Merge pull request #83 from UC-Davis-molecular-computing/dev

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UC-Davis-molecular-computing · Jun 20, 2020 · f54b629 · f54b629
2 parents 3d3e455 + 59305e8
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diff --git a/dist/scadnano-0.9.1.tar.gz b/dist/scadnano-0.9.1.tar.gz
diff --git a/examples/1_staple_1_helix_origami.py b/examples/1_staple_1_helix_origami.py
@@ -3,8 +3,8 @@
 def main():
     length = 9
     helices = [sc.Helix(max_offset=length, major_ticks=[2, 5])]
-    stap_ss = sc.Domain(0, sc.forward, 0, length)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, True, 0, length)
+    scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/1_staple_1_helix_origami_idt_duplicate_names.py b/examples/1_staple_1_helix_origami_idt_duplicate_names.py
@@ -1,10 +1,10 @@
 import scadnano as sc
 
 def main():
-    ss1_r = sc.Domain(0, sc.forward, 0, 4)
-    ss2_r = sc.Domain(0, sc.forward, 4, 8)
-    ss3_r = sc.Domain(0, sc.forward, 8, 12)
-    ss_l = sc.Domain(0, sc.reverse, 0, 12)
+    ss1_r = sc.Domain(0, True, 0, 4)
+    ss2_r = sc.Domain(0, True, 4, 8)
+    ss3_r = sc.Domain(0, True, 8, 12)
+    ss_l = sc.Domain(0, False, 0, 12)
 
     s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r'))
     s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r'))

diff --git a/examples/1_staple_1_helix_origami_mismatches.py b/examples/1_staple_1_helix_origami_mismatches.py
@@ -3,8 +3,8 @@
 
 def main():
     length = 10
-    stap_ss = sc.Domain(0, sc.forward, 0, length)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, True, 0, length)
+    scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/1_staple_1_helix_origami_position_nondefault.py b/examples/1_staple_1_helix_origami_position_nondefault.py
@@ -5,8 +5,8 @@ def main():
     length = 9
     helices = [
         sc.Helix(max_offset=length, major_ticks=[2, 5], position=sc.Position3D(x=1, y=2, z=3), pitch=90)]
-    stap_ss = sc.Domain(0, sc.forward, 0, length)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, True, 0, length)
+    scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/1_staple_1_helix_origami_roll.py b/examples/1_staple_1_helix_origami_roll.py
@@ -5,8 +5,8 @@
 def main():
     length = 9
     helices = [sc.Helix(max_offset=length, roll=90)]
-    stap_ss = sc.Domain(0, sc.forward, 0, length)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, True, 0, length)
+    scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/2_staple_2_helix_modifications.py b/examples/2_staple_2_helix_modifications.py
@@ -3,13 +3,13 @@
 import dataclasses
 
 def main():
-    stap_left_ss1 = sc.Domain(1, sc.forward, 0, 16)
-    stap_left_ss0 = sc.Domain(0, sc.reverse, 0, 16)
-    stap_right_ss0 = sc.Domain(0, sc.reverse, 16, 32)
-    stap_right_ss1 = sc.Domain(1, sc.forward, 16, 32)
-    scaf_ss1_left = sc.Domain(1, sc.reverse, 0, 16)
-    scaf_ss0 = sc.Domain(0, sc.forward, 0, 32)
-    scaf_ss1_right = sc.Domain(1, sc.reverse, 16, 32)
+    stap_left_ss1 = sc.Domain(1, True, 0, 16)
+    stap_left_ss0 = sc.Domain(0, False, 0, 16)
+    stap_right_ss0 = sc.Domain(0, False, 16, 32)
+    stap_right_ss1 = sc.Domain(1, True, 16, 32)
+    scaf_ss1_left = sc.Domain(1, False, 0, 16)
+    scaf_ss0 = sc.Domain(0, True, 0, 32)
+    scaf_ss1_right = sc.Domain(1, False, 16, 32)
     stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
     stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
     scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right], color=sc.default_scaffold_color)

