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Merge pull request #250 from UC-Davis-molecular-computing/dev
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Dev
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dave-doty authored Nov 30, 2022
2 parents 724a4a8 + 8e78237 commit 786c809
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2 changes: 1 addition & 1 deletion .github/workflows/run_unit_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.6, 3.7, 3.8, 3.9]
python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]

steps:
- uses: actions/checkout@v2
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29 changes: 29 additions & 0 deletions examples/extension_and_loopout_oxdna_export.py
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@@ -0,0 +1,29 @@
import scadnano as sc


def main() -> None:
d = create_design()
d.write_scadnano_file(directory='output_designs')
d.write_oxdna_files(directory='oxdna')


def create_design() -> sc.Design:
width = 21
helices = [sc.Helix(max_offset=32) for _ in range(3)]
helices[0].roll = 210
helices[1].roll = 20
helices[2].roll = 210
design = sc.Design(helices=helices, grid=sc.square)

design.draw_strand(0, 0).extension_5p(5) \
.move(width) \
.cross(1).move(-width) \
.loopout(2, 32) \
.move(width) \
.extension_3p(7)

return design


if __name__ == '__main__':
main()
33 changes: 25 additions & 8 deletions examples/extensions.py
Original file line number Diff line number Diff line change
@@ -1,22 +1,39 @@
import scadnano as sc


def main() -> None:
d = create_design()
d.write_scadnano_file(directory='output_designs')
d.write_oxdna_files(directory='oxdna')


def create_design() -> sc.Design:
width = 8
helices = [sc.Helix(max_offset=32) for _ in range(3)]
design = sc.Design(helices=helices, grid=sc.square)
helices[2].roll = 30

design.draw_strand(0, 0).extension_5p(5, display_length=2.5, display_angle=45)\
.move(width).cross(1).move(-width).loopout(2, 3).move(width)\
.extension_3p(7).with_domain_name("ext_3p")
design.draw_strand(0, 0).extension_5p(5, display_length=2.5, display_angle=45) \
.with_domain_name("ext_5p 1") \
.move(width).with_domain_name('domain 1') \
.cross(1).move(-width) \
.loopout(2, 3).with_domain_name('loopout 1') \
.move(width) \
.extension_3p(7).with_domain_name("ext_3p 1") \
.with_name('strand1') \
.with_sequence('TATTT' + 'G' * width + 'C' * width + 'T' * 3 + 'G' * width + 'ATAAAAA') \
.with_modification_5p(sc.cy5_5p) \
.with_modification_3p(sc.cy3_3p)

design.draw_strand(0, 24).extension_5p(5, display_length=3.5, display_angle=60)\
.move(-width).cross(1).move(width).loopout(2, 3).move(-width)\
.extension_3p(7).with_domain_name("ext_3p_top")
design.draw_strand(0, 24).extension_5p(5, display_length=3.5, display_angle=60) \
.with_domain_name("ext_5p 2") \
.move(-width).cross(1).move(width).loopout(2, 3).move(-width) \
.extension_3p(7).with_domain_name("ext_3p 2") \
.with_name('strand2') \
.with_sequence('ATAAA' + 'C' * width + 'G' * width + 'A' * 3 + 'C' * width + 'TATTTTT') \

return design


if __name__ == '__main__':
d = create_design()
d.write_scadnano_file(directory='output_designs')
main()
22 changes: 22 additions & 0 deletions examples/output_designs/extension_and_loopout_oxdna_export.sc
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@@ -0,0 +1,22 @@
{
"version": "0.17.6",
"grid": "square",
"helices": [
{"max_offset": 32, "grid_position": [0, 0], "roll": 210},
{"max_offset": 32, "grid_position": [0, 1], "roll": 20},
{"max_offset": 32, "grid_position": [0, 2], "roll": 210}
],
"strands": [
{
"color": "#f74308",
"domains": [
{"extension_num_bases": 5},
{"helix": 0, "forward": true, "start": 0, "end": 21},
{"helix": 1, "forward": false, "start": 0, "end": 21},
{"loopout": 32},
{"helix": 2, "forward": true, "start": 0, "end": 21},
{"extension_num_bases": 7}
]
}
]
}
38 changes: 29 additions & 9 deletions examples/output_designs/extensions.sc
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@@ -1,32 +1,52 @@
{
"version": "0.17.3",
"version": "0.17.5",
"grid": "square",
"helices": [
{"max_offset": 32, "grid_position": [0, 0]},
{"max_offset": 32, "grid_position": [0, 1]},
{"max_offset": 32, "grid_position": [0, 2]}
{"max_offset": 32, "grid_position": [0, 2], "roll": 30}
],
"modifications_in_design": {
"/3Cy3Sp/": {
"display_text": "Cy3",
"idt_text": "/3Cy3Sp/",
"display_connector": false,
"location": "3'"
},
"/5Cy5/": {
"display_text": "Cy5",
"idt_text": "/5Cy5/",
"display_connector": false,
"location": "5'"
}
},
"strands": [
{
"name": "strand1",
"color": "#f74308",
"sequence": "TATTTGGGGGGGGCCCCCCCCTTTGGGGGGGGATAAAAA",
"domains": [
{"extension_num_bases": 5, "display_length": 2.5},
{"helix": 0, "forward": true, "start": 0, "end": 8},
{"extension_num_bases": 5, "display_length": 2.5, "name": "ext_5p 1"},
{"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8},
{"helix": 1, "forward": false, "start": 0, "end": 8},
{"loopout": 3},
{"loopout": 3, "name": "loopout 1"},
{"helix": 2, "forward": true, "start": 0, "end": 8},
{"extension_num_bases": 7, "name": "ext_3p"}
]
{"extension_num_bases": 7, "name": "ext_3p 1"}
],
"5prime_modification": "/5Cy5/",
"3prime_modification": "/3Cy3Sp/"
},
{
"name": "strand2",
"color": "#57bb00",
"sequence": "ATAAACCCCCCCCGGGGGGGGAAACCCCCCCCTATTTTT",
"domains": [
{"extension_num_bases": 5, "display_length": 3.5, "display_angle": 60},
{"extension_num_bases": 5, "display_length": 3.5, "display_angle": 60, "name": "ext_5p 2"},
{"helix": 0, "forward": false, "start": 16, "end": 24},
{"helix": 1, "forward": true, "start": 16, "end": 24},
{"loopout": 3},
{"helix": 2, "forward": false, "start": 16, "end": 24},
{"extension_num_bases": 7, "name": "ext_3p_top"}
{"extension_num_bases": 7, "name": "ext_3p 2"}
]
}
]
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110 changes: 110 additions & 0 deletions examples/oxdna/extension_and_loopout_oxdna_export.dat
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@@ -0,0 +1,110 @@
t = 0
b = 27.636671979913565 27.636671979913565 27.636671979913565
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