From 22d446eced1fccae06974ce84342af9421842e9c Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 15 Dec 2020 18:20:20 -0800 Subject: [PATCH] updated tutorial script (still not completely in line with #154, however, since issue #111 still need to be implemented) --- ...helix_origami_rectangle_twist_corrected.py | 84 - ...helix_origami_rectangle_twist_corrected.sc | 1990 --------------- .../24_helix_rectangle_twist_corrected.sc | 1749 ------------- examples/6_helix_bundle_honeycomb.py | 70 +- .../tutorial-examples/24_helix_rectangle.py | 86 + .../tutorial-examples/24_helix_rectangle.sc | 2182 +++++++++++++++++ .../24_helix_rectangle.xls} | Bin 30208 -> 30208 bytes .../24_helix_rectangle_manual.sc} | 0 scadnano/scadnano.py | 70 +- tests/scadnano_tests.py | 43 +- 10 files changed, 2373 insertions(+), 3901 deletions(-) delete mode 100644 examples/24_helix_origami_rectangle_twist_corrected.py delete mode 100644 examples/24_helix_origami_rectangle_twist_corrected.sc delete mode 100644 examples/24_helix_rectangle_twist_corrected.sc create mode 100644 examples/tutorial-examples/24_helix_rectangle.py create mode 100644 examples/tutorial-examples/24_helix_rectangle.sc rename examples/{24_helix_origami_rectangle_twist_corrected.xls => tutorial-examples/24_helix_rectangle.xls} (57%) rename examples/{24_helix_rectangle.sc => tutorial-examples/24_helix_rectangle_manual.sc} (100%) diff --git a/examples/24_helix_origami_rectangle_twist_corrected.py b/examples/24_helix_origami_rectangle_twist_corrected.py deleted file mode 100644 index 856f0e5b..00000000 --- a/examples/24_helix_origami_rectangle_twist_corrected.py +++ /dev/null @@ -1,84 +0,0 @@ -import scadnano as sc - - -def create_design(): - design = precursor_scaffolds() - add_scaffold_nicks(design) - add_scaffold_crossovers(design) - design.strands[0].set_scaffold() - add_precursor_staples(design) - add_staple_nicks(design) - add_staple_crossovers(design) - add_deletions(design) - design.assign_m13_to_scaffold() - export_idt_plate_file(design) - return design - - -def export_idt_plate_file(design: sc.Design): - for strand in design.strands: - if strand != design.scaffold: - strand.set_default_idt(use_default_idt=True) - design.write_idt_plate_excel_file(use_default_plates=True) - - -def add_deletions(design: sc.Design): - for helix in range(24): - for offset in range(27, 294, 48): - design.add_deletion(helix, offset) - - -def add_staple_crossovers(design: sc.Design): - for helix in range(23): - start_offset = 24 if helix % 2 == 0 else 40 - for offset in range(start_offset, 296, 32): - if offset != 152: # skip crossover near seam - design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, - forward=helix % 2 == 1) - - -def add_staple_nicks(design: sc.Design): - for helix in range(24): - start_offset = 32 if helix % 2 == 0 else 48 - for offset in range(start_offset, 280, 32): - design.add_nick(helix, offset, forward=helix % 2 == 1) - - -def add_precursor_staples(design: sc.Design): - staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)]) - for helix in range(24)] - for staple in staples: - design.add_strand(staple) - - -def precursor_scaffolds() -> sc.Design: - helices = [sc.Helix(max_offset=304) for _ in range(24)] - scaffolds = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 0, start=8, end=296)]) - for helix in range(24)] - return sc.Design(helices=helices, strands=scaffolds, grid=sc.square) - - -def add_scaffold_nicks(design: sc.Design): - for helix in range(1, 24): - design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0) - - -def add_scaffold_crossovers(design: sc.Design): - crossovers = [] - - # scaffold interior - for helix in range(1, 23, 2): - crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=152, forward=False)) - - # scaffold edges - for helix in range(0, 23, 2): - crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=8, forward=True, half=True)) - crossovers.append( - sc.Crossover(helix=helix, helix2=helix + 1, offset=295, forward=True, half=True)) - - design.add_crossovers(crossovers) - - -if __name__ == '__main__': - design = create_design() - design.write_scadnano_file() \ No newline at end of file diff --git a/examples/24_helix_origami_rectangle_twist_corrected.sc b/examples/24_helix_origami_rectangle_twist_corrected.sc deleted file mode 100644 index ecb3af72..00000000 --- a/examples/24_helix_origami_rectangle_twist_corrected.sc +++ /dev/null @@ -1,1990 +0,0 @@ -{ - "version": "0.11.0", - "grid": "square", - "helices": [ - {"max_offset": 304, "grid_position": [0, 0]}, - {"max_offset": 304, "grid_position": [0, 1]}, - {"max_offset": 304, "grid_position": [0, 2]}, - {"max_offset": 304, "grid_position": [0, 3]}, - {"max_offset": 304, "grid_position": [0, 4]}, - {"max_offset": 304, "grid_position": [0, 5]}, - {"max_offset": 304, "grid_position": [0, 6]}, - {"max_offset": 