Merge pull request #129 from UC-Davis-molecular-computing/dev

Dev

examples/24_helix_origami_rectangle_twist_corrected.py

@@ -5,8 +5,7 @@ def create_design():
     design = precursor_scaffolds()
     add_scaffold_nicks(design)
     add_scaffold_crossovers(design)
-    scaffold = design.strands[0]
-    scaffold.set_scaffold()
+    design.strands[0].set_scaffold()
     add_precursor_staples(design)
     add_staple_nicks(design)
     add_staple_crossovers(design)
@@ -82,4 +81,4 @@ def add_scaffold_crossovers(design: sc.Design):
 
 if __name__ == '__main__':
     design = create_design()
-    design.write_scadnano_file()
+    design.write_scadnano_file()

examples/flatish_sst_ribbon.py

@@ -0,0 +1,162 @@
+import argparse
+
+import scadnano as sc
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description='Create a scadnano design for a flat(ish) SST zig-zag ribbon of a specified width.')
+    upper_limit_width = 50
+    parser.add_argument('-w', '--width', required=True, type=int,
+                        help='width of ribbon (number of tiles in one zig or one zag); '
+                             f'must be even number between 4 and {upper_limit_width}',
+                        choices=range(4, upper_limit_width + 1, 2))
+    parser.add_argument('-d', '--duple', action='store_true',
+                        help='whether to use duples (double-tiles) to turn direction; '
+                             'otherwise 1.5-tiles are used')
+    args = parser.parse_args()
+    width: int = args.width
+    duple: bool = args.duple
+    design = create_design(width=width, duple=duple)
+    print(design.to_json())
+    design.write_scadnano_file(directory='output_designs')
+
+
+def create_design(width: int, duple: bool) -> sc.Design:
+    helices = [sc.Helix() for _ in range(width + 4)]
+    design = sc.Design(helices=helices, grid=sc.Grid.none)
+
+    add_tick_marks(design)
+    add_zig_tiles(design, width)
+    add_zag_tiles(design, width)
+    add_zig_seed_tiles(design, width)
+    add_duples(design, width, duple)
+    add_seed(design, width)
+
+    return design
+
+
+def add_tick_marks(design: sc.Design) -> None:
+    num_helices = len(design.helices)
+    for idx, helix in design.helices.items():
+        tick_start = num_helices - idx - 2
+        if tick_start % 2 == 1:
+            tick_start += 1
+        helix.major_tick_start = tick_start
+        helix.major_tick_periodic_distances = [12, 9] if idx % 2 == 0 else [10, 11]
+
+
+def add_zig_tiles(design: sc.Design, width: int) -> None:
+    green = sc.Color(hex_string='#009900')
+    low_helix_idx = 4
+    high_helix_idx = low_helix_idx + width - 3
+    offset_5p_even = design.helices[low_helix_idx].major_tick_start + 12 + (width // 2 + 1) * 21
+    offset_5p_odd = offset_5p_even - 12
+    for idx in range(low_helix_idx, high_helix_idx + 1, 2):
+        # 12-9-11-10 strand ("even" strand)
+        design.strand(idx, offset_5p_even).move(-12).move(-9) \
+            .cross(idx - 1).move(11).move(10).with_color(green)
+        offset_5p_even -= 23
+
+        # 11-10-12-9 strand ("odd" strand)
+        design.strand(idx + 1, offset_5p_odd).move(-11).move(-10) \
+            .cross(idx).move(12).move(9).with_color(green)
+        offset_5p_odd -= 23
+
+
+def add_zag_tiles(design: sc.Design, width: int) -> None:
+    red = sc.Color(hex_string='#ff0000')
+    low_helix_idx = 3
+    high_helix_idx = low_helix_idx + width - 3
+    offset_5p_odd = design.helices[low_helix_idx].major_tick_start + (width // 2 + 1) * 21
