct['row']}")
 
     @staticmethod
     def _cadnano_v2_color_of_stap(color: Color, domain: Domain) -> List[int]:
@@ -6784,13 +6795,13 @@ 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}')

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}
+      ]
+    }
+  ]
+}