304, "grid_position": [0, 7]}, - {"max_offset": 304, "grid_position": [0, 8]}, - {"max_offset": 304, "grid_position": [0, 9]}, - {"max_offset": 304, "grid_position": [0, 10]}, - {"max_offset": 304, "grid_position": [0, 11]}, - {"max_offset": 304, "grid_position": [0, 12]}, - {"max_offset": 304, "grid_position": [0, 13]}, - {"max_offset": 304, "grid_position": [0, 14]}, - {"max_offset": 304, "grid_position": [0, 15]}, - {"max_offset": 304, "grid_position": [0, 16]}, - {"max_offset": 304, "grid_position": [0, 17]}, - {"max_offset": 304, "grid_position": [0, 18]}, - {"max_offset": 304, "grid_position": [0, 19]}, - {"max_offset": 304, "grid_position": [0, 20]}, - {"max_offset": 304, "grid_position": [0, 21]}, - {"max_offset": 304, "grid_position": [0, 22]}, - {"max_offset": 304, "grid_position": [0, 23]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGT", - "domains": [ - {"helix": 23, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 22, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 21, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 20, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 19, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 18, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 17, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 16, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 15, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 14, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 13, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 12, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 11, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 10, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 9, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 8, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 7, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 6, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 5, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 4, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 3, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 2, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 1, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 0, "forward": true, "start": 8, "end": 296, "deletions": [27, 75, 123, 171, 219, 267]}, - {"helix": 1, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 2, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 3, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 4, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 5, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 6, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 7, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 8, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 9, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 10, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 11, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 12, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 13, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 14, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 15, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 16, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 17, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 18, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 19, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 20, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 21, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 22, "forward": true, "start": 152, "end": 296, "deletions": [171, 219, 267]}, - {"helix": 23, "forward": false, "start": 152, "end": 296, "deletions": [171, 219, 267]} - ], - "is_scaffold": true - }, - { - "sequence": "ATAGTTAGCGTAACGATCTAAAGTTTTGTCGT", - "idt": {"name": "ST0[159]0[128]", "scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 0, "forward": false, "start": 128, "end": 160} - ] - }, - { - "sequence": "GAAGGGAAACCAGTAATAAAAGGGACATTCT", - "idt": {"name": "ST23[144]23[175]", "scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 23, "forward": true, "start": 144, "end": 176, "deletions": [171]} - ] - }, - { - "color": "#f7931e", - "sequence": "TCACGTTGAAAATCTCGCGAATAATAATTTTT", - "idt": {"name": "ST1[8]0[8]", "scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 24}, - {"helix": 0, "forward": false, "start": 8, "end": 24} - ] - }, - { - "sequence": "CCTTTAATGTGAGAATAGAAAGGAACAACTAA", - 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index 961970d0..d4cf539f 100644 --- a/examples/6_helix_bundle_honeycomb.py +++ b/examples/6_helix_bundle_honeycomb.py @@ -1,7 +1,7 @@ import scadnano as sc -def create_design(): +def create_design() -> sc.Design: m13_rotation = 6702 m13_variant = sc.M13Variant.p7560 # print(sc.m13(m13_rotation, m13_variant)) @@ -16,10 +16,9 @@ def create_design(): return design -def initial_design(): +def