re-ran examples to produce latest version

UC-Davis-molecular-computing · Aug 6, 2020 · 3f59e6d · 3f59e6d
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diff --git a/examples/1_staple_1_helix_origami_position_nondefault.py b/examples/1_staple_1_helix_origami_position_nondefault.py
@@ -10,7 +10,7 @@ def create_design():
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]
-    design = sc.Design(helices=helices, strands=strands, grid=sc.square)
+    design = sc.Design(helices=helices, strands=strands, grid=sc.Grid.none)
     design.assign_dna(scaf, 'AACT' * (length // 4))
 
     return design

diff --git a/examples/24_helix_origami_rectangle_twist_corrected.sc b/examples/24_helix_origami_rectangle_twist_corrected.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 304, "grid_position": [0, 0]},

diff --git a/examples/24_helix_rectangle_twist_corrected.sc b/examples/24_helix_rectangle_twist_corrected.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "e",
   "helices": [
     {"max_offset": 304, "grid_position": [0, -3]},

diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/16_helix_origami_rectangle.sc b/examples/output_designs/16_helix_origami_rectangle.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.sc b/examples/output_designs/16_helix_origami_rectangle_idt.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.sc b/examples/output_designs/16_helix_origami_rectangle_no_seq.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.sc b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.sc b/examples/output_designs/16_helix_origami_rectangle_no_twist.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.sc b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/1_staple_1_helix_origami.sc b/examples/output_designs/1_staple_1_helix_origami.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.sc b/examples/output_designs/1_staple_1_helix_origami_mismatches.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc
@@ -1,6 +1,6 @@
 {
-  "version": "0.10.1",
-  "grid": "square",
+  "version": "0.11.0",
+  "grid": "none",
   "helices": [
     {
       "position": {"x": 1, "y": 2, "z": 3},

diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.sc b/examples/output_designs/1_staple_1_helix_origami_roll.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0], "roll": 90}

diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.sc b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_modifications.sc b/examples/output_designs/2_staple_2_helix_modifications.sc
@@ -1,16 +1,22 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},
     {"grid_position": [0, 1]}
   ],
   "modifications_in_design": {
-    "/5Biosg/": {
-      "display_text": "B",
-      "idt_text": "/5Biosg/",
+    "/3Cy3Sp/": {
+      "display_text": "Cy3",
+      "idt_text": "/3Cy3Sp/",
       "display_connector": false,
-      "location": "5'"
+      "location": "3'"
+    },
+    "/iCy5/": {
+      "display_text": "Cy5",
+      "idt_text": "/iCy5/",
+      "display_connector": false,
+      "location": "internal"
     },
     "/iBiodT/": {
       "display_text": "B",
@@ -25,12 +31,6 @@
       "display_connector": false,
       "location": "5'"
     },
-    "/iCy5/": {
-      "display_text": "Cy5",
-      "idt_text": "/iCy5/",
-      "display_connector": false,
-      "location": "internal"
-    },
     "/iCy3/": {
       "display_text": "Cy3",
       "idt_text": "/iCy3/",
@@ -43,11 +43,11 @@
       "display_connector": false,
       "location": "3'"
     },
-    "/3Cy3Sp/": {
-      "display_text": "Cy3",
-      "idt_text": "/3Cy3Sp/",
+    "/5Biosg/": {
+      "display_text": "B",
+      "idt_text": "/5Biosg/",
       "display_connector": false,
-      "location": "3'"
+      "location": "5'"
     }
   },
   "strands": [

diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.sc b/examples/output_designs/2_staple_2_helix_origami_deletions.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/...ples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc b/...ples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "geometry": {
     "rise_per_base_pair": 0.2,

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/3_helix_deletions_insertions.sc b/examples/output_designs/3_helix_deletions_insertions.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 64, "grid_position": [0, 0]},

diff --git a/examples/output_designs/4_helix_grid_none.sc b/examples/output_designs/4_helix_grid_none.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "none",
   "helices": [
     {

diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "none",
   "helices": [
     {

diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.sc b/examples/output_designs/4_helix_min_offsets_nonzero.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 30, "grid_position": [0, 0]},

diff --git a/examples/output_designs/56_helix_origami_rectangle.sc b/examples/output_designs/56_helix_origami_rectangle.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 160, "grid_position": [0, 0]},

diff --git a/examples/output_designs/64_helix_origami_rectangle.sc b/examples/output_designs/64_helix_origami_rectangle.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 128, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.sc b/examples/output_designs/6_helix_6_col_origami_rectangle.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_bundle_honeycomb.sc b/examples/output_designs/6_helix_bundle_honeycomb.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.3",
+  "version": "0.11.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 1295, "grid_position": [1, 1]},

diff --git a/examples/output_designs/6_helix_origami_rectangle.sc b/examples/output_designs/6_helix_origami_rectangle.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/empty.sc b/examples/output_designs/empty.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [],
   "strands": []

diff --git a/examples/output_designs/hairpin.sc b/examples/output_designs/hairpin.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/helices_out_of_order_nonconsecutive.sc b/examples/output_designs/helices_out_of_order_nonconsecutive.sc
@@ -1,12 +1,12 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "none",
   "helices": [
-    {"max_offset": 20, "grid_position": [0, 2], "idx": 2},
-    {"max_offset": 20, "grid_position": [0, 3], "idx": 3},
-    {"max_offset": 20, "grid_position": [0, 5], "idx": 5},
-    {"max_offset": 20, "grid_position": [0, 7], "idx": 7},
-    {"max_offset": 20, "grid_position": [0, 11], "idx": 11}
+    {"max_offset": 20, "grid_position": null, "idx": 2},
+    {"max_offset": 20, "grid_position": null, "idx": 3},
+    {"max_offset": 20, "grid_position": null, "idx": 5},
+    {"max_offset": 20, "grid_position": null, "idx": 7},
+    {"max_offset": 20, "grid_position": null, "idx": 11}
   ],
   "strands": []
 }
diff --git a/examples/output_designs/hex_lattice_10x10.sc b/examples/output_designs/hex_lattice_10x10.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0]},

diff --git a/examples/output_designs/hex_lattice_10x10_with_negative.sc b/examples/output_designs/hex_lattice_10x10_with_negative.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [-4, -4]},

diff --git a/examples/output_designs/honeycomb_lattice_10x10.sc b/examples/output_designs/honeycomb_lattice_10x10.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0]},

diff --git a/examples/output_designs/honeycomb_lattice_10x10_with_negative.sc b/examples/output_designs/honeycomb_lattice_10x10_with_negative.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 16, "grid_position": [-4, -4]},

diff --git a/examples/output_designs/idt-plates-explicit.sc b/examples/output_designs/idt-plates-explicit.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/long_range_crossovers.sc b/examples/output_designs/long_range_crossovers.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/loopouts_all_types.sc b/examples/output_designs/loopouts_all_types.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/many_big_helices.sc b/examples/output_designs/many_big_helices.sc
@@ -1,5 +1,5 @@
 {
-  "version": "0.10.1",
+  "version": "0.11.0",
   "grid": "square",
   "helices": [
     {"max_offset": 2000, "grid_position": [0, 0]},