Merge pull request #258 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Jul 22, 2023 · 4d0c152 · 4d0c152
2 parents 13d4e0e + f198708
commit 4d0c152
Show file tree

Hide file tree

Showing 12 changed files with 8,753 additions and 8,337 deletions.
diff --git a/examples/output_designs/domain_colors.sc b/examples/output_designs/domain_colors.sc
@@ -1,24 +1,24 @@
-{
-  "version": "0.17.7",
-  "grid": "square",
-  "helices": [
-    {"max_offset": 100, "grid_position": [0, 0]},
-    {"max_offset": 100, "grid_position": [0, 1]},
-    {"max_offset": 100, "grid_position": [0, 2]},
-    {"max_offset": 100, "grid_position": [0, 3]}
-  ],
-  "strands": [
-    {
-      "color": "#0000ff",
-      "domains": [
-        {"extension_num_bases": 5, "color": "#ff0000"},
-        {"helix": 0, "forward": true, "start": 0, "end": 8, "color": "#00ff00"},
-        {"loopout": 5, "color": "#000096"},
-        {"helix": 1, "forward": false, "start": 0, "end": 8, "color": "#960000"},
-        {"helix": 2, "forward": true, "start": 0, "end": 8, "color": "#009600"},
-        {"helix": 3, "forward": false, "start": 0, "end": 8},
-        {"extension_num_bases": 5, "color": "#000000"}
-      ]
-    }
-  ]
+{
+  "version": "0.17.8",
+  "grid": "square",
+  "helices": [
+    {"max_offset": 100, "grid_position": [0, 0]},
+    {"max_offset": 100, "grid_position": [0, 1]},
+    {"max_offset": 100, "grid_position": [0, 2]},
+    {"max_offset": 100, "grid_position": [0, 3]}
+  ],
+  "strands": [
+    {
+      "color": "#0000ff",
+      "domains": [
+        {"extension_num_bases": 5, "color": "#ff0000"},
+        {"helix": 0, "forward": true, "start": 0, "end": 8, "color": "#00ff00"},
+        {"loopout": 5, "color": "#000096"},
+        {"helix": 1, "forward": false, "start": 0, "end": 8, "color": "#960000"},
+        {"helix": 2, "forward": true, "start": 0, "end": 8, "color": "#009600"},
+        {"helix": 3, "forward": false, "start": 0, "end": 8},
+        {"extension_num_bases": 5, "color": "#000000"}
+      ]
+    }
+  ]
 }
diff --git a/examples/output_designs/oxdna_export_with_pitch.sc b/examples/output_designs/oxdna_export_with_pitch.sc
@@ -0,0 +1,28 @@
+{
+  "version": "0.17.8",
+  "groups": {
+    "default_group": {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "pitch": 45,
+      "grid": "square"
+    }
+  },
+  "helices": [
+    {"max_offset": 100, "grid_position": [0, 0]},
+    {"max_offset": 100, "grid_position": [0, 1]}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 21}
+      ]
+    },
+    {
+      "color": "#57bb00",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 0, "end": 21}
+      ]
+    }
+  ]
+}
diff --git a/examples/output_designs/oxdna_export_with_pitch.zip b/examples/output_designs/oxdna_export_with_pitch.zip
diff --git a/examples/output_designs/oxdna_export_with_pitch_0.sc b/examples/output_designs/oxdna_export_with_pitch_0.sc
@@ -0,0 +1,22 @@
+{
+  "version": "0.17.8",
+  "grid": "square",
+  "helices": [
+    {"max_offset": 100, "grid_position": [0, 0]},
+    {"max_offset": 100, "grid_position": [0, 1]}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 21}
+      ]
+    },
+    {
+      "color": "#57bb00",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 0, "end": 21}
+      ]
+    }
+  ]
+}
diff --git a/examples/output_designs/oxdna_export_with_pitch_45.sc b/examples/output_designs/oxdna_export_with_pitch_45.sc
@@ -0,0 +1,28 @@
+{
+  "version": "0.17.8",
+  "groups": {
+    "default_group": {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "pitch": 45,
+      "grid": "square"
+    }
+  },
+  "helices": [
+    {"max_offset": 100, "grid_position": [0, 0]},
+    {"max_offset": 100, "grid_position": [0, 1]}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 21}
+      ]
+    },
+    {
+      "color": "#57bb00",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 0, "end": 21}
+      ]
+    }
+  ]
+}
diff --git a/examples/oxdna/oxdna_export_with_pitch_0.dat b/examples/oxdna/oxdna_export_with_pitch_0.dat