initial_design() -> sc.Design: max_offset = 1295 helices = [ - # below uses cadnano honeycomb coordinates # https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/master/misc/cadnano-format-specs/v2.txt sc.Helix(grid_position=(1, 1), max_offset=max_offset), @@ -28,38 +27,6 @@ def initial_design(): sc.Helix(grid_position=(1, 2), max_offset=max_offset), sc.Helix(grid_position=(2, 2), max_offset=max_offset), sc.Helix(grid_position=(2, 1), max_offset=max_offset), - - # below uses original mistaken convention from mistaken cadnano specs - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # # below uses odd-q coordinates: - # sc.Helix(grid_position=(1, -1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # below uses even-q coordinates: - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # below uses odd-r coordinates: - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), ] scafs = [ sc.Strand([sc.Domain(helix=0, forward=True, start=16, end=1276)]), @@ -81,7 +48,7 @@ def initial_design(): return sc.Design(helices=helices, strands=strands, grid=sc.honeycomb) -def add_nicks(design: sc.Design): +def add_nicks(design: sc.Design) -> None: design.add_nick(helix=5, offset=399, forward=False) # scaffold for offset in range(56, 1246, 42): design.add_nick(helix=0, offset=offset, forward=False) @@ -94,7 +61,7 @@ def add_nicks(design: sc.Design): design.add_nick(helix=5, offset=offset, forward=True) -def add_crossovers(design: sc.Design): +def add_crossovers(design: sc.Design) -> None: # staples interior for offset in range(84, 1246, 42): design.add_full_crossover(helix=0, helix2=1, offset=offset, forward=False) @@ -115,27 +82,28 @@ def add_crossovers(design: sc.Design): design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False) # scaffold interior - crossovers = [] for offset in range(58, 1250, 42): - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=offset, forward=True)) + design.add_full_crossover(helix=0, helix2=1, offset=offset, forward=True) for offset in range(30, 1250, 42): - crossovers.append(sc.Crossover(helix=1, helix2=2, offset=offset, forward=False)) + design.add_full_crossover(helix=1, helix2=2, offset=offset, forward=False) for offset in range(54, 1250, 42): - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=offset, forward=True)) + design.add_full_crossover(helix=2, helix2=3, offset=offset, forward=True) for offset in range(26, 1250, 42): - crossovers.append(sc.Crossover(helix=3, helix2=4, offset=offset, forward=False)) + design.add_full_crossover(helix=3, helix2=4, offset=offset, forward=False) # scaffold edges - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=16, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=12, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=4, helix2=5, offset=19, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=1275, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=1271, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=4, helix2=5, offset=1278, forward=True, half=True)) + design.add_half_crossover(helix=0, helix2=1, offset=16, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=12, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=19, forward=True) + design.add_half_crossover(helix=0, helix2=1, offset=1275, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=1271, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=1278, forward=True) - design.add_crossovers(crossovers) - -if __name__ == '__main__': +def main() -> None: design = create_design() design.write_scadnano_file(directory='output_designs') + + +if __name__ == '__main__': + main() diff --git a/examples/tutorial-examples/24_helix_rectangle.py b/examples/tutorial-examples/24_helix_rectangle.py new file mode 100644 index 00000000..82439310 --- /dev/null +++ b/examples/tutorial-examples/24_helix_rectangle.py @@ -0,0 +1,86 @@ +import scadnano as sc + + +def main() -> None: + design = create_design() + export_idt_plate_file(design) + design.write_scadnano_file() + + +def create_design() -> sc.Design: + design = helices_only() + + add_scaffold_precursors(design) + add_scaffold_crossovers(design) + + add_staple_precursors(design) + add_staple_crossovers(design) + add_staple_nicks(design) + + add_twist_correction_deletions(design) + design.assign_m13_to_scaffold() + + return design + + +def helices_only() -> sc.Design: + helices = [sc.Helix(max_offset=288) for _ in range(24)] + return sc.Design(helices=helices, grid=sc.square) + + +def add_scaffold_precursors(design: sc.Design) -> None: + for helix in range(0, 23, 2): # scaffold goes forward on even helices + design.strand(helix, 0).move(288).as_scaffold() + for helix in range(1, 23, 2): # scaffold goes reverse on odd helices + design.strand(helix, 288).move(-288).as_scaffold() + design.strand(23, 288).move(-144).as_scaffold() + design.strand(23, 