From 054a8bf0f96bbd66e13050cce5c262da3482d0ec Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 11 Jul 2020 15:13:10 -0700 Subject: [PATCH] updated examples to v0.9.9 --- ...igami_deletions_insertions_new_geometry.py | 2 +- ...elix_origami_barrel_from_algoSST_paper.dna | 2 +- .../16_helix_origami_rectangle.dna | 2 +- .../16_helix_origami_rectangle_idt.dna | 2 +- .../16_helix_origami_rectangle_no_seq.dna | 2 +- ...elix_origami_rectangle_no_seq_no_twist.dna | 2 +- .../16_helix_origami_rectangle_no_twist.dna | 2 +- ...ami_rectangle_seed_tiles_grow_from_top.dna | 2 +- ..._origami_rectangle_shifted_seam_no_seq.dna | 2 +- .../1_staple_1_helix_origami.dna | 2 +- .../1_staple_1_helix_origami_mismatches.dna | 2 +- ...le_1_helix_origami_position_nondefault.dna | 2 +- .../1_staple_1_helix_origami_roll.dna | 2 +- ...elix_origami_rectangle_twist_corrected.dna | 2 +- ...x_2_strands_multiple_substrands_no_seq.dna | 2 +- .../2_staple_2_helix_modifications.dna | 38 +++++++++---------- .../2_staple_2_helix_origami_6bases_wide.dna | 2 +- .../2_staple_2_helix_origami_deletions.dna | 2 +- ...e_2_helix_origami_deletions_insertions.dna | 2 +- ...ix_origami_deletions_insertions_labels.dna | 2 +- ...elix_origami_deletions_insertions_mods.dna | 2 +- ...etions_insertions_mods_chained_methods.dna | 2 +- ...gami_deletions_insertions_new_geometry.dna | 4 +- ...ix_origami_deletions_insertions_no_seq.dna | 2 +- .../3_helix_deletions_insertions.dna | 2 +- examples/output_designs/4_helix_grid_none.dna | 2 +- ..._none_min_offset_position_x_nondefault.dna | 2 +- .../4_helix_min_offsets_nonzero.dna | 2 +- .../56_helix_origami_rectangle.dna | 2 +- .../64_helix_origami_rectangle.dna | 2 +- .../6_helix_6_col_origami_rectangle.dna | 2 +- .../6_helix_bundle_honeycomb.dna | 2 +- .../6_helix_origami_rectangle.dna | 2 +- ...origami_rectangle_helices_out_of_order.dna | 2 +- .../add_deletions_to_24_helix_rectangle.dna | 2 +- examples/output_designs/empty.dna | 2 +- examples/output_designs/hairpin.dna | 2 +- .../helices_out_of_order_nonconsecutive.dna | 2 +- examples/output_designs/hex_lattice_10x10.dna | 2 +- .../hex_lattice_10x10_with_negative.dna | 2 +- .../honeycomb_lattice_10x10.dna | 2 +- .../honeycomb_lattice_10x10_with_negative.dna | 2 +- .../output_designs/idt-plates-explicit.dna | 2 +- .../output_designs/long_range_crossovers.dna | 2 +- .../output_designs/loopouts_all_types.dna | 2 +- examples/output_designs/many_big_helices.dna | 2 +- .../many_helices_modifications.dna | 14 +++---- examples/output_designs/proposal.dna | 2 +- examples/output_designs/sst-motif-3_2.dna | 2 +- examples/output_designs/sst-motif-4_1.dna | 2 +- .../output_designs/very_large_origami.dna | 2 +- ...st_16_helix_origami_rectangle_no_twist.dna | 2 +- ...e_2_helix_origami_deletions_insertions.dna | 2 +- ...stape_2_helix_origami_extremely_simple.dna | 2 +- ...ape_2_helix_origami_extremely_simple_2.dna | 2 +- .../test_6_helix_origami_rectangle.dna | 2 +- 56 files changed, 81 insertions(+), 81 deletions(-) diff --git a/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py b/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py index 30e3ca26..bd30a948 100644 --- a/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py +++ b/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py @@ -23,7 +23,7 @@ def main(): scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True) # geometry - geometry = sc.Geometry(z_step=0.2, helix_radius=1.2, inter_helix_gap=1.0) + geometry = sc.Geometry(rise_per_base_pair=0.2, helix_radius=1.2, inter_helix_gap=1.0) # whole design design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square, diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna index c9e4445d..d7185a81 100644 --- a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna +++ b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ { diff --git a/examples/output_designs/16_helix_origami_rectangle.dna b/examples/output_designs/16_helix_origami_rectangle.dna index 8a58b0c8..63901a62 100644 --- a/examples/output_designs/16_helix_origami_rectangle.dna +++ b/examples/output_designs/16_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.dna b/examples/output_designs/16_helix_origami_rectangle_idt.dna index d1b5569c..1e5009d6 100644 --- a/examples/output_designs/16_helix_origami_rectangle_idt.dna +++ b/examples/output_designs/16_helix_origami_rectangle_idt.