@@ -0,0 +1,45 @@
+t = 0
+b = 19.19288565390937 19.19288565390937 19.19288565390937
+E = 0 0 0
+-0.20521208599540122 -0.563815572471545 0.0 0.3420201433256687 0.9396926207859084 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.14805443861417622 -0.5814463717374467 0.3897628551303123 -0.2467573976902937 0.969077286229078 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.4498687217806405 -0.39701150255811557 0.7795257102606246 -0.7497812029677342 0.6616858375968593 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5953435239601033 -0.07460622278849112 1.1692885653909368 -0.9922392066001721 0.1243437046474852 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5339230852868811 0.2737263944118978 1.5590514205212491 -0.8898718088114685 -0.456210657353163 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.2869523871727911 0.5269329440221371 1.9488142756515616 -0.47825397862131847 -0.8782215733702284 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.059740707957489946 0.5970184652192408 2.3385771307818737 0.09956784659581658 -0.9950307753654014 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.3856725658119234 0.459626665871387 2.728339985912186 0.642787609686539 -0.7660444431189783 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5775745481700072 0.16250428088580296 3.1181028410424982 0.962624246950012 -0.27084046814300494 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.568756407700279 -0.19109199015101058 3.5078656961728107 0.9479273461671318 0.3184866502516843 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.36228264619528666 -0.47827950433375327 3.8976285513031232 0.6038044103254778 0.7971325072229222 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.02990753139641875 -0.5992541527313534 4.287391406433435 0.04984588566069792 0.9987569212189223 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.31286112202769867 -0.5119745289792934 4.677154261563747 -0.5214352033794978 0.8532908816321557 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5469035113870039 -0.24677226187836673 5.06691711669406 -0.9115058523116732 0.41128710313061123 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.590884651807325 0.10418890660015769 5.456679971824372 -0.9848077530122084 -0.17364817766692947 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.429520109555832 0.41894209085164286 5.846442826954685 -0.71586684925972 -0.6982368180860714 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.11888768591963841 0.5881034927091263 6.2362056820849965 -0.19814614319939736 -0.9801724878485439 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.23306087776481726 0.5528857271222444 6.625968537215309 0.38843479627469546 -0.9214762118704074 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5040155538904627 0.32552775831945585 7.0157313923456215 0.8400259231507712 -0.5425462638657598 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5998135092004897 -0.014958415042842765 7.405494247475934 0.9996891820008162 0.024930691738071276 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.48716280342951424 -0.3502462033408734 7.7952571026062465 0.8119380057158571 0.5837436722347891 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.20521208599540122 2.95813793774212 0.0 0.3420201433256687 0.9396926207859084 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.14805443861417622 2.9405071384762183 0.3897628551303123 -0.2467573976902937 0.969077286229078 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.4498687217806405 3.1249420076555494 0.7795257102606246 -0.7497812029677342 0.6616858375968593 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5953435239601033 3.447347287425174 1.1692885653909368 -0.9922392066001721 0.1243437046474852 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5339230852868811 3.7956799046255627 1.5590514205212491 -0.8898718088114685 -0.456210657353163 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.2869523871727911 