closes #111: write_idt_plate_excel_file uses reasonable defaults even…

… when some strands have no IDT field set; bumped version
UC-Davis-molecular-computing · Dec 17, 2020 · d2e924c · d2e924c
1 parent 22d446e
commit d2e924c
Show file tree

Hide file tree

Showing 62 changed files with 2,291 additions and 1,056 deletions.
diff --git a/examples/16_helix_origami_barrel_from_algoSST_paper.py b/examples/16_helix_origami_barrel_from_algoSST_paper.py
@@ -6,7 +6,7 @@ def create_design():
     design = rect.create(num_helices=16, num_cols=28, seam_left_column=12, assign_seq=False,
                          num_flanking_columns=2,
                          num_flanking_helices=2, edge_staples=False,
-                         scaffold_nick_offset=102, use_idt_defaults=True)
+                         scaffold_nick_offset=102)
 
     # # need this to match original design, but doesn't leave room for left-side adapters
     # design.move_strand_offsets(8)

diff --git a/examples/16_helix_origami_rectangle_idt.py b/examples/16_helix_origami_rectangle_idt.py
@@ -3,7 +3,7 @@
 
 
 def create_design():
-    design = rect.create(num_helices=16, num_cols=26, use_idt_defaults=True)
+    design = rect.create(num_helices=16, num_cols=26)
     return design
 
 

diff --git a/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py b/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py
@@ -5,7 +5,7 @@
 def create_design():
     design = rect.create(num_helices=16, num_cols=28, seam_left_column=12, assign_seq=False,
                          num_flanking_columns=2, num_flanking_helices=2, edge_staples=False,
-                         scaffold_nick_offset=102, use_idt_defaults=True)
+                         scaffold_nick_offset=102)
 
     # # need this to match original design, but doesn't leave room for left-side adapters
     # design.move_strand_offsets(8)

diff --git a/examples/add_deletions_to_24_helix_rectangle.py b/examples/add_deletions_to_24_helix_rectangle.py
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
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": "0.11.0",
+  "version": "0.14.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},