diff --git a/examples/1_staple_1_helix_origami_position_nondefault.py b/examples/1_staple_1_helix_origami_position_nondefault.py index 5bb0129b..bb1c887e 100644 --- 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 index bd6b4a79..ecb3af72 100644 --- 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 index ce6fa603..c0061337 100644 --- 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 index 01a0c9e8..17992dd9 100644 --- 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 index c363a634..50e5b0cb 100644 --- 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 index 92a1b609..02a2482a 100644 --- 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 index b530c221..ea5c31c2 100644 --- 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 index af18b177..af33e13d 100644 --- 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 index 130c5250..a373b8c1 100644 --- 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 index 3a74746d..daaa0762 100644 --- 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 index 85fc390e..ee8d78b2 100644 --- 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 index 2d866bea..d69910df 100644 --- 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 index 806263ac..79edc8ea 100644 --- 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 index b89565d0..ae69ba1d 100644 --- 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 index 40b84278..adf02995 100644 --- 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 index 49a02c06..4f3aa98b 100644 --- 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 index f1eeea7f..907f762d 100644 --- 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 index 71ee21ba..abbe91fe 100644 --- 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 index f358aa00..d4187658 100644 --- 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 index 809e35ea..1b2219d2 100644 --- 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 index 7aba6c8a..4243d482 100644 --- 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 index 51d62189..57555ea9 100644 --- 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/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc index ff72a1f6..a3b76941 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc +++ b/examples/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 index d07d3144..e76b1bb3 100644 --- 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 index edd8a72e..2d935d0e 100644 --- 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 index ecc6378f..86f377f8 100644 --- 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 index 20d274c0..f221aa48 100644 --- 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 index c61362b7..682c5cbc 100644 --- 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 index 5459bc80..537610a3 100644 --- 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 index 2ecdd4e2..334ba0bf 100644 --- 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 index e63c9d31..862ff3a0 100644 --- 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 index 3f68747e..f0cbbcb6 100644 --- 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 index 229ef827..01fc85ae 100644 --- 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 index c4a54466..eb4ca2b5 100644 --- 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 index a340501b..de0e6a63 100644 --- 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 index aab2617f..126033ec 100644 --- 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 index 2846fffc..674ce6de 100644 --- 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 index d6049b93..adcc96ab 100644 --- 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": [] } \ No newline at end of file diff --git a/examples/output_designs/hex_lattice_10x10.sc b/examples/output_designs/hex_lattice_10x10.sc index 5ffb8d2f..70a9ee2a 100644 --- 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 index 1f825bef..4980301b 100644 --- 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 index aec2ccb5..77db916d 100644 --- 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 index 04f6e11a..3a77728e 100644 --- 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 index 45a51367..5ce41929 100644 --- 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 index a54aedfe..286d170f 100644 --- 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 index 045dbed0..6c078e67 100644 --- 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 index ab3bedc9..17459ccf 100644 --- 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]}, diff --git a/examples/output_designs/many_helices_modifications.sc b/examples/output_designs/many_helices_modifications.sc index 6f0f0f4c..0564573a 100644 --- a/examples/output_designs/many_helices_modifications.sc +++ b/examples/output_designs/many_helices_modifications.sc @@ -1,5 +1,5 @@ { - "version": "0.10.1", + "version": "0.11.0", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -12,13 +12,6 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, "/iCy3/": { "display_text": "Cy3", "idt_text": "/iCy3/", @@ -36,6 +29,13 @@ "idt_text": "/5Biosg/", "display_connector": false, "location": "5'" + }, + "/iBiodT/": { + "display_text": "B", + "idt_text": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] } }, "strands": [ diff --git a/examples/output_designs/very_large_origami.sc b/examples/output_designs/very_large_origami.sc index b24e9b11..24a98356 100644 --- a/examples/output_designs/very_large_origami.sc +++ b/examples/output_designs/very_large_origami.sc @@ -1,5 +1,5 @@ { - "version": "0.10.1", + "version": "0.11.0", "grid": "square", "helices": [ {"max_offset": 672, "grid_position": [0, 0]},