144).move(-144).as_scaffold() + + +def add_scaffold_crossovers(design: sc.Design) -> None: + for helix in range(1, 23, 2): # scaffold interior crossovers + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=144, forward=False) + + for helix in range(0, 23, 2): # scaffold edges crossovers + design.add_half_crossover(helix=helix, helix2=helix + 1, offset=0, forward=True) + design.add_half_crossover(helix=helix, helix2=helix + 1, offset=287, forward=True) + + +def add_staple_precursors(design: sc.Design) -> None: + staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=0, end=288)]) # noqa + for helix in range(24)] + for staple in staples: + design.add_strand(staple) + + +def add_staple_crossovers(design: sc.Design) -> None: + for helix in range(23): + start_offset = 16 if helix % 2 == 0 else 32 + for offset in range(start_offset, 288, 32): + if offset != 144: # skip crossover near seam + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, + forward=helix % 2 == 1) + + +def add_staple_nicks(design: sc.Design) -> None: + for helix in range(24): + start_offset = 24 if helix % 2 == 0 else 40 + for offset in range(start_offset, 272, 32): + design.add_nick(helix, offset, forward=helix % 2 == 1) + + +def add_twist_correction_deletions(design: sc.Design) -> None: + for helix in range(24): + for offset in range(19, 286, 48): + design.add_deletion(helix, offset) + + +def export_idt_plate_file(design: sc.Design) -> None: + for strand in design.strands: + if strand != design.scaffold: + strand.set_default_idt(use_default_idt=True) + design.write_idt_plate_excel_file(use_default_plates=True) + + +if __name__ == '__main__': + main() diff --git a/examples/tutorial-examples/24_helix_rectangle.sc b/examples/tutorial-examples/24_helix_rectangle.sc new file mode 100644 index 00000000..40f3c8fc --- /dev/null +++ b/examples/tutorial-examples/24_helix_rectangle.sc @@ -0,0 +1,2182 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]}, + {"grid_position": [0, 3]}, + {"grid_position": [0, 4]}, + {"grid_position": [0, 5]}, + {"grid_position": [0, 6]}, + {"grid_position": [0, 7]}, + {"grid_position": [0, 8]}, + {"grid_position": [0, 9]}, + {"grid_position": [0, 10]}, + {"grid_position": [0, 11]}, + {"grid_position": [0, 12]}, + {"grid_position": [0, 13]}, + {"grid_position": [0, 14]}, + {"grid_position": [0, 15]}, + {"grid_position": [0, 16]}, + {"grid_position": [0, 17]}, + {"grid_position": [0, 18]}, + {"grid_position": [0, 19]}, + {"grid_position": [0, 20]}, + {"grid_position": [0, 21]}, + {"grid_position": [0, 22]}, + {"grid_position": [0, 23]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGT", + "domains": [ + {"helix": 23, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 22, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 21, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 20, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 19, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 18, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 17, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 16, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 15, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 14, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 13, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 12, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 11, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 10, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 9, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 8, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 7, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 6, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 5, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 4, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 3, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 2, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 1, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 0, "forward": true, "start": 0, "end": 288, "deletions": [19, 67, 115, 163, 211, 259]}, + {"helix": 1, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 2, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 3, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 4, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 5, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 6, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 7, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 8, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 9, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 10, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 11, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 12, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 13, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 14, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 15, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 16, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 17, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 18, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 19, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 20, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 21, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 22, "forward": true, "start": 144, "end": 288, "deletions": [163, 211, 259]}, + {"helix": 23, "forward": false, "start": 144, "end": 288, "deletions": [163, 211, 259]} + ], + "is_scaffold": true + }, + { + "color": "#b8056c", + "sequence": "TCACGTTGAAAATCTCGCGAATAATAATTTTT", + "idt": {"name": "ST1[0]0[0]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16}, + {"helix": 0, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#aaaa00", + "sequence": "CAGAACCGCCACCCTCTCAGAACCGCCACCCT", + "idt": {"name": "ST0[287]1[287]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 0, "forward": false, "start": 272, "end": 288}, + {"helix": 1, "forward": true, "start": 272, "end": 288} + ] + }, + { + "color": "#cc0000", + "sequence": "AGGAAGTTTCCATTAATAAAGACTTTTTCATG", + "idt": {"name": "ST3[0]2[0]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 3, "forward": true, "start": 0, "end": 16}, + {"helix": 2, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#007200", + "sequence": "ATACAGGAGTGTACTGTACATGGCTTTTGATG", + "idt": {"name": "ST2[287]3[287]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 2, "forward": false, "start": 272, "end": 288}, + {"helix": 3, "forward": true, "start": 272, "end": 288} + ] + }, + { + "color": "#f74308", + "sequence": "CAGGCGCATAGGCTGGTGAACGGTGTACAGAC", + "idt": {"name": "ST5[0]4[0]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 5, "forward": true, "start": 0, "end": 16}, + {"helix": 4, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#f7931e", + "sequence": "CGTTTGCCATCTTTTCATAGCCCCCTTATTAG", + "idt": {"name": "ST4[287]5[287]", "scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 4, "forward": false, "start": 272, "end": 288}, + {"helix": 5, "forward": true, "start": 272, "end": 288} + ] + }, + { + "color": "#888888", + "sequence": 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support dropped + """ + :return: The :any:`Strand` that contains this :any:`Loopout`. + """ if self._parent_strand is None: raise ValueError('_parent_strand has not yet been set') return self._parent_strand @@ -1854,6 +1857,14 @@ def from_json(json_map: Dict[str, Any]) -> 'Loopout': # remove quotes when Py3. label = json_map.get(domain_label_key) return Loopout(length=length, name=name, label=label) + def strand(self) -> 'Strand': # remove quotes when Py3.6 support dropped + """ + :return: The :any:`Strand` that contains this :any:`Loopout`. + """ + if self._parent_strand is None: + raise ValueError('_parent_strand has not yet been set') + return self._parent_strand + def __repr__(self) -> str: return f'Loopout(' + \ (f'{self.name}, ' if self.name is not None else '') + \ @@ -2574,20 +2585,7 @@ class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): def __post_init__(self) -> None: self._helix_idx_domain_map = defaultdict(list) - for domain in self.domains: - if isinstance(domain, Domain): - self._helix_idx_domain_map[domain.helix].append(domain) - - for domain in self.domains: - domain._parent_strand = self - - if len(self.domains) == 1: - if isinstance(self.domains[0], Loopout): - raise StrandError(self, 'strand cannot have a single Loopout as its only domain') - - for domain1, domain2 in _pairwise(self.domains): - if isinstance(domain1, Loopout) and isinstance(domain2, Loopout): - raise StrandError(self, 'cannot have two consecutive Loopouts in a strand') + self.set_domains(self.domains) if self.use_default_idt: self.set_default_idt(True) @@ -2750,6 +2748,44 @@ def set_linear(self) -> None: """ self.set_circular(False) + def set_domains(self, domains: Iterable[Union[Domain[DomainLabel], Loopout]]) -> None: + """ + Sets the :any:`Domain`'s/:any:`Loopout`'s of this :any:`Strand` to be `domains`, + which can contain a mix of :any:`Domain`'s and :any:`Loopout`'s, + just like the field :py:data:`Strand.domains`. + + :param domains: + The new sequence of :any:`Domain`'s/:any:`Loopout`'s to use for this :any:`Strand`. + :raises StrandError: + if domains has two consecutive :any:`Loopout`'s, consists of just a single :any:`Loopout`'s, + or starts or ends with a :any:`Loopout` + """ + self.domains = domains + + for domain in self.domains: + if isinstance(domain, Domain): + self._helix_idx_domain_map[domain.helix].append(domain) + + for domain in self.domains: + domain._parent_strand = self + + if len(self.domains) == 1: + if isinstance(self.domains[0], Loopout): + raise StrandError(self, 'strand cannot have a single Loopout as its only