diff --git a/examples/2_staple_2_helix_origami_6bases_wide.py b/examples/2_staple_2_helix_origami_6bases_wide.py
@@ -3,13 +3,13 @@
 def main():
     width = 6
     width_h = width // 2
-    stap_left_ss1 = sc.Domain(1, sc.forward, 0, width_h)
-    stap_left_ss0 = sc.Domain(0, sc.reverse, 0, width_h)
-    stap_right_ss0 = sc.Domain(0, sc.reverse, width_h, width)
-    stap_right_ss1 = sc.Domain(1, sc.forward, width_h, width)
-    scaf_ss1_left = sc.Domain(1, sc.reverse, 0, width_h)
-    scaf_ss0 = sc.Domain(0, sc.forward, 0, width)
-    scaf_ss1_right = sc.Domain(1, sc.reverse, width_h, width)
+    stap_left_ss1 = sc.Domain(1, True, 0, width_h)
+    stap_left_ss0 = sc.Domain(0, False, 0, width_h)
+    stap_right_ss0 = sc.Domain(0, False, width_h, width)
+    stap_right_ss1 = sc.Domain(1, True, width_h, width)
+    scaf_ss1_left = sc.Domain(1, False, 0, width_h)
+    scaf_ss0 = sc.Domain(0, True, 0, width)
+    scaf_ss1_right = sc.Domain(1, False, width_h, width)
     stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
     stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
     scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right], color=sc.default_scaffold_color)

diff --git a/examples/2_staple_2_helix_origami_deletions.py b/examples/2_staple_2_helix_origami_deletions.py
@@ -2,13 +2,13 @@
 
 
 def main():
-    stap_left_ss1 = sc.Domain(1, sc.forward, 0, 16)
-    stap_left_ss0 = sc.Domain(0, sc.reverse, 0, 16)
-    stap_right_ss0 = sc.Domain(0, sc.reverse, 16, 32)
-    stap_right_ss1 = sc.Domain(1, sc.forward, 16, 32)
-    scaf_ss1_left = sc.Domain(1, sc.reverse, 0, 16)
-    scaf_ss0 = sc.Domain(0, sc.forward, 0, 32)
-    scaf_ss1_right = sc.Domain(1, sc.reverse, 16, 32)
+    stap_left_ss1 = sc.Domain(1, True, 0, 16)
+    stap_left_ss0 = sc.Domain(0, False, 0, 16)
+    stap_right_ss0 = sc.Domain(0, False, 16, 32)
+    stap_right_ss1 = sc.Domain(1, True, 16, 32)
+    scaf_ss1_left = sc.Domain(1, False, 0, 16)
+    scaf_ss0 = sc.Domain(0, True, 0, 32)
+    scaf_ss1_right = sc.Domain(1, False, 16, 32)
     stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
     stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
     scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right], color=sc.default_scaffold_color)

diff --git a/examples/4_helix_grid_none.py b/examples/4_helix_grid_none.py
@@ -9,8 +9,8 @@ def main():
         sc.Helix(max_offset=length, position=sc.Position3D(x=0, y=-3, z=8), pitch=0, roll=0, yaw=0),
         sc.Helix(max_offset=length, position=sc.Position3D(x=0, y=1, z=11), pitch=0, roll=0, yaw=0),
     ]
-    stap_ss = sc.Domain(0, sc.forward, 0, length)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, True, 0, length)
+    scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/4_helix_grid_none_min_offset_position_x_nondefault.py b/examples/4_helix_grid_none_min_offset_position_x_nondefault.py
@@ -0,0 +1,28 @@
+import scadnano as sc
+
+
+def main():
+    length = 16
+    helices = [
+        sc.Helix(major_tick_distance=4, max_offset=length, position=sc.Position3D(x=0, y=0, z=0),
+                 min_offset=0),
+        sc.Helix(major_tick_distance=4, max_offset=length, position=sc.Position3D(x=0, y=3, z=3),
+                 min_offset=8),
+        sc.Helix(major_tick_distance=4, max_offset=length, position=sc.Position3D(x=2.5, y=-3, z=8),
+                 min_offset=0),
+        sc.Helix(major_tick_distance=4, max_offset=length, position=sc.Position3D(x=2.5, y=1, z=11),
+                 min_offset=8),
+    ]
+    design = sc.DNADesign(helices=helices, strands=[
+        sc.Strand([sc.Domain(0, True, 0, length)]),
+        sc.Strand([sc.Domain(1, True, 8, length)]),
+        sc.Strand([sc.Domain(2, True, 0, length)]),
+        sc.Strand([sc.Domain(3, True, 8, length)]),
+    ], grid=sc.Grid.none)
+
+    return design
+
+
+if not sc.in_browser() and __name__ == '__main__':
+    design = main()
+    design.write_scadnano_file(directory='output_designs')
diff --git a/examples/4_helix_min_offsets_nonzero.py b/examples/4_helix_min_offsets_nonzero.py
@@ -9,8 +9,8 @@ def main():
         sc.Helix(min_offset=2, max_offset=length, grid_position=(0, 2)),
         sc.Helix(min_offset=3, max_offset=length, grid_position=(0, 3)),
     ]
-    stap_ss = sc.Domain(0, sc.forward, 0, length - 1)
-    scaf_ss = sc.Domain(0, sc.reverse, 0, length - 1)
+    stap_ss = sc.Domain(0, True, 0, length - 1)
+    scaf_ss = sc.Domain(0, False, 0, length - 1)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

diff --git a/examples/long_range_crossovers.py b/examples/long_range_crossovers.py
@@ -11,12 +11,12 @@ def main():
         helix_top = helices[bot]
         helix_bot = helices[top]
 