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna index e65aceb2..274a172f 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna index 9aeca60e..cffdf3f0 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna index 907dfc40..074e6257 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "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.dna b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna index 4c71ecdd..3cd28b7e 100644 --- a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna +++ b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ { diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna index f9ff0b84..b1711a66 100644 --- a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/1_staple_1_helix_origami.dna b/examples/output_designs/1_staple_1_helix_origami.dna index c940a532..30b36a04 100644 --- a/examples/output_designs/1_staple_1_helix_origami.dna +++ b/examples/output_designs/1_staple_1_helix_origami.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ { diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna index d79aeea3..e73f415c 100644 --- a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna +++ b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]} diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna index 3a814be1..aefd4fc6 100644 --- a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna +++ b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ { diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.dna b/examples/output_designs/1_staple_1_helix_origami_roll.dna index e41f6827..42f91dc5 100644 --- a/examples/output_designs/1_staple_1_helix_origami_roll.dna +++ b/examples/output_designs/1_staple_1_helix_origami_roll.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0], "roll": 90} diff --git a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna index c9211bb4..29ff1df3 100644 --- a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna +++ b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 304, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna index ca6f8090..a0ebc48d 100644 --- a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna +++ b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index 2b0f047b..9ebcaf32 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -1,22 +1,28 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, {"grid_position": [0, 1]} ], "modifications_in_design": { - "/5Cy5/": { + "/iCy5/": { "display_text": "Cy5", - "idt_text": "/5Cy5/", + "idt_text": "/iCy5/", "display_connector": false, - "location": "5'" + "location": "internal" }, - "/3Bio/": { + "/5Biosg/": { "display_text": "B", - "idt_text": "/3Bio/", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "3'" + "location": "5'" + }, + "/5Cy5/": { + "display_text": "Cy5", + "idt_text": "/5Cy5/", + "display_connector": false, + "location": "5'" }, "/iBiodT/": { "display_text": "B", @@ -25,18 +31,6 @@ "location": "internal", "allowed_bases": ["T"] }, - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - }, "/iCy3/": { "display_text": "Cy3", "idt_text": "/iCy3/", @@ -48,6 +42,12 @@ "idt_text": "/3Cy3Sp/", "display_connector": false, "location": "3'" + }, + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", + "display_connector": false, + "location": "3'" } }, "strands": [ diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna index b04218ba..7ad405f7 100644 --- a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna +++ b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions.dna index d4a07656..afcc9f58 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna index 29295ec1..da79fb7d 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 48, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna index 2dd4b33b..ee15c48d 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 48, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna index a186cda3..b364a16e 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "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.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna index f3267f9d..b088c0f6 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "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.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna index f051a64a..2f85553e 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna @@ -1,8 +1,8 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "geometry": { - "z_step": 0.2, + "rise_per_base_pair": 0.2, "helix_radius": 1.2, "inter_helix_gap": 1.0 }, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna index efb1f765..9638d6b2 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna index f065f31b..a369e09e 100644 --- a/examples/output_designs/3_helix_deletions_insertions.dna +++ b/examples/output_designs/3_helix_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 64, "grid_position": [0, 0]}, diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna index 6e420fe7..c764c0e9 100644 --- a/examples/output_designs/4_helix_grid_none.dna +++ b/examples/output_designs/4_helix_grid_none.