domain') + + if len(self.domains) == 0: + raise StrandError(self, 'domains cannot be empty') + + for domain1, domain2 in _pairwise(self.domains): + if isinstance(domain1, Loopout) and isinstance(domain2, Loopout): + raise StrandError(self, 'cannot have two consecutive Loopouts in a strand') + + if isinstance(self.domains[0], Loopout): + raise StrandError(self, 'strand cannot begin with a loopout') + + if isinstance(self.domains[-1], Loopout): + raise StrandError(self, 'strand cannot end with a loopout') + def set_default_idt(self, use_default_idt: bool = True, skip_scaffold: bool = True, unique_names: bool = False) -> None: """ @@ -5426,7 +5462,7 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru if strand.circular: # if strand is circular, we modify its domains in place domains = domains_after + domains_before - strand.domains = domains + strand.set_domains(domains) # DNA sequence was rotated, so re-assign it if seq_before_whole is not None and seq_after_whole is not None: @@ -5960,13 +5996,13 @@ class Crossover: forward: bool """direction of :any:`Strand` on `helix` to which to add half crossover""" - offset2: int + offset2: Optional[int] = None """ offset on `helix2` at which to add half crossover. If not specified, defaults to `offset` """ - forward2: bool + forward2: Optional[bool] = None """ direction of :any:`Strand` on `helix2` to which to add half crossover. If not specified, defaults to the negation of `forward` diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 4fefa46b..9d3289f1 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3496,10 +3496,12 @@ def test_consecutive_domains_loopout(self) -> None: with self.assertRaises(sc.IllegalDesignError): sc.Strand([ss1, ss2, ss3]) - strand = sc.Strand([ss1, ss2]) - strand.domains.append(ss3) - with self.assertRaises(sc.IllegalDesignError): - sc.Design(helices=helices, strands=[strand], grid=sc.square) + #XXX: we used to allow Strands to violate the loopout rules and caught it only at the design level + # now the Strand constructor checks, so that means we can't set up a bad Strand for the Design check + # strand = sc.Strand([ss1, ss2]) + # strand.domains.append(ss3) + # with self.assertRaises(sc.IllegalDesignError): + # sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_singleton_loopout(self) -> None: helices = [sc.Helix(max_offset=10)] @@ -3507,10 +3509,12 @@ def test_singleton_loopout(self) -> None: with self.assertRaises(sc.StrandError): sc.Strand([loopout]) - strand = sc.Strand([]) - strand.domains.append(loopout) - with self.assertRaises(sc.StrandError): - sc.Design(helices=helices, strands=[strand], grid=sc.square) + # XXX: we used to allow Strands to violate the loopout rules and caught it only at the design level + # now the Strand constructor checks, so that means we can't set up a bad Strand for the Design check + # strand = sc.Strand([]) + # strand.domains.append(loopout) + # with self.assertRaises(sc.StrandError): + # sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_strand_offset_beyond_maxbases(self) -> None: helices = [sc.Helix(max_offset=10)] @@ -3864,6 +3868,9 @@ def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_first_domain( self.assertEqual(40, d2.start) self.assertEqual(45, d2.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_second_domain(self) -> None: # nick strand 5 r''' @@ -3897,6 +3904,9 @@ def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_second_domain self.assertEqual(45, d2.start) self.assertEqual(50, d2.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain(self) -> None: # nick strand 4 r''' @@ -3939,6 +3949,9 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain( self.assertEqual(30, d3.start) self.assertEqual(35, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain(self) -> None: # nick strand 4 r''' @@ -3981,6 +3994,9 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain self.assertEqual(35, d3.start) self.assertEqual(40, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(self) -> None: # nick strand 4 r''' @@ -4023,15 +4039,22 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(s self.assertEqual(30, d3.start) self.assertEqual(35, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_ligate_linear_strand_to_itself_makes_it_circular(self) -> None: self.assertFalse(self.design.strands[1].circular) self.assertEqual(3, len(self.design.strands[1].domains)) self.design.ligate(0, 15, True) + strand = self.design.strands[1] self.assertEqual(self.num_strands, len(self.design.strands)) - self.assertTrue(self.design.strands[1].circular) - self.assertEqual(2, len(self.design.strands[1].domains)) + self.assertTrue(strand.circular) + self.assertEqual(2, len(strand.domains)) + + for domain in strand.domains: + self.assertIs(strand, domain.strand()) #TODO: add functionality for removing crossovers and loopouts, and test that here