names_domains_strands.py

import scadnano as sc


def create_design() -> sc.Design:
    num_domains = 9
    helices = [sc.Helix(max_offset=(num_domains) * 8)]
    design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square)
    design.draw_strand(0, (num_domains - 1) * 8) \
        .move(-8).with_domain_name('domain 8*') \
        .move(-8).with_domain_name('domain 7*') \
        .move(-8).with_domain_name('domain 6*') \
        .move(-8).with_domain_name('domain 5*') \
        .move(-8).with_domain_name('domain 4*') \
        .move(-8).with_domain_name('domain 3*') \
        .move(-8).with_domain_name('domain 2*') \
        .move(-8).with_domain_name('domain 1*') \
        .with_name('bottom strand')

    # domain names match
    design.draw_strand(0, 0).move(8).with_domain_name('domain 1').with_name('top strand 1')

    # domains are aligns but names mismatch
    design.draw_strand(0, 8).move(8).with_domain_name('domain 50').with_name('top strand 2')

    # domain names match
    design.draw_strand(0, 16).move(8).with_domain_name('domain 3').with_name('top strand 3')

    # domain names are the same, not complementary
    design.draw_strand(0, 24).move(8).with_domain_name('domain 4*').with_name('top strand 4')

    # domain names match but domains are mis-aligned
    design.draw_strand(0, 32).move(9).with_domain_name('domain 5').with_name('top strand 5')

    # domain names match but domains are mis-aligned
    design.draw_strand(0, 48).move(7).with_domain_name('domain 7').with_name('top strand 7')

    # no overlap so no mismatch
    design.draw_strand(0, 64).move(8).with_domain_name('domain 9').with_name('top strand 9')

    return design


if __name__ == '__main__':
    d = create_design()
    d.write_scadnano_file(directory='output_designs')