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "none", "helices": [ { 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 index 9400da45..437e231f 100644 --- 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 @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "none", "helices": [ { diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna index f21827d9..680a7b55 100644 --- a/examples/output_designs/4_helix_min_offsets_nonzero.dna +++ b/examples/output_designs/4_helix_min_offsets_nonzero.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 30, "grid_position": [0, 0]}, diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna index aeaa2cda..4cbc15ec 100644 --- a/examples/output_designs/56_helix_origami_rectangle.dna +++ b/examples/output_designs/56_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 160, "grid_position": [0, 0]}, diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna index ba774cef..e05e013a 100644 --- a/examples/output_designs/64_helix_origami_rectangle.dna +++ b/examples/output_designs/64_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 128, "grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna index d6aacd04..29b8a4d4 100644 --- a/examples/output_designs/6_helix_6_col_origami_rectangle.dna +++ b/examples/output_designs/6_helix_6_col_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna index 9592fa96..f769efd1 100644 --- a/examples/output_designs/6_helix_bundle_honeycomb.dna +++ b/examples/output_designs/6_helix_bundle_honeycomb.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "honeycomb", "helices": [ {"max_offset": 1295, "grid_position": [1, 1, 0]}, diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna index c33f6377..41aabd46 100644 --- a/examples/output_designs/6_helix_origami_rectangle.dna +++ b/examples/output_designs/6_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna index a9cb37d5..914c64c5 100644 --- a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna +++ b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]}, diff --git a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna index d2875005..9ed0698c 100644 --- a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna +++ b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "e", "helices": [ {"max_offset": 304, "grid_position": [0, -3]}, diff --git a/examples/output_designs/empty.dna b/examples/output_designs/empty.dna index 13fe4dfd..cc1b4601 100644 --- a/examples/output_designs/empty.dna +++ b/examples/output_designs/empty.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [], "strands": [] diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna index 16306317..363bfb8f 100644 --- a/examples/output_designs/hairpin.dna +++ b/examples/output_designs/hairpin.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]} diff --git a/examples/output_designs/helices_out_of_order_nonconsecutive.dna b/examples/output_designs/helices_out_of_order_nonconsecutive.dna index 10a971a3..25ef8580 100644 --- a/examples/output_designs/helices_out_of_order_nonconsecutive.dna +++ b/examples/output_designs/helices_out_of_order_nonconsecutive.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "none", "helices": [ {"max_offset": 20, "grid_position": [0, 2], "idx": 2}, diff --git a/examples/output_designs/hex_lattice_10x10.dna b/examples/output_designs/hex_lattice_10x10.dna index 629d3227..ff4f2aee 100644 --- a/examples/output_designs/hex_lattice_10x10.dna +++ b/examples/output_designs/hex_lattice_10x10.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "hex", "helices": [ {"max_offset": 16, "grid_position": [0, 0, 0]}, diff --git a/examples/output_designs/hex_lattice_10x10_with_negative.dna b/examples/output_designs/hex_lattice_10x10_with_negative.dna index cfc61094..b26b5821 100644 --- a/examples/output_designs/hex_lattice_10x10_with_negative.dna +++ b/examples/output_designs/hex_lattice_10x10_with_negative.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "hex", "helices": [ {"max_offset": 16, "grid_position": [-4, -4, 0]}, diff --git a/examples/output_designs/honeycomb_lattice_10x10.dna b/examples/output_designs/honeycomb_lattice_10x10.dna index a24f2649..f9e0d614 100644 --- a/examples/output_designs/honeycomb_lattice_10x10.dna +++ b/examples/output_designs/honeycomb_lattice_10x10.