Merge pull request #307 from UC-Davis-molecular-computing/306-allow-p…

…er-helix-group-geometry

306 allow per helix group geometry

.github/workflows/run_unit_tests.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.7, 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ 3.7, 3.8, 3.9, "3.10", "3.11", "3.12" ]
 
     steps:
       - uses: actions/checkout@v2
@@ -21,8 +21,8 @@ jobs:
         with:
           activate-conda: true
       - name: Install openpyxl,tabulate with conda
-        run: conda install openpyxl=3.0.10 tabulate=0.8.10
+        run: conda install openpyxl=3.1 tabulate=0.9
       - name: Install docutils with conda
-        run: conda install docutils=0.16
+        run: conda install docutils=0.18
       - name: Test with unittest
         run: python -m unittest -v tests/scadnano_tests.py

environment.yml

@@ -4,7 +4,6 @@ channels:
   - defaults
 dependencies:
   - python=3.7
-  - xlwt=1.3.0=py37_0
   - pip
   - pip:
     - sphinx

examples/1_staple_1_helix_origami_roll.py

@@ -1,5 +1,3 @@
-import math
-
 import scadnano as sc
 
 def create_design() -> sc.Design:

examples/2_staple_2_helix_helixgroup_geometry.py

@@ -0,0 +1,24 @@
+import scadnano as sc
+
+
+def create_design() -> sc.Design:
+    group0 = sc.HelixGroup(grid=sc.square)
+    group1 = sc.HelixGroup(grid=sc.square, geometry=sc.Geometry(bases_per_turn=18),
+                           position=sc.Position3D(0, 3, 0))
+    groups = {"group 0": group0, "group 1": group1}
+    helices = [sc.Helix(idx=idx, max_offset=40, group=group) for idx, group in
+               [(0, "group 0"), (1, "group 1")]]
+    design = sc.Design(helices=helices, groups=groups, strands=[])
+    design.draw_strand(0, 0).move(40)
+    design.draw_strand(0, 40).move(-40)
+    design.draw_strand(1, 0).move(40)
+    design.draw_strand(1, 40).move(-40)
+
+    return design
+
+
+if __name__ == '__main__':
+    d = create_design()
+    d.write_scadnano_file(directory='output_designs')
+    d.from_scadnano_file('output_designs/2_staple_2_helix_helixgroup_geometry.sc')
+    print(f'design: {d.to_json()}')

examples/output_designs/2_staple_2_helix_helixgroup_geometry.sc

@@ -0,0 +1,46 @@
+{
+  "version": "0.19.4",
+  "groups": {
+    "group 0": {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "grid": "square"
+    },
+    "group 1": {
+      "position": {"x": 0, "y": 3, "z": 0},
+      "grid": "square",
+      "geometry": {
+        "bases_per_turn": 18
+      }
+    }
+  },
+  "helices": [
+    {"group": "group 0", "grid_position": [0, 0]},
+    {"group": "group 1", "grid_position": [0, 0]}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#57bb00",
+      "domains": [
+        {"helix": 0, "forward": false, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#888888",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#32b86c",
+      "domains": [
+        {"helix": 1, "forward": false, "start": 0, "end": 40}
+      ]
+    }
+  ]
+}

scadnano/scadnano.py

@@ -54,7 +54,7 @@
 # needed to use forward annotations: https://docs.python.org/3/whatsnew/3.7.html#whatsnew37-pep563
 from __future__ import annotations
 
-__version__ = "0.19.4"  # version line; WARNING: do not remove or change this line or comment
+__version__ = "0.19.5"  # version line; WARNING: do not remove or change this line or comment
 
 import collections
 import dataclasses
@@ -1315,6 +1315,14 @@ class HelixGroup(_JSONSerializable):
     grid: Grid = Grid.none
     """:any:`Grid` of this :any:`HelixGroup` used to interpret the field :data:`Helix.grid_position`."""
 
+    geometry: Optional[Geometry] = None
+    """
+    Optional custom :any:`Geometry` to specify for this :any:`HelixGroup`. If specified then
+    it is assumed to override the field :data:`Design.geometry`. This will affect, for instance,
+    where nucleotides and phosphate groups are placed when exporting to oxDNA or oxView via
+    :meth:`Design.to_oxview_format` or :meth:`Design.to_oxdna_format`.
+    """
+
     def has_default_position_and_orientation(self):
         # we don't bother checking grid or helices_view_order because those are written to top-level
         # fields of Design if the group is otherwise default
@@ -1341,6 +1349,9 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
         if self.helices_view_order != default_helices_view_order:
             dct[helices_view_order_key] = NoIndent(self.helices_view_order)
 
+        if self.geometry is not None:
+            dct[geometry_key] = self.geometry.to_json_serializable(suppress_indent)
+
         return dct
 
     def _assign_default_helices_view_order(self, helices_in_group: Dict[int, 'Helix']) -> None:
@@ -1372,12 +1383,19 @@ def from_json(json_map: dict, **kwargs: Any) -> HelixGroup:
         roll = json_map.get(roll_key, default_roll)
         yaw = json_map.get(yaw_key, default_yaw)
 
-        return HelixGroup(position=position,
-                          pitch=pitch,
-                          yaw=yaw,
-                          roll=roll,
-                          helices_view_order=helices_view_order,
-                          grid=grid)
+        geometry = None
+        if geometry_key in json_map:
+            geometry = Geometry.from_json(json_map[geometry_key])
+
+        return HelixGroup(
+            position=position,
+            pitch=pitch,
+            yaw=yaw,
+            roll=roll,
+            helices_view_order=helices_view_order,
+            grid=grid,
+            geometry=geometry,
+        )
 
     def helices_view_order_inverse(self, idx: int) -> int:
         """

tests/scadnano_tests.py

@@ -1282,7 +1282,7 @@ def test_write_idt_plate_excel_file(self) -> None:
         # add 10 strands in excess of 3 plates
         for plate_type in [sc.PlateType.wells96, sc.PlateType.wells384]:
             num_strands = 3 * plate_type.num_wells_per_plate() + 10
-            filename = f'test_excel_export_{plate_type.num_wells_per_plate()}.xlsx'
+            filename = f'tests/test_excel_export_{plate_type.num_wells_per_plate()}.xlsx'
             max_offset = num_strands * strand_len
             helices = [sc.Helix(max_offset=max_offset) for _ in range(1)]
             design = sc.Design(helices=helices, strands=[], grid=sc.square)
@@ -1307,7 +1307,10 @@ def test_write_idt_plate_excel_file(self) -> None:
 
                 self.assertEqual(expected_wells + 1, sheet.max_row)
 
-            os.remove(filename)
+            try:
+                os.remove(filename)
+            except PermissionError as e:
+                print(f'could not remove file "{filename}" due to permission error')
 
     def test_export_dna_sequences_extension_5p(self) -> None:
         design = sc.Design(helices=[sc.Helix(max_offset=100)])