+    offset_5p_even = offset_5p_odd - 11
+    for idx in range(low_helix_idx, high_helix_idx + 1, 2):
+        # 11-10-12-9 strand ("odd" strand)
+        design.strand(idx, offset_5p_odd).move(-11).move(-10) \
+            .cross(idx - 1).move(12).move(9).with_color(red)
+        offset_5p_odd -= 23
+
+        # 12-9-11-10 strand ("even" strand)
+        design.strand(idx + 1, offset_5p_even).move(-12).move(-9) \
+            .cross(idx).move(11).move(10).with_color(red)
+        offset_5p_even -= 23
+
+
+def add_zig_seed_tiles(design: sc.Design, width: int) -> None:
+    dark_green = sc.Color(hex_string='#006600')
+    low_helix_idx = 1
+    high_helix_idx = low_helix_idx + width - 2
+    offset_5p_odd = design.helices[low_helix_idx].major_tick_start + (width // 2 + 1) * 21
+    offset_5p_even = offset_5p_odd - 11
+
+    for idx in range(low_helix_idx, high_helix_idx + 1, 2):
+        # 11-10-12-9 strand ("odd" strand)
+        design.strand(idx, offset_5p_odd).move(-11).move(-10) \
+            .cross(idx - 1).move(12).move(9).with_color(dark_green)
+        offset_5p_odd -= 23
+
+        if idx < high_helix_idx:
+            # 12-9-11-10 strand ("even" strand)
+            design.strand(idx + 1, offset_5p_even).move(-12).move(-9) \
+                .cross(idx).move(11).move(10).with_color(dark_green)
+            offset_5p_even -= 23
+
+
+def duple_at(design: sc.Design, color: sc.Color, duple: bool, start_offset: int, top_helix: int) -> None:
+    mid_helix = top_helix - 1
+    bot_helix = mid_helix - 1
+    if duple:
+        design.strand(top_helix, start_offset) \
+            .move(-11).move(-10) \
+            .cross(mid_helix) \
+            .move(4).loopout(mid_helix, 4).move(-4) \
+            .move(-9) \
+            .cross(bot_helix) \
+            .move(11).move(10) \
+            .cross(mid_helix) \
+            .move(-4).loopout(mid_helix, 4).move(4) \
+            .move(9) \
+            .with_color(color)
+    else:
+        raise NotImplementedError()
+
+
+def add_seed_duple(design: sc.Design, width: int, duple: bool, color: sc.Color) -> None:
+    top_helix = width + 1
+    start_offset = 2 + 21 * 2
+    duple_at(design, color, duple, start_offset, top_helix)
+
+
+def add_zig_to_zag_duple(design: sc.Design, width: int, duple: bool, color: sc.Color) -> None:
+    top_helix = width + 3
+    start_offset = 21 * 3
+    duple_at(design, color, duple, start_offset, top_helix)
+
+
+def add_zag_to_zig_duple(design: sc.Design, width: int, duple: bool, color: sc.Color) -> None:
+    top_helix = 3
+    start_offset = design.helices[top_helix].major_tick_start + (width // 2 + 2) * 21
+    duple_at(design, color, duple, start_offset, top_helix)
+
+
+def add_duples(design: sc.Design, width: int, duple: bool) -> None:
+    black = sc.Color(hex_string='#000000')
+    add_seed_duple(design, width, duple, black)
+    add_zig_to_zag_duple(design, width, duple, black)
+    add_zag_to_zig_duple(design, width, duple, black)
+
+
+def add_seed(design: sc.Design, width: int) -> None:
+    blue = sc.Color(hex_string='#0066cc')
+    start_helix = 0
+    start_offset = design.helices[start_helix].major_tick_start + (width // 2 + 1) * 21
+    strand_builder = design.strand(start_helix, start_offset).move(-9)
+    for helix in range(1, width + 1, 2):
+        strand_builder.move(-12).loopout(helix, 8).move(-11)
+        if helix < width:
+            strand_builder.loopout(helix + 1, 8)
+    strand_builder.with_color(blue)
+
+
+if __name__ == '__main__':
+    main()