Merge pull request #133 from UC-Davis-molecular-computing/dev-export-…

…helix-groups

Dev export helix groups

scadnano/scadnano.py

@@ -4133,23 +4133,19 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict,
                 self._cadnano_v2_place_crossover(which_helix, next_helix,
                                                  domain, next_domain, strand_type)
 
-    def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int) -> Dict[int, int]:
+    def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) ->  Dict[int, int]:
         """Creates blank cadnanov2 helices in and initialized all their fields.
         """
         helices_ids_reverse = {}
         for i, helix in self.helices.items():
             helix_dct: Dict[str, Any] = OrderedDict()
             helix_dct['num'] = helix.idx
 
-            if self.grid == Grid.square:
-                if helix.grid_position is None:
-                    raise ValueError('cannot have grid_position == None if grid is square')
+            if design_grid == Grid.square:
                 helix_dct['row'] = helix.grid_position[1]
                 helix_dct['col'] = helix.grid_position[0]
 
-            elif self.grid == Grid.honeycomb:
-                if helix.grid_position is None:
-                    raise ValueError('cannot have grid_position == None if grid is honeycomb')
+            if design_grid == Grid.honeycomb:
                 helix_dct['row'], helix_dct['col'] = helix.grid_position[1], helix.grid_position[0]
 
             helix_dct['scaf'] = []
@@ -4178,9 +4174,22 @@ def to_cadnano_v2(self) -> Dict[str, Any]:
         dct: Dict[str, Any] = OrderedDict()
         dct['vstrands'] = []
 
-        if self.__class__ != Design:
-            raise ValueError(
-                'Please export DNAOrigamiDesign only as we need to know which strand is the scaffold.')
+        '''Check if helix group are used or if only one grid is used'''
+        design_grid = None
+        if self._has_default_groups():
+            design_grid = self.grid
+        else:
+            gridUsed = {}
+            grid_type = None
+            for group_name in self.groups:
+                gridUsed[self.groups[group_name].grid] = True
+                grid_type = self.groups[group_name].grid
+            if len(gridUsed) > 1:
+                raise ValueError('Designs using helix groups can be exported to cadnano v2 \
+                    only if all groups share the same grid type.')
+            else:
+                design_grid = grid_type
+
 
         '''Figuring out the type of grid.
         In cadnano v2, all helices have the same max offset 
@@ -4194,9 +4203,9 @@ def to_cadnano_v2(self) -> Dict[str, Any]:
                 raise ValueError('must have helix.max_offset set')
             num_bases = max(num_bases, helix.max_offset)
 
-        if self.grid == Grid.square:
+        if design_grid == Grid.square:
             num_bases = self._get_multiple_of_x_sup_closest_to_y(32, num_bases)
-        elif self.grid == Grid.honeycomb:
+        elif design_grid == Grid.honeycomb:
             num_bases = self._get_multiple_of_x_sup_closest_to_y(21, num_bases)
         else:
             raise NotImplementedError('We can export to cadnano v2 `square` and `honeycomb` grids only.')
@@ -4219,7 +4228,7 @@ def to_cadnano_v2(self) -> Dict[str, Any]:
 
         '''Filling the helices with blank.
         '''
-        helices_ids_reverse: Dict[int, int] = self._cadnano_v2_fill_blank(dct, num_bases)
+        helices_ids_reverse = self._cadnano_v2_fill_blank(dct, num_bases, design_grid)
         '''Putting the scaffold in place.
         '''
 

tests/scadnano_tests.py

@@ -607,7 +607,65 @@ class TestExportCadnanoV2(unittest.TestCase):
     output_path = os.path.join('tests_outputs', folder)
     ext = sc.default_scadnano_file_extension
 
-    def test_2_staple_2_helix_origami_extremely_simple(self) -> None:
+    def test_export_design_with_helix_group(self):
+        e = 'east'
+        s = 'south'
+        helices = [
+            sc.Helix(max_offset=24, group=s), 
+            sc.Helix(max_offset=25, group=s),  
+        ]
+        helices.extend([
+            sc.Helix(max_offset=22, group=e),  
+            sc.Helix(max_offset=23, group=e),
+        ])
+
+        group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0),
+                                    grid=sc.square)
+        group_east = sc.HelixGroup(position=sc.Position3D(x=10, y=0, z=0), grid=sc.square)
+
+        groups = {
+            e: group_east,
+            s: group_south
+        }
+
+        design = sc.Design(helices=helices, groups=groups, strands=[])
+        design.write_scadnano_file(directory=self.input_path,
+                                filename=f'test_export_design_with_helix_group.{self.ext}')
+        design.export_cadnano_v2(directory=self.output_path,
+                                filename='test_export_design_with_helix_group.json')
+
+    def test_export_design_with_helix_group_not_same_grid(self):
+        e = 'east'
+        s = 'south'
+        helices = [
+            sc.Helix(max_offset=24, group=s), 
+            sc.Helix(max_offset=25, group=s),  
+        ]
+        helices.extend([
+            sc.Helix(max_offset=22, group=e),  
+            sc.Helix(max_offset=23, group=e),
+        ])
+
+        group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0),
+                                    grid=sc.square)
+        group_east = sc.HelixGroup(position=sc.Position3D(x=10, y=0, z=0), grid=sc.honeycomb)
+
+        groups = {
+            e: group_east,
+            s: group_south
+        }
+
+        design = sc.Design(helices=helices, groups=groups, strands=[])
+        design.write_scadnano_file(directory=self.input_path,
+                                filename=f'test_export_design_with_helix_group_not_same_grid.{self.ext}')
+
+        with self.assertRaises(ValueError) as context:
+            design.export_cadnano_v2(directory=self.output_path,
+                                    filename='test_export_design_with_helix_group_not_same_grid.json')
+        self.assertTrue('helix groups' in context.exception.args[0])
+
+
+    def test_2_staple_2_helix_origami_extremely_simple(self):
         helices = [sc.Helix(max_offset=32), sc.Helix(max_offset=32)]
         scaf_part = sc.Domain(helix=0, forward=True, start=0, end=32)
         scaf = sc.Strand(domains=[scaf_part], is_scaffold=True)
@@ -676,7 +734,6 @@ def test_6_helix_origami_rectangle(self) -> None:
         design.export_cadnano_v2(directory=self.output_path,
                                  filename='test_6_helix_origami_rectangle.json')
 
-    @unittest.skip('DD: I cannot find where this file is. Is it supposed to be generated by some code?')
     def test_6_helix_bundle_honeycomb(self) -> None:
         design = sc.Design.from_scadnano_file(
             os.path.join(self.input_path, f'test_6_helix_bundle_honeycomb.{self.ext}'))