├── .gitattributes ├── .github ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── dart.yml │ ├── dart_formatting.yml │ ├── gh-pages-dev.yml │ ├── gh-pages.yml │ └── release.yml ├── .gitignore ├── CODEOWNERS ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.txt ├── README.md ├── analysis_options.yaml ├── clean.bat ├── code snippets.txt ├── compile-upload-readme.sh ├── compile_and_upload_to_ucdavis.sh ├── dart_test.yaml ├── define_root_dir.sh ├── doc-images ├── grid_hex.svg ├── grid_honeycomb.svg ├── grid_honeycomb_wrong_convention.svg ├── grid_none.svg ├── grid_square.svg ├── screenshot-initial.png └── screenshot-initial.pptx ├── drawing.svg ├── example_designs ├── .gitignore ├── 2_helix_origami.sc ├── 32-helix-rectangle-scaffold.sc ├── 6_helix_bundle_honeycomb.sc ├── origami_cross_tile_strong_strong.sc └── tetrahedron.sc ├── fix-index.sh ├── gh-pages.bat ├── gh-pages.sh ├── images ├── bounding-box-loopouts.png ├── circular-strand.png ├── github-CI-checks-complete.png ├── github-CI-checks-incomplete.png ├── github-vote.png ├── location-of-scadnano-sources-unit-testing.png ├── rope-select-fail-select-entire-bounding-box.png ├── screenshot-polygon-illegal.png └── screenshot-polygon.png ├── json_schema.json ├── lib ├── scadnano.dart └── src │ ├── .gitignore │ ├── actions │ ├── .gitignore │ └── actions.dart │ ├── app.dart │ ├── constants.dart │ ├── dna_file_type.dart │ ├── dna_sequence_constants.dart │ ├── extension_methods.dart │ ├── json_serializable.dart │ ├── middleware │ ├── .gitignore │ ├── adjust_grid_position.dart │ ├── all_middleware.dart │ ├── assign_dna.dart │ ├── autostaple_and_autobreak.dart │ ├── check_mirror_strands_legal.dart │ ├── dna_ends_move_start.dart │ ├── dna_extensions_move_start.dart │ ├── edit_select_mode_change.dart │ ├── example_design_selected.dart │ ├── export_cadnano_file.dart │ ├── export_dna_sequences.dart │ ├── export_svg.dart │ ├── forbid_create_circular_strand_no_crossovers_middleware.dart │ ├── group_remove.dart │ ├── helices_positions_set_based_on_crossovers.dart │ ├── helix_grid_change.dart │ ├── helix_group_move_start.dart │ ├── helix_hide_all.dart │ ├── helix_idxs_change.dart │ ├── helix_offsets_change.dart │ ├── helix_remove.dart │ ├── insertion_deletion_batching.dart │ ├── invalidate_png.dart │ ├── load_file.dart │ ├── local_storage.dart │ ├── oxdna_export.dart │ ├── oxview_update_view.dart │ ├── periodic_save_design_local_storage.dart │ ├── reselect_moved_copied_strands.dart │ ├── reselect_moved_dna_ends.dart │ ├── reselect_moved_dna_extension_ends.dart │ ├── reselect_moved_domains.dart │ ├── reset_local_storage.dart │ ├── save_file.dart │ ├── selections_intersect_box_compute.dart │ ├── strand_create.dart │ ├── system_clipboard.dart │ ├── throttle.dart │ └── zoom_speed.dart │ ├── reducers │ ├── app_state_reducer.dart │ ├── app_ui_state_reducer.dart │ ├── assign_domain_names_reducer.dart │ ├── assign_or_remove_dna_reducer.dart │ ├── change_loopout_ext_properties.dart │ ├── context_menu_reducer.dart │ ├── delete_reducer.dart │ ├── design_reducer.dart │ ├── dialog_reducer.dart │ ├── dna_ends_move_reducer.dart │ ├── dna_extensions_move_reducer.dart │ ├── domains_move_reducer.dart │ ├── edit_modes_reducer.dart │ ├── groups_reducer.dart │ ├── helices_reducer.dart │ ├── helix_group_move_reducer.dart │ ├── inline_insertions_deletions_reducer.dart │ ├── insertion_deletion_reducer.dart │ ├── load_dna_file_reducer.dart │ ├── mouseover_datas_reducer.dart │ ├── nick_ligate_join_by_crossover_reducers.dart │ ├── potential_crossover_reducer.dart │ ├── select_mode_state_reducer.dart │ ├── selection_reducer.dart │ ├── strand_creation_reducer.dart │ ├── strands_copy_info_reducer.dart │ ├── strands_move_reducer.dart │ ├── strands_reducer.dart │ ├── undo_redo_reducer.dart │ └── util_reducer.dart │ ├── serializers.dart │ ├── state │ ├── .gitignore │ ├── address.dart │ ├── app_state.dart │ ├── app_ui_state.dart │ ├── app_ui_state_storables.dart │ ├── base_pair_display_type.dart │ ├── clipboard.dart │ ├── context_menu.dart │ ├── copy_info.dart │ ├── crossover.dart │ ├── design.dart │ ├── design_side_rotation_data.dart │ ├── dialog.dart │ ├── dna_assign_options.dart │ ├── dna_end.dart │ ├── dna_ends_move.dart │ ├── dna_extensions_move.dart │ ├── domain.dart │ ├── domain_name_mismatch.dart │ ├── domains_move.dart │ ├── edit_mode.dart │ ├── example_designs.dart │ ├── export_dna_format.dart │ ├── export_dna_format_strand_order.dart │ ├── extension.dart │ ├── geometry.dart │ ├── grid.dart │ ├── grid_position.dart │ ├── group.dart │ ├── helix.dart │ ├── helix_group_move.dart │ ├── linker.dart │ ├── local_storage_design_choice.dart │ ├── loopout.dart │ ├── modification.dart │ ├── modification_type.dart │ ├── mouseover_data.dart │ ├── position3d.dart │ ├── potential_crossover.dart │ ├── potential_vertical_crossover.dart │ ├── select_mode.dart │ ├── select_mode_state.dart │ ├── selectable.dart │ ├── selection_box.dart │ ├── selection_rope.dart │ ├── strand.dart │ ├── strand_creation.dart │ ├── strand_maker.dart │ ├── strand_part.dart │ ├── strands_move.dart │ ├── substrand.dart │ ├── undo_redo.dart │ ├── unused_fields.dart │ └── vendor_fields.dart │ ├── util.dart │ └── view │ ├── 3p_end.dart │ ├── 5p_end.dart │ ├── axis_arrows_main.dart │ ├── axis_arrows_side.dart │ ├── design.dart │ ├── design_context_menu.dart │ ├── design_dialog_form.dart │ ├── design_footer.dart │ ├── design_loading_dialog.dart │ ├── design_main.dart │ ├── design_main_base_pair_lines.dart │ ├── design_main_base_pair_rectangle.dart │ ├── design_main_dna_mismatches.dart │ ├── design_main_dna_sequence.dart │ ├── design_main_dna_sequences.dart │ ├── design_main_domain_moving.dart │ ├── design_main_domain_name_mismatches.dart │ ├── design_main_domains_moving.dart │ ├── design_main_error_boundary.dart │ ├── design_main_helices.dart │ ├── design_main_helix.dart │ ├── design_main_loopout_extension_length.dart │ ├── design_main_loopout_extension_lengths.dart │ ├── design_main_potential_vertical_crossover.dart │ ├── design_main_potential_vertical_crossovers.dart │ ├── design_main_slice_bar.dart │ ├── design_main_strand.dart │ ├── design_main_strand_and_domain_texts.dart │ ├── design_main_strand_creating.dart │ ├── design_main_strand_crossover.dart │ ├── design_main_strand_deletion.dart │ ├── design_main_strand_dna_end.dart │ ├── design_main_strand_dna_end_moving.dart │ ├── design_main_strand_dna_extension_end_moving.dart │ ├── design_main_strand_domain.dart │ ├── design_main_strand_domain_text.dart │ ├── design_main_strand_extension.dart │ ├── design_main_strand_extension_text.dart │ ├── design_main_strand_insertion.dart │ ├── design_main_strand_loopout.dart │ ├── design_main_strand_loopout_name.dart │ ├── design_main_strand_modification.dart │ ├── design_main_strand_modifications.dart │ ├── design_main_strand_moving.dart │ ├── design_main_strand_paths.dart │ ├── design_main_strands.dart │ ├── design_main_strands_moving.dart │ ├── design_main_unpaired_insertion_deletions.dart │ ├── design_main_warning_star.dart │ ├── design_side.dart │ ├── design_side_helix.dart │ ├── design_side_potential_helix.dart │ ├── design_side_rotation.dart │ ├── design_side_rotation_arrow.dart │ ├── edit_and_select_modes.dart │ ├── edit_mode.dart │ ├── error_message.dart │ ├── helix_context_menu.dart │ ├── helix_group_moving.dart │ ├── menu.dart │ ├── menu_boolean.dart │ ├── menu_dropdown_item.dart │ ├── menu_dropdown_right.dart │ ├── menu_form_file.dart │ ├── menu_number.dart │ ├── menu_side.dart │ ├── oxview.dart │ ├── potential_crossover_view.dart │ ├── potential_extensions_view.dart │ ├── pure_component.dart │ ├── react_bootstrap.dart │ ├── react_color.dart │ ├── react_dnd.dart │ ├── redraw_counter_component_mixin.dart │ ├── select_mode.dart │ ├── selection_box_view.dart │ ├── selection_rope_view.dart │ ├── strand_color_picker.dart │ ├── svg_filters.dart │ ├── transform_by_helix_group.dart │ └── view.dart ├── pubspec-old.yaml ├── pubspec.lock ├── pubspec.yaml ├── remove_g.sh ├── run_docker.sh ├── test.bat ├── test.sh ├── test ├── _templates │ └── react_components_test_template.html ├── assign_dna_unit_test.dart ├── assign_domain_name_complement_domain_test.dart ├── assign_domain_name_complement_strand_test.dart ├── assign_name_unit_test.dart ├── base_pairs_test.dart ├── circular_strands_unit_test.dart ├── components │ ├── connected_edit_mode_test.dart │ ├── connected_menu_test_old.dart │ └── connected_select_mode_test.dart ├── domain_label_move_test.dart ├── export_cadnano_v2_test.dart ├── extensions_test.dart ├── helix_groups_test.dart ├── helix_reducer_test.dart ├── helix_relax_rolls_test.dart ├── helix_rotation_set_test.dart ├── idt_unit_test.dart ├── import_cadnano_v2_test.dart ├── inline_insertions_deletions_test.dart ├── join_strands_by_crossovers_test.dart ├── json_export_import_test.dart ├── middleware_test.dart ├── move_linker_test.dart ├── other_unit_test.dart ├── oxdna_export_test.dart ├── paste_test.dart ├── reducer_test.dart ├── tests_inputs │ ├── cadnano_v2_export │ │ ├── test_16_helix_origami_rectangle_no_twist.sc │ │ ├── test_6_helix_bundle_honeycomb.sc │ │ ├── test_6_helix_origami_rectangle.sc │ │ ├── test_big_circular_staples.sc │ │ ├── test_big_circular_staples_hex.sc │ │ ├── test_circular_strand.sc │ │ ├── test_paranemic_crossover.sc │ │ └── test_paranemic_crossover_other_direction.sc │ └── cadnano_v2_import │ │ ├── test_2_stape_2_helix_origami_deletions_insertions.json │ │ ├── test_32_helix_rectangle.json │ │ ├── test_Nature09_monolith.json │ │ ├── test_Science09_prot120_98_v3.json │ │ ├── test_circular_auto_staple.json │ │ ├── test_circular_auto_staple_hex.json │ │ ├── test_helices_order.json │ │ ├── test_huge_hex.json │ │ └── test_paranemic_crossover.json ├── undo_redo_test.dart └── utils.dart ├── toc.sh ├── tutorial ├── 24_helix_rectangle.sc ├── images │ ├── 24_helices_empty_default_length.png │ ├── M13_sequence_near_5p.png │ ├── adjust_helix_max_offset.png │ ├── adjust_helix_max_offset_dialog.png │ ├── all_edge_staples.png │ ├── all_seam_staples.png │ ├── all_staples.png │ ├── all_staples_except_near_seam.png │ ├── all_staples_except_top_bottom_at_seam.png │ ├── assign_DNA_click.png │ ├── assign_DNA_dialog.png │ ├── assign_m13.png │ ├── complete_design.png │ ├── complete_design_no_DNA.png │ ├── crossover.png │ ├── deletion_edit_mode.png │ ├── deletions_full_column.png │ ├── download_raw_sc_file.png │ ├── draw_one_strand.png │ ├── eight_edge_staples.png │ ├── empty.png │ ├── example_empty.png │ ├── excel_spreadsheet.png │ ├── export_DNA.png │ ├── file_menu.png │ ├── first_column_inner_staples.png │ ├── first_inner_staple.png │ ├── first_two_columns_inner_staples.png │ ├── first_two_columns_with_top_bottom_staples.png │ ├── first_two_seam_staples.png │ ├── four_edge_staples.png │ ├── full_scaffold.png │ ├── helices_lengthed.png │ ├── idt_plate_options.png │ ├── idt_upload_plates.png │ ├── initial.png │ ├── lengthen_strand.png │ ├── ligate_after_clicking.png │ ├── ligate_click.png │ ├── ligate_mode.png │ ├── load_empty.png │ ├── load_file_button.png │ ├── manual_deletions.png │ ├── nick_first_two_domains.png │ ├── nick_first_two_domains_zoomed_out.png │ ├── one_helix_initial.png │ ├── one_helix_zoomed_in.png │ ├── paste_scaffold_domains_16_to_19.png │ ├── pasted_strands_new_color_menu_option.png │ ├── pencil_mode.png │ ├── potential_crossover.png │ ├── potential_vertical_crossover.png │ ├── reflect_horizontal_error_message.png │ ├── reflect_strand_horizontally.png │ ├── right_edge_staples_backwards.png │ ├── scaffold_complete.png │ ├── scaffold_complete_with_nick_at_top.png │ ├── scaffold_crossovers_seam_21_22.png │ ├── scaffold_domain_first_copy.png │ ├── scaffold_domains_16_to_23.png │ ├── scaffold_domains_22_23_selected.png │ ├── scaffold_domains_8_to_23.png │ ├── scaffold_domains_all_helices_missing_crossovers_seam.png │ ├── scaffold_domains_helices_22_23_crossovers.png │ ├── scaffold_helix_23_full_length.png │ ├── scaffold_just_turned_blue.png │ ├── scaffold_pasted_helices_20_21.png │ ├── select_all_not_in_select_mode.png │ ├── select_mode.png │ ├── selection_5p_3p_strand.png │ ├── selection_box_over_5p_end.png │ ├── set_scaffold.png │ ├── shift_drag_select_scaffold_domains_20_to_23.png │ ├── show_dna.png │ ├── show_offsets_all_helices.png │ ├── strand_lengthened.png │ ├── strand_selectable.png │ ├── strand_selected.png │ ├── top_left_edge_staple.png │ ├── top_left_edge_staple_no_crossover.png │ ├── twelve_edge_staples.png │ ├── two_left_edge_staples.png │ └── unselect_text.png ├── sequences.xlsx └── tutorial.md ├── up.sh ├── up_all.sh └── web ├── .gitignore ├── 24-helix-rectangle-origami.dna ├── CNAME ├── bootstrap.min.css ├── compile_script.py ├── copy_python_scripts.sh ├── examples ├── .gitignore ├── 16_helix_origami_barrel_from_algoSST_paper.py ├── 16_helix_origami_rectangle.py ├── 16_helix_origami_rectangle_idt.py ├── 16_helix_origami_rectangle_no_seq.py ├── 16_helix_origami_rectangle_no_seq_no_twist.py ├── 16_helix_origami_rectangle_no_twist.py ├── 16_helix_origami_rectangle_seed_tiles_grow_from_top.py ├── 16_helix_origami_rectangle_shifted_seam_no_seq.py ├── 1_staple_1_helix_origami.py ├── 1_staple_1_helix_origami_idt_duplicate_names.py ├── 1_staple_1_helix_origami_mismatches.py ├── 1_staple_1_helix_origami_position_nondefault.py ├── 1_staple_1_helix_origami_roll.py ├── 24_helix_origami_rectangle_twist_corrected.py ├── 24_helix_origami_rectangle_twist_corrected.sc ├── 24_helix_origami_rectangle_twist_corrected.xls ├── 24_helix_rectangle.sc ├── 24_helix_rectangle_twist_corrected.sc ├── 2_helix_2_strands_multiple_substrands_no_seq.py ├── 2_staple_2_helix_modifications.py ├── 2_staple_2_helix_origami_6bases_wide.py ├── 2_staple_2_helix_origami_deletions.py ├── 2_staple_2_helix_origami_deletions_insertions.py ├── 2_staple_2_helix_origami_deletions_insertions_labels.py ├── 2_staple_2_helix_origami_deletions_insertions_mods.py ├── 2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py ├── 2_staple_2_helix_origami_deletions_insertions_new_geometry.py ├── 2_staple_2_helix_origami_deletions_insertions_no_seq.py ├── 3_helix_deletions_insertions.py ├── 4_helix_grid_none.py ├── 4_helix_grid_none_min_offset_position_x_nondefault.py ├── 4_helix_min_offsets_nonzero.py ├── 56_helix_origami_rectangle.py ├── 64_helix_origami_rectangle.py ├── 6_helix_6_col_origami_rectangle.py ├── 6_helix_bundle_honeycomb.py ├── 6_helix_origami_rectangle.py ├── 6_helix_origami_rectangle_helices_out_of_order.py ├── M13_seq_from5588.txt ├── _16-helix-barrel-to-order.json ├── add_deletions_to_24_helix_rectangle.py ├── empty.py ├── hairpin.py ├── helices_out_of_order_nonconsecutive.py ├── helix_groups.py ├── hex_lattice_10x10.py ├── hex_lattice_10x10_with_negative.py ├── honeycomb_lattice_10x10.py ├── honeycomb_lattice_10x10_with_negative.py ├── idt-plates-explicit.py ├── idt │ ├── .gitignore │ ├── 16_helix_origami_barrel_from_algoSST_paper.idt │ ├── 16_helix_origami_rectangle.idt │ ├── 16_helix_origami_rectangle_384well.xls │ ├── 16_helix_origami_rectangle_96well.xls │ ├── 16_helix_origami_rectangle_idt.idt │ ├── 16_helix_origami_rectangle_seed_tiles_grow_from_top.idt │ ├── 16_helix_origami_rectangle_seed_tiles_grow_from_top.xls │ ├── 1_staple_1_helix_origami_idt_duplicate_names.idt │ ├── idt-plates-explicit.idt │ └── idt-plates-explicit.xls ├── long_range_crossovers.py ├── loopouts_all_types.py ├── many_big_helices.py ├── many_helices_modifications.py ├── names_domains_strands.py ├── output_designs │ ├── .gitignore │ ├── 16_helix_origami_barrel_from_algoSST_paper.sc │ ├── 16_helix_origami_rectangle.sc │ ├── 16_helix_origami_rectangle_idt.sc │ ├── 16_helix_origami_rectangle_no_seq.sc │ ├── 16_helix_origami_rectangle_no_seq_no_twist.sc │ ├── 