4.048886454235802 1.9488142756515616 -0.47825397862131847 -0.8782215733702284 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.059740707957489946 4.118971975432906 2.3385771307818737 0.09956784659581658 -0.9950307753654014 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.3856725658119234 3.981580176085052 2.728339985912186 0.642787609686539 -0.7660444431189783 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5775745481700072 3.684457791099468 3.1181028410424982 0.962624246950012 -0.27084046814300494 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.568756407700279 3.3308615200626543 3.5078656961728107 0.9479273461671318 0.3184866502516843 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.36228264619528666 3.043674005879912 3.8976285513031232 0.6038044103254778 0.7971325072229222 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.02990753139641875 2.9226993574823115 4.287391406433435 0.04984588566069792 0.9987569212189223 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.31286112202769867 3.0099789812343714 4.677154261563747 -0.5214352033794978 0.8532908816321557 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.5469035113870039 3.2751812483352984 5.06691711669406 -0.9115058523116732 0.41128710313061123 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.590884651807325 3.6261424168138228 5.456679971824372 -0.9848077530122084 -0.17364817766692947 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.429520109555832 3.940895601065308 5.846442826954685 -0.71586684925972 -0.6982368180860714 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+0.11888768591963841 4.110057002922791 6.2362056820849965 -0.19814614319939736 -0.9801724878485439 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.23306087776481726 4.074839237335909 6.625968537215309 0.38843479627469546 -0.9214762118704074 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5040155538904627 3.847481268533121 7.0157313923456215 0.8400259231507712 -0.5425462638657598 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.5998135092004897 3.506995095170822 7.405494247475934 0.9996891820008162 0.024930691738071276 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
+-0.48716280342951424 3.1717073068727917 7.7952571026062465 0.8119380057158571 0.5837436722347891 -0.0 -0.0 -0.0 -1.0 0 0 0 0 0 0
diff --git a/examples/oxdna/oxdna_export_with_pitch_0.top b/examples/oxdna/oxdna_export_with_pitch_0.top
@@ -0,0 +1,43 @@
+42 2
+1 T 1 -1
+1 T 2 0
+1 T 3 1
+1 T 4 2
+1 T 5 3
+1 T 6 4
+1 T 7 5
+1 T 8 6
+1 T 9 7
+1 T 10 8
+1 T 11 9
+1 T 12 10
+1 T 13 11
+1 T 14 12
+1 T 15 13
+1 T 16 14
+1 T 17 15
+1 T 18 16
+1 T 19 17
+1 T 20 18
+1 T -1 19
+2 T 22 -1
+2 T 23 21
+2 T 24 22
+2 T 25 23
+2 T 26 24
+2 T 27 25
+2 T 28 26
+2 T 29 27
+2 T 30 28
+2 T 31 29
+2 T 32 30
+2 T 33 31
+2 T 34 32
+2 T 35 33
+2 T 36 34
+2 T 37 35
+2 T 38 36
+2 T 39 37
+2 T 40 38
+2 T 41 39
+2 T -1 40
diff --git a/examples/oxdna/oxdna_export_with_pitch_45.dat b/examples/oxdna/oxdna_export_with_pitch_45.dat
@@ -0,0 +1,45 @@
+t = 0
+b = 21.051049002838713 21.051049002838713 21.051049002838713
+E = 0 0 0
+-0.20521208599540125 -0.3986778146332049 0.3986778146332049 0.34202014332566877 0.6644630243886749 -0.6644630243886749 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.14805443861417625 -0.1355407144345891 0.6867486302691366 -0.24675739769029376 0.6852411205864382 -0.6852411205864382 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.4498687217806406 0.27047839016664355 0.8319374415024515 -0.7497812029677343 0.46788254277984 -0.46788254277984 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.5953435239601033 0.774057307699365 0.8795664398042778 -0.9922392066001722 0.08792427675409403 -0.08792427675409403 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.5339230852868813 1.2959696213474916 0.9088620419906985 -0.8898718088114688 -0.32258964946399415 0.32258964946399415 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.2869523871727911 