Merge pull request #128 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Aug 6, 2020 · e03a5ea · e03a5ea
2 parents 1895aa9 + dceefc1
commit e03a5ea
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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/helix_groups.py b/examples/helix_groups.py
@@ -1,50 +1,76 @@
 import scadnano as sc
 
+
 def create_design():
+    include_rot = False
+    include_rot = True
     n = 'north'
     e = 'east'
     s = 'south'
     w = 'west'
     helices = [
-        sc.Helix(max_offset=20, group=n, grid_position=(1, 1)),                     # 0
-        sc.Helix(max_offset=21, group=n, grid_position=(0, 1)),                     # 1
-        sc.Helix(max_offset=19, group=n, grid_position=(0, 2)),                     # 2
-        sc.Helix(max_offset=18, group=n, grid_position=(1, 2)),                     # 3
-        sc.Helix(max_offset=17, group=n, grid_position=(2, 2)),                     # 4
-        sc.Helix(max_offset=16, group=n, grid_position=(2, 1)),                     # 5
-        sc.Helix(max_offset=24, group=s),                                           # 6
-        sc.Helix(max_offset=25, group=s),                                           # 7
-        sc.Helix(max_offset=26, group=w, position=sc.Position3D(x=0, y=0, z=0)),    # 8
-        sc.Helix(max_offset=27, group=w, position=sc.Position3D(x=0, y=2.5, z=0)),  # 9
-        sc.Helix(idx=13, max_offset=22, group=e),                                   # 13
-        sc.Helix(idx=15, max_offset=23, group=e),                                   # 15
+        sc.Helix(max_offset=20, group=n, grid_position=(0, 0)),  # 0
+        sc.Helix(max_offset=21, group=n, grid_position=(1, 0)),  # 1
+        sc.Helix(max_offset=19, group=n, grid_position=(1, 1)),  # 2
+        sc.Helix(max_offset=18, group=n, grid_position=(0, 1)),  # 3
+        sc.Helix(max_offset=17, group=n, grid_position=(-1, 1)),  # 4
+        sc.Helix(max_offset=16, group=n, grid_position=(-1, 0)),  # 5
+        sc.Helix(max_offset=24, group=s),  # 6
+        sc.Helix(max_offset=25, group=s),  # 7
+        sc.Helix(max_offset=26, group=w, position=sc.Position3D(x=0, y=0, z=0)),  # 8
+        sc.Helix(max_offset=27, group=w, position=sc.Position3D(x=0, y=3, z=0)),  # 9
     ]
-    group_north = sc.HelixGroup(position=sc.Position3D(x=0, y=-200, z=0), grid=sc.honeycomb)
-    group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=70, z=0), helices_view_order=[7, 6],
+    if include_rot:
+        helices.extend([
+            sc.Helix(max_offset=26, group='r', grid_position=(0, 0)),  # 10
+            sc.Helix(max_offset=27, group='r', grid_position=(0, 1)),  # 11
+        ])
+    helices.extend([
+        sc.Helix(idx=13, max_offset=22, group=e),  # 13
+        sc.Helix(idx=15, max_offset=23, group=e),  # 15
+    ])
+
+    group_north = sc.HelixGroup(position=sc.Position3D(x=0, y=-10, z=0), grid=sc.honeycomb)
+    group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0), helices_view_order=[7, 6],
                                 grid=sc.square)
-    group_east = sc.HelixGroup(position=sc.Position3D(x=0, y=0, z=100), pitch=45, grid=sc.square)
-    group_west = sc.HelixGroup()
+    group_east = sc.HelixGroup(position=sc.Position3D(x=10, y=0, z=0), grid=sc.square)
+    group_west = sc.HelixGroup(position=sc.Position3D(x=-10, y=0, z=0), grid=sc.Grid.none)
     groups = {
         n: group_north,
         e: group_east,
         s: group_south,
         w: group_west,
     }
+
+    if include_rot:
+        group_rot = sc.HelixGroup(position=sc.Position3D(x=10, y=10, z=0), pitch=45, grid=sc.square)
+        groups['r'] = group_rot
+
     design = sc.Design(helices=helices, groups=groups, strands=[])
 
-    design.strand(0, 0).to(8)\
-        .cross(1).to(0)\
-        .cross(2).to(8)\
-        .cross(3).to(0)\
-        .cross(4).to(8)\
+    design.strand(0, 0).to(8) \
+        .cross(1).to(0) \
+        .cross(2).to(8) \
+        .cross(3).to(0) \
+        .cross(4).to(8) \
         .cross(5).to(0)
 
+    design.strand(4, 10).to(13)
+
     design.strand(6, 0).to(8).cross(7).to(0)
     design.strand(8, 0).to(8).cross(9).to(0)
     design.strand(13, 0).to(8).cross(15).to(0)
 
+    design.strand(8, 8).to(11)
+    design.strand(13, 8).to(11)
+
+
+    if include_rot:
+        design.strand(10, 0).to(8).cross(11).to(0)
+
     return design
 
+
 if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')
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]},