added example of oxDNA export of extension and loopouts

UC-Davis-molecular-computing · Nov 30, 2022 · 8e78237 · 8e78237
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diff --git a/examples/extension_and_loopout_oxdna_export.py b/examples/extension_and_loopout_oxdna_export.py
@@ -0,0 +1,29 @@
+import scadnano as sc
+
+
+def main() -> None:
+    d = create_design()
+    d.write_scadnano_file(directory='output_designs')
+    d.write_oxdna_files(directory='oxdna')
+
+
+def create_design() -> sc.Design:
+    width = 21
+    helices = [sc.Helix(max_offset=32) for _ in range(3)]
+    helices[0].roll = 210
+    helices[1].roll = 20
+    helices[2].roll = 210
+    design = sc.Design(helices=helices, grid=sc.square)
+
+    design.draw_strand(0, 0).extension_5p(5) \
+        .move(width) \
+        .cross(1).move(-width) \
+        .loopout(2, 32) \
+        .move(width) \
+        .extension_3p(7)
+
+    return design
+
+
+if __name__ == '__main__':
+    main()
diff --git a/examples/output_designs/extension_and_loopout_oxdna_export.sc b/examples/output_designs/extension_and_loopout_oxdna_export.sc
@@ -0,0 +1,22 @@
+{
+  "version": "0.17.6",
+  "grid": "square",
+  "helices": [
+    {"max_offset": 32, "grid_position": [0, 0], "roll": 210},
+    {"max_offset": 32, "grid_position": [0, 1], "roll": 20},
+    {"max_offset": 32, "grid_position": [0, 2], "roll": 210}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"extension_num_bases": 5},
+        {"helix": 0, "forward": true, "start": 0, "end": 21},
+        {"helix": 1, "forward": false, "start": 0, "end": 21},
+        {"loopout": 32},
+        {"helix": 2, "forward": true, "start": 0, "end": 21},
+        {"extension_num_bases": 7}
+      ]
+    }
+  ]
+}
diff --git a/examples/oxdna/extension_and_loopout_oxdna_export.dat b/examples/oxdna/extension_and_loopout_oxdna_export.dat
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diff --git a/examples/oxdna/extension_and_loopout_oxdna_export.top b/examples/oxdna/extension_and_loopout_oxdna_export.top
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+1 T 98 96
+1 T 99 97
+1 T 100 98
+1 T 101 99
+1 T 102 100
+1 T 103 101
+1 T 104 102
+1 T 105 103
+1 T 106 104
+1 T -1 105
diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py
@@ -2181,7 +2181,7 @@ class Extension(_JSONSerializable, Generic[DomainLabel]):
         design = sc.Design(helices=[sc.Helix(max_offset=10)])
         design.draw_strand(0,0).extension_5p(3).move(10).extension_3p(2)
 
-    which makes this strand with an :any:`Extension` on side of the length-10 :any:`Domain`:
+    which makes this strand with an :any:`Extension` on the side of the length-10 :any:`Domain`:
 
     .. code-block:: none