1.7506176475350137 1.0054219316377244 -0.4782539786213185 -0.6209964299144077 0.6209964299144077 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.05974070795748991 2.075779552753753 1.2314679422535326 0.09956784659581652 -0.7035930087501837 0.7035930087501837 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.3856725658119235 2.254232837672738 1.6042225731690951 0.6427876096865391 -0.5416752204197022 0.5416752204197022 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5775745481700073 2.3197395423243847 2.0899237843519956 0.9626242469500121 -0.19151313164365794 0.19151313164365794 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5687564077002791 2.345313179189252 2.615558063321677 0.9479273461671319 0.22520407011035426 -0.22520407011035426 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.36228264619528666 2.4178448983558005 3.0942342599896757 0.6038044103254778 0.563657801361563 -0.563657801361563 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.029907531396418784 2.6079068620394725 3.4553802121405504 0.049845885660697975 0.7062277917508986 -0.7062277917508986 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.3128611220276987 2.9452268337712386 3.6692681562433327 -0.5214352033794979 0.603367768726745 -0.603367768726745 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.546903511387004 3.4083571131416237 3.757345792707495 -0.9115058523116734 0.2908238996382262 -0.2908238996382262 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.590884651807325 3.9321280932232163 3.784782728460449 -0.9848077530122084 -0.12278780396897232 0.12278780396897232 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.429520109555832 4.430296162124774 3.837822575393439 -0.71586684925972 -0.493727988942779 0.493727988942779 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.11888768591963843 4.825515294410497 3.9938113589422635 -0.19814614319939738 -0.6930866128901945 0.6930866128901945 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.23306087776481724 5.076216531463048 4.29431803772426 0.3884347962746954 -0.6515820781156569 0.6515820781156569 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5040155538904627 5.1910541278830715 4.730688357138786 0.8400259231507713 -0.38363814228690474 0.38363814228690474 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5998135092004898 5.225898003715605 5.2470523971407985 0.9996891820008165 0.017628661187661654 -0.017628661187661654 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.4871628034295143 5.264417692878302 5.75974062381265 0.8119380057158572 0.41276910911195674 -0.41276910911195674 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.20521208599540125 3.12327569558046 0.3986778146332049 0.34202014332566877 0.6644630243886749 -0.6644630243886749 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.14805443861417625 3.386412795779076 0.6867486302691366 -0.24675739769029376 0.6852411205864382 -0.6852411205864382 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.4498687217806406 3.7924319003803086 0.8319374415024515 -0.7497812029677343 0.46788254277984 -0.46788254277984 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.5953435239601033 4.29601081791303 0.8795664398042778 -0.9922392066001722 0.08792427675409403 -0.08792427675409403 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.5339230852868813 4.817923131561156 0.9088620419906985 -0.8898718088114688 -0.32258964946399415 0.32258964946399415 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.2869523871727911 5.272571157748678 1.0054219316377244 -0.4782539786213185 -0.6209964299144077 0.6209964299144077 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.05974070795748991 5.597733062967418 1.2314679422535326 0.09956784659581652 -0.7035930087501837 0.7035930087501837 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.3856725658119235 5.776186347886402 1.6042225731690951 0.6427876096865391 -0.5416752204197022 0.5416752204197022 