def create_design() -> sc.Design:
design = rect.create(num_helices=16,
num_cols=28,
seam_left_column=12,
assign_seq=False,
num_flanking_columns=2,
num_flanking_helices=2,
edge_staples=False,
scaffold_nick_offset=102)
# # need this to match original design, but doesn't leave room for left-side adapters
# design.move_strand_offsets(8)
set_helix_major_tickets(design)
move_top_and_bottom_staples_within_column_boundaries(design)
add_domains_for_barrel_seam(design)
add_toeholds_for_seam_displacement(design)
add_adapters(design)
add_twist_correct_deletions(design)
add_angle_inducing_insertions_deletions(design)
add_tiles_and_assign_dna(design)
assign_dna_to_unzipper_toeholds(design)
design.assign_m13_to_scaffold()
return design
def create_design():
design = rect.create(num_helices=16,
num_cols=26,
assign_seq=False,
twist_correction_deletion_spacing=3,
twist_correction_start_col=2)
return design
def main():
design = rect.create(num_helices=6,
num_cols=10,
nick_pattern=rect.staggered,
twist_correction_deletion_spacing=3)
design.set_helices_view_order([5, 4, 3, 2, 1, 0])
return design
def create_design() -> sc.Design:
design = rect.create(num_helices=16, num_cols=28, seam_left_column=12, assign_seq=False,
num_flanking_columns=2, edge_staples=False,
scaffold_nick_offset=102)
design.set_major_tick_distance(8)
adjust_helix_grid_and_positions(design)
move_top_and_bottom_staples_within_column_boundaries(design)
add_domains_for_barrel_seam(design)
add_twist_correct_deletions(design)
add_angle_inducing_insertions_deletions(design)
design.set_helices_view_order(list(reversed(range(16))))
design.set_default_idt()
design.assign_m13_to_scaffold()
return design
def main():
design = rect.create(num_helices=16,
num_cols=28,
seam_left_column=12,
assign_seq=False,
num_flanking_columns=2,
num_flanking_helices=2,
edge_staples=False,
scaffold_nick_offset=102)
# # need this to match original design, but doesn't leave room for left-side adapters
# design.move_strand_offsets(8)
set_helix_major_ticks(design)
# move_top_and_bottom_staples_within_column_boundaries(design)
# add_adapters(design)
# add_twist_correct_deletions(design)
# add_tiles_and_assign_dna(design)
design.assign_m13_to_scaffold()
return design
def main():
design = rect.create(num_helices=16,
num_cols=26,
assign_seq=False,
seam_left_column=2)
return design
def create_design() -> sc.Design:
return rect.create(num_helices=64, num_cols=6)
def create_design() -> sc.Design:
return rect.create(num_helices=56, num_cols=8, seam_left_column=4)
def main():
design = rect.create(num_helices=6, num_cols=10, nick_pattern=rect.staggered, twist_correction_deletion_spacing=3)
return design
def main():
# this is a very large origami (taking ~25,000 bases). It is useful for testing the performance of
# rendering code, since at the time it was created, it is very janky to update, particularly for
# things that edit strands such as adding a strand or adding a nick in a strand
design = rect.create(num_helices=40, num_cols=40)
return design
def main():
design = rect.create(num_helices=56, num_cols=8, seam_left_column=4)
return design
def create_design() -> sc.Design:
design = rect.create(num_helices=6, num_cols=6, num_flanking_columns=0)
return design
def create_design():
design = rect.create(num_helices=16, num_cols=26)
return design
def create_design() -> sc.Design:
return rect.create(num_helices=16, num_cols=26, assign_seq=False, seam_left_column=2)
def main():
design = rect.create(num_helices=16,
num_cols=26,
assign_seq=True,
twist_correction_deletion_spacing=3)
return design
def create_design() -> sc.Design:
return rect.create(num_helices=16,
num_cols=26,
assign_seq=True,
twist_correction_deletion_spacing=3)
def create_design():
design = rect.create(num_helices=16, num_cols=26, use_idt_defaults=True)
return design
def create_design():
design = rect.create(num_helices=16, num_cols=26, assign_seq=False)
return design
def main():
design = rect.create(num_helices=64, num_cols=6)
return design
def main():
design = rect.create(num_helices=6, num_cols=6, num_flanking_columns=0)
return design