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "honeycomb", "helices": [ {"max_offset": 16, "grid_position": [0, 0, 0]}, diff --git a/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna b/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna index c7426ac3..ff21b834 100644 --- a/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna +++ b/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "honeycomb", "helices": [ {"max_offset": 16, "grid_position": [-4, -4, 0]}, diff --git a/examples/output_designs/idt-plates-explicit.dna b/examples/output_designs/idt-plates-explicit.dna index cef66c11..3a8cb953 100644 --- a/examples/output_designs/idt-plates-explicit.dna +++ b/examples/output_designs/idt-plates-explicit.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/long_range_crossovers.dna b/examples/output_designs/long_range_crossovers.dna index dd9abbee..b53ad433 100644 --- a/examples/output_designs/long_range_crossovers.dna +++ b/examples/output_designs/long_range_crossovers.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/loopouts_all_types.dna b/examples/output_designs/loopouts_all_types.dna index f2d7c0ac..643b6148 100644 --- a/examples/output_designs/loopouts_all_types.dna +++ b/examples/output_designs/loopouts_all_types.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/many_big_helices.dna b/examples/output_designs/many_big_helices.dna index 38d7035c..3557a203 100644 --- a/examples/output_designs/many_big_helices.dna +++ b/examples/output_designs/many_big_helices.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 2000, "grid_position": [0, 0]}, diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index 1ca606cb..5161d523 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -12,11 +12,11 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/3Cy3Sp/": { + "/iCy3/": { "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "idt_text": "/iCy3/", "display_connector": false, - "location": "3'" + "location": "internal" }, "/5Biosg/": { "display_text": "B", @@ -24,11 +24,11 @@ "display_connector": false, "location": "5'" }, - "/iCy3/": { + "/3Cy3Sp/": { "display_text": "Cy3", - "idt_text": "/iCy3/", + "idt_text": "/3Cy3Sp/", "display_connector": false, - "location": "internal" + "location": "3'" }, "/iBiodT/": { "display_text": "B", diff --git a/examples/output_designs/proposal.dna b/examples/output_designs/proposal.dna index e47a19ee..6b1949e7 100644 --- a/examples/output_designs/proposal.dna +++ b/examples/output_designs/proposal.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "none", "helices": [ { diff --git a/examples/output_designs/sst-motif-3_2.dna b/examples/output_designs/sst-motif-3_2.dna index 477375f2..037141b3 100644 --- a/examples/output_designs/sst-motif-3_2.dna +++ b/examples/output_designs/sst-motif-3_2.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "major_tick_distance": 10, "helices": [ diff --git a/examples/output_designs/sst-motif-4_1.dna b/examples/output_designs/sst-motif-4_1.dna index fc358406..efb7f83b 100644 --- a/examples/output_designs/sst-motif-4_1.dna +++ b/examples/output_designs/sst-motif-4_1.dna @@ -1,5 +1,5 @@ { - "version": "0.9.1", + "version": "0.9.9", "grid": "square", "major_tick_distance": 10, "helices": [ diff --git a/examples/output_designs/very_large_origami.dna b/examples/output_designs/very_large_origami.dna index aa51b36a..02908eb9 100644 --- a/examples/output_designs/very_large_origami.dna +++ b/examples/output_designs/very_large_origami.dna @@ -1,5 +1,5 @@ { - "version": "0.9.6", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 672, "grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index 3d32454d..074e6257 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.3", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index e180d5a2..b085f97d 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.3", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna index 46694d67..f1591484 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna @@ -1,5 +1,5 @@ { - "version": "0.9.3", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna index 5b4b8236..7672ed35 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna @@ -1,5 +1,5 @@ { - "version": "0.9.3", + "version": "0.9.9", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index 77191d25..41aabd46 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.3", + "version": "0.9.9", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]},