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5775745481700073 5.84169305253805 2.0899237843519956 0.9626242469500121 -0.19151313164365794 0.19151313164365794 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5687564077002791 5.867266689402917 2.615558063321677 0.9479273461671319 0.22520407011035426 -0.22520407011035426 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.36228264619528666 5.939798408569465 3.0942342599896757 0.6038044103254778 0.563657801361563 -0.563657801361563 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.029907531396418784 6.1298603722531375 3.4553802121405504 0.049845885660697975 0.7062277917508986 -0.7062277917508986 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.3128611220276987 6.467180343984904 3.6692681562433327 -0.5214352033794979 0.603367768726745 -0.603367768726745 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.546903511387004 6.93031062335529 3.757345792707495 -0.9115058523116734 0.2908238996382262 -0.2908238996382262 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.590884651807325 7.454081603436881 3.784782728460449 -0.9848077530122084 -0.12278780396897232 0.12278780396897232 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.429520109555832 7.952249672338439 3.837822575393439 -0.71586684925972 -0.493727988942779 0.493727988942779 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+0.11888768591963843 8.347468804624162 3.9938113589422635 -0.19814614319939738 -0.6930866128901945 0.6930866128901945 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.23306087776481724 8.598170041676713 4.29431803772426 0.3884347962746954 -0.6515820781156569 0.6515820781156569 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5040155538904627 8.713007638096736 4.730688357138786 0.8400259231507713 -0.38363814228690474 0.38363814228690474 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.5998135092004898 8.747851513929268 5.2470523971407985 0.9996891820008165 0.017628661187661654 -0.017628661187661654 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
+-0.4871628034295143 8.786371203091967 5.75974062381265 0.8119380057158572 0.41276910911195674 -0.41276910911195674 -0.0 -0.7071067811865476 -0.7071067811865476 0 0 0 0 0 0
diff --git a/examples/oxdna/oxdna_export_with_pitch_45.top b/examples/oxdna/oxdna_export_with_pitch_45.top
@@ -0,0 +1,43 @@
+42 2
+1 T 1 -1
+1 T 2 0
+1 T 3 1
+1 T 4 2
+1 T 5 3
+1 T 6 4
+1 T 7 5
+1 T 8 6
+1 T 9 7
+1 T 10 8
+1 T 11 9
+1 T 12 10
+1 T 13 11
+1 T 14 12
+1 T 15 13
+1 T 16 14
+1 T 17 15
+1 T 18 16
+1 T 19 17
+1 T 20 18
+1 T -1 19
+2 T 22 -1
+2 T 23 21
+2 T 24 22
+2 T 25 23
+2 T 26 24
+2 T 27 25
+2 T 28 26
+2 T 29 27
+2 T 30 28
+2 T 31 29
+2 T 32 30
+2 T 33 31
+2 T 34 32
+2 T 35 33
+2 T 36 34
+2 T 37 35
+2 T 38 36
+2 T 39 37
+2 T 40 38
+2 T 41 39
+2 T -1 40
diff --git a/examples/oxdna_export_with_pitch.py b/examples/oxdna_export_with_pitch.py
@@ -0,0 +1,20 @@
+import scadnano as sc
+
+
+def create_design(pitch: float) -> sc.Design:
+    helices = [sc.Helix(max_offset=100) for _ in range(2)]
+    design = sc.Design(helices=helices, grid=sc.square)
+
+    design.groups[sc.default_group_name].pitch = pitch
+
+    design.draw_strand(0, 0).to(21)
+    design.draw_strand(1, 0).to(21)
+
+    return design
+
+
+if __name__ == '__main__':
+    for pitch in [0, 45]:
+        d = create_design(pitch)
+        d.write_scadnano_file(filename=f'oxdna_export_with_pitch_{pitch}.sc', directory='output_designs')
+        d.write_oxdna_files(filename_no_extension=f'oxdna_export_with_pitch_{pitch}', directory='oxdna')
-Original file line number
+Diff line change
@@ -0,0 +1,43 @@
+2
+T 1 -1
+T 2 0
+T 3 1
+T 4 2
+T 5 3
+T 6 4
+T 7 5
+T 8 6
+T 9 7
+T 10 8
+T 11 9
+T 12 10
+T 13 11
+T 14 12
+T 15 13
+T 16 14
+T 17 15
+T 18 16
+T 19 17
+T 20 18
+T -1 19
+T 22 -1
+T 23 21
+T 24 22
+T 25 23
+T 26 24
+T 27 25
+T 28 26
+T 29 27
+T 30 28
+T 31 29
+T 32 30
+T 33 31
+T 34 32
+T 35 33
+T 36 34
+T 37 35
+T 38 36
+T 39 37
+T 40 38
+T 41 39
+T -1 40