Merge pull request #241 from UC-Davis-molecular-computing/240-support…

…-extensions-in-oxdna-export 240 support extensions in oxdna export
UC-Davis-molecular-computing · Sep 8, 2022 · a46e4ad · a46e4ad
2 parents 4ae1d93 + b477328
commit a46e4ad
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diff --git a/examples/extensions.py b/examples/extensions.py
@@ -4,20 +4,33 @@
 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 = 8
     helices = [sc.Helix(max_offset=32) for _ in range(3)]
     design = sc.Design(helices=helices, grid=sc.square)
+    helices[2].roll = 30
 
     design.draw_strand(0, 0).extension_5p(5, display_length=2.5, display_angle=45) \
-        .move(width).cross(1).move(-width).loopout(2, 3).move(width) \
-        .extension_3p(7).with_domain_name("ext_3p")
+        .with_domain_name("ext_5p 1") \
+        .move(width).with_domain_name('domain 1') \
+        .cross(1).move(-width) \
+        .loopout(2, 3).with_domain_name('loopout 1') \
+        .move(width) \
+        .extension_3p(7).with_domain_name("ext_3p 1") \
+        .with_name('strand1') \
+        .with_sequence('TATTT' + 'G' * width + 'C' * width + 'T' * 3 + 'G' * width + 'ATAAAAA') \
+        .with_modification_5p(sc.cy5_5p) \
+        .with_modification_3p(sc.cy3_3p)
 
     design.draw_strand(0, 24).extension_5p(5, display_length=3.5, display_angle=60) \
+        .with_domain_name("ext_5p 2") \
         .move(-width).cross(1).move(width).loopout(2, 3).move(-width) \
-        .extension_3p(7).with_domain_name("ext_3p_top")
+        .extension_3p(7).with_domain_name("ext_3p 2") \
+        .with_name('strand2') \
+        .with_sequence('ATAAA' + 'C' * width + 'G' * width + 'A' * 3 + 'C' * width + 'TATTTTT') \
 
     return design
 

diff --git a/examples/output_designs/extensions.sc b/examples/output_designs/extensions.sc
@@ -4,29 +4,49 @@
   "helices": [
     {"max_offset": 32, "grid_position": [0, 0]},
     {"max_offset": 32, "grid_position": [0, 1]},
-    {"max_offset": 32, "grid_position": [0, 2]}
+    {"max_offset": 32, "grid_position": [0, 2], "roll": 30}
   ],
+  "modifications_in_design": {
+    "/3Cy3Sp/": {
+      "display_text": "Cy3",
+      "idt_text": "/3Cy3Sp/",
+      "display_connector": false,
+      "location": "3'"
+    },
+    "/5Cy5/": {
+      "display_text": "Cy5",
+      "idt_text": "/5Cy5/",
+      "display_connector": false,
+      "location": "5'"
+    }
+  },
   "strands": [
     {
+      "name": "strand1",
       "color": "#f74308",
+      "sequence": "TATTTGGGGGGGGCCCCCCCCTTTGGGGGGGGATAAAAA",
       "domains": [
-        {"extension_num_bases": 5, "display_length": 2.5},
-        {"helix": 0, "forward": true, "start": 0, "end": 8},
+        {"extension_num_bases": 5, "display_length": 2.5, "name": "ext_5p 1"},
+        {"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8},
         {"helix": 1, "forward": false, "start": 0, "end": 8},
-        {"loopout": 3},
+        {"loopout": 3, "name": "loopout 1"},
         {"helix": 2, "forward": true, "start": 0, "end": 8},
-        {"extension_num_bases": 7, "name": "ext_3p"}
-      ]
+        {"extension_num_bases": 7, "name": "ext_3p 1"}
+      ],
+      "5prime_modification": "/5Cy5/",
+      "3prime_modification": "/3Cy3Sp/"
     },
     {
+      "name": "strand2",
       "color": "#57bb00",
+      "sequence": "ATAAACCCCCCCCGGGGGGGGAAACCCCCCCCTATTTTT",
       "domains": [
-        {"extension_num_bases": 5, "display_length": 3.5, "display_angle": 60},
+        {"extension_num_bases": 5, "display_length": 3.5, "display_angle": 60, "name": "ext_5p 2"},
         {"helix": 0, "forward": false, "start": 16, "end": 24},
         {"helix": 1, "forward": true, "start": 16, "end": 24},
         {"loopout": 3},
         {"helix": 2, "forward": false, "start": 16, "end": 24},
-        {"extension_num_bases": 7, "name": "ext_3p_top"}
+        {"extension_num_bases": 7, "name": "ext_3p 2"}
       ]
     }
   ]

diff --git a/examples/oxdna/extensions.dat b/examples/oxdna/extensions.dat
@@ -0,0 +1,81 @@
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+E = 0 0 0
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diff --git a/examples/oxdna/extensions.top b/examples/oxdna/extensions.top
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