-        stap_left_ss_top = sc.Domain(top, sc.forward, 0, bases // 3)
-        stap_left_ss_bot = sc.Domain(bot, sc.reverse, 0, bases // 3)
-        stap_mid_ss_bot = sc.Domain(bot, sc.reverse, bases // 3, bases * 2 // 3)
-        stap_mid_ss_top = sc.Domain(top, sc.forward, bases // 3, bases * 2 // 3)
-        stap_right_ss_top = sc.Domain(top, sc.forward, bases * 2 // 3, bases)
-        stap_right_ss_bot = sc.Domain(bot, sc.reverse, bases * 2 // 3, bases)
+        stap_left_ss_top = sc.Domain(top, True, 0, bases // 3)
+        stap_left_ss_bot = sc.Domain(bot, False, 0, bases // 3)
+        stap_mid_ss_bot = sc.Domain(bot, False, bases // 3, bases * 2 // 3)
+        stap_mid_ss_top = sc.Domain(top, True, bases // 3, bases * 2 // 3)
+        stap_right_ss_top = sc.Domain(top, True, bases * 2 // 3, bases)
+        stap_right_ss_bot = sc.Domain(bot, False, bases * 2 // 3, bases)
         stap_left = sc.Strand([stap_left_ss_bot, stap_left_ss_top])
         stap_mid = sc.Strand([stap_mid_ss_top, stap_mid_ss_bot])
         stap_right = sc.Strand([stap_right_ss_bot, stap_right_ss_top])

diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna
@@ -12,6 +12,12 @@
       "display_connector": false,
       "location": "5'"
     },
+    "/3Cy3Sp/": {
+      "display_text": "Cy3",
+      "idt_text": "/3Cy3Sp/",
+      "display_connector": false,
+      "location": "3'"
+    },
     "/iCy3/": {
       "display_text": "Cy3",
       "idt_text": "/iCy3/",
@@ -31,12 +37,6 @@
       "display_connector": false,
       "location": "3'"
     },
-    "/3Cy3Sp/": {
-      "display_text": "Cy3",
-      "idt_text": "/3Cy3Sp/",
-      "display_connector": false,
-      "location": "3'"
-    },
     "/5Biosg/": {
       "display_text": "B",
       "idt_text": "/5Biosg/",

diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna
@@ -20,7 +20,7 @@
   ],
   "strands": [
     {
-      "color": "#f74308",
+      "color": "#32b86c",
       "domains": [
         {"helix": 0, "forward": true, "start": 0, "end": 10}
       ]

diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna
@@ -0,0 +1,50 @@
+{
+  "version": "0.9.0",
+  "grid": "none",
+  "helices": [
+    {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "major_tick_distance": 4
+    },
+    {
+      "min_offset": 8,
+      "position": {"x": 0, "y": 3, "z": 3},
+      "major_tick_distance": 4
+    },
+    {
+      "position": {"x": 2.5, "y": -3, "z": 8},
+      "major_tick_distance": 4
+    },
+    {
+      "min_offset": 8,
+      "position": {"x": 2.5, "y": 1, "z": 11},
+      "major_tick_distance": 4
+    }
+  ],
+  "strands": [
+    {
+      "color": "#333333",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 16}
+      ]
+    },
+    {
+      "color": "#320096",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 8, "end": 16}
+      ]
+    },
+    {
+      "color": "#03b6a2",
+      "domains": [
+        {"helix": 2, "forward": true, "start": 0, "end": 16}
+      ]
+    },
+    {
+      "color": "#7300de",
+      "domains": [
+        {"helix": 3, "forward": true, "start": 8, "end": 16}
+      ]
+    }
+  ]
+}
diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna
@@ -9,7 +9,7 @@
   ],
   "strands": [
     {
-      "color": "#f74308",
+      "color": "#aaaa00",
       "domains": [
         {"helix": 0, "forward": true, "start": 0, "end": 29}
       ]