16_helix_origami_rectangle_no_twist.sc │ ├── 16_helix_origami_rectangle_seed_tiles_grow_from_top.sc │ ├── 16_helix_origami_rectangle_shifted_seam_no_seq.sc │ ├── 1_staple_1_helix_origami.sc │ ├── 1_staple_1_helix_origami_mismatches.sc │ ├── 1_staple_1_helix_origami_position_nondefault.sc │ ├── 1_staple_1_helix_origami_roll.sc │ ├── 2_helix_2_strands_multiple_substrands_no_seq.sc │ ├── 2_staple_2_helix_modifications.sc │ ├── 2_staple_2_helix_origami_6bases_wide.sc │ ├── 2_staple_2_helix_origami_deletions.sc │ ├── 2_staple_2_helix_origami_deletions_insertions.sc │ ├── 2_staple_2_helix_origami_deletions_insertions_labels.sc │ ├── 2_staple_2_helix_origami_deletions_insertions_mods.sc │ ├── 2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc │ ├── 2_staple_2_helix_origami_deletions_insertions_new_geometry.sc │ ├── 2_staple_2_helix_origami_deletions_insertions_no_seq.sc │ ├── 3_helix_deletions_insertions.sc │ ├── 4_helix_grid_none.sc │ ├── 4_helix_grid_none_min_offset_position_x_nondefault.sc │ ├── 4_helix_min_offsets_nonzero.sc │ ├── 56_helix_origami_rectangle.sc │ ├── 64_helix_origami_rectangle.sc │ ├── 6_helix_6_col_origami_rectangle.sc │ ├── 6_helix_bundle_honeycomb.sc │ ├── 6_helix_origami_rectangle.sc │ ├── 6_helix_origami_rectangle_helices_out_of_order.sc │ ├── _error_badly_formatted_file.sc │ ├── _error_empty_file.sc │ ├── _error_json_file_not_a_map.sc │ ├── empty.sc │ ├── hairpin.sc │ ├── helices_out_of_order_nonconsecutive.sc │ ├── helix_groups.sc │ ├── hex_lattice_10x10.sc │ ├── hex_lattice_10x10_with_negative.sc │ ├── honeycomb_lattice_10x10.sc │ ├── honeycomb_lattice_10x10_with_negative.sc │ ├── idt-plates-explicit.sc │ ├── long_range_crossovers.sc │ ├── loopouts_all_types.sc │ ├── many_big_helices.sc │ ├── many_helices_modifications.sc │ ├── names_domains_strands.sc │ ├── sst-motif-3_2.sc │ ├── sst-motif-4_1.sc │ └── very_large_origami.sc ├── proposal.py ├── run_all_examples.py ├── sst-motif-3_2.py ├── sst-motif-4_1.py └── very_large_origami.py ├── excel-spreadsheets ├── idt-plates-empty-10plate.xlsx ├── idt-plates-empty-1plate.xlsx ├── idt-plates-empty-2plate.xlsx ├── idt-plates-empty-3plate.xlsx ├── idt-plates-empty-4plate.xlsx ├── idt-plates-empty-5plate.xlsx ├── idt-plates-empty-6plate.xlsx ├── idt-plates-empty-7plate.xlsx ├── idt-plates-empty-8plate.xlsx └── idt-plates-empty-9plate.xlsx ├── external-libs ├── EventSource.js ├── autosizer │ ├── index.js │ └── vendor │ │ └── detectElementResize.js ├── eventsource.min.js ├── hammer.min.js ├── pablo.js ├── pablo.min.js ├── panzoom.js ├── panzoom.min.js ├── polyfill.js ├── react-bootstrap.js ├── react-color.min.js ├── react-dnd │ ├── ReactDnD.js │ ├── ReactDnD.min.js │ ├── ReactDnDHTML5Backend.js │ └── ReactDnDHTML5Backend.min.js ├── react-svg-pan-zoom │ ├── prop-types.js │ ├── react-svg-pan-zoom.min.js │ └── react_svg_pan_zoom.js ├── simpledrag.js ├── svg-pan-zoom.js └── svg-pan-zoom.min.js ├── images ├── edit_mode_icons │ ├── deletion.svg │ ├── insertion.svg │ ├── ligate.svg │ ├── move_group.svg │ ├── nick.svg │ ├── pencil.svg │ ├── rope_select.svg │ └── select.svg 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