├── CHANGELOG.md ├── Cargo.toml ├── LICENSE ├── README.md ├── ensnano-design ├── Cargo.toml └── src │ ├── bezier_plane.rs │ ├── bezier_plane │ └── import_from_svg.rs │ ├── cocentric_spheres.rs │ ├── codenano.rs │ ├── collection.rs │ ├── curves │ ├── bezier.rs │ ├── bezier │ │ └── instantiator.rs │ ├── discretization.rs │ ├── legacy.rs │ ├── mod.rs │ ├── revolution.rs │ ├── sphere_like_spiral.rs │ ├── supertwist.rs │ ├── time_nucl_map.rs │ ├── torus.rs │ ├── tube_spiral.rs │ └── twist.rs │ ├── design_operations.rs │ ├── elements.rs │ ├── external_3d_objects.rs │ ├── grid.rs │ ├── grid │ ├── copy_grid.rs │ ├── deserialize.rs │ ├── grid_collection.rs │ └── hyperboloid.rs │ ├── group_attributes.rs │ ├── helices.rs │ ├── insertions.rs │ ├── interpolated_torus.rs │ ├── interpolated_two_ball.rs │ ├── lib.rs │ ├── parameters.rs │ ├── scadnano.rs │ ├── strands │ ├── formating.rs │ └── mod.rs │ ├── tests │ ├── mod.rs │ └── strand_with_insertion.json │ ├── torus_radius.rs │ └── utils.rs ├── ensnano-exports ├── Cargo.toml ├── dd12_na.pdb ├── ds_rna_Helix.pdb └── src │ ├── cadnano.rs │ ├── cadnano │ └── parity_graph.rs │ ├── cando.rs │ ├── lib.rs │ ├── oxdna.rs │ └── pdb.rs ├── ensnano-flatscene ├── Cargo.toml └── src │ ├── controller.rs │ ├── controller │ └── automata.rs │ ├── data.rs │ ├── data │ ├── design.rs │ ├── helix.rs │ └── strand.rs │ ├── flattypes.rs │ ├── lib.rs │ ├── view.rs │ └── view │ ├── background.frag │ ├── background.frag.spv │ ├── background.rs │ ├── background.vert │ ├── background.vert.spv │ ├── border.frag │ ├── border.frag.spv │ ├── border.vert │ ├── border.vert.spv │ ├── grid.frag │ ├── grid.frag.spv │ ├── grid.vert │ ├── grid.vert.spv │ ├── helix_view.rs │ ├── insertion.rs │ ├── insertion.vert │ ├── insertion.vert.spv │ ├── rectangle.frag │ ├── rectangle.frag.spv │ ├── rectangle.rs │ ├── rectangle.vert │ ├── rectangle.vert.spv │ ├── strand.frag │ ├── strand.frag.spv │ ├── strand.vert │ └── strand.vert.spv ├── ensnano-gui ├── Cargo.toml └── src │ ├── consts.rs │ ├── icon.rs │ ├── left_panel.rs │ ├── left_panel │ ├── color_picker.rs │ ├── contextual_panel.rs │ ├── contextual_panel │ │ └── value_constructor.rs │ ├── discrete_value.rs │ ├── export_menu.rs │ ├── sequence_input.rs │ ├── tabs.rs │ └── tabs │ │ ├── camera_shortcut.rs │ │ ├── camera_tab.rs │ │ ├── edition_tab.rs │ │ ├── grids_tab.rs │ │ ├── parameters_tab.rs │ │ ├── pen_tab.rs │ │ ├── revolution_tab.rs │ │ ├── sequence_tab.rs │ │ └── simulation_tab.rs │ ├── lib.rs │ ├── material_icons_light.rs │ ├── status_bar.rs │ ├── top_bar.rs │ └── ui_size.rs ├── ensnano-interactor ├── Cargo.toml ├── m13-p8064.txt ├── p7249-Tilibit.txt ├── p7560.txt ├── pUC19.txt └── src │ ├── application.rs │ ├── consts.rs │ ├── graphics.rs │ ├── lib.rs │ ├── operation.rs │ ├── operation_labels.rs │ ├── selection.rs │ ├── strand_builder.rs │ ├── surfaces.rs │ └── torsion.rs ├── ensnano-organizer ├── Cargo.toml ├── icons │ ├── bootstrap-LICENSE.md │ ├── bootstrap-icons.ttf │ ├── bootstrap-icons.ttf.old │ └── icons.ttf └── src │ ├── drag_drop_target.rs │ ├── element.rs │ ├── hoverable_button.rs │ ├── lib.rs │ ├── theme.rs │ └── tree.rs ├── ensnano-scene ├── Cargo.toml └── src │ ├── camera.rs │ ├── controller.rs │ ├── controller │ ├── automata.rs │ └── automata │ │ ├── dragging_state.rs │ │ ├── event_context.rs │ │ └── point_and_click_state.rs │ ├── data.rs │ ├── data │ ├── design3d.rs │ └── design3d │ │ └── bezier_paths.rs │ ├── element_selector.rs │ ├── lib.rs │ ├── maths_3d.rs │ ├── view.rs │ └── view │ ├── direction_cube.frag │ ├── direction_cube.frag.spv │ ├── direction_cube.rs │ ├── direction_cube.vert │ ├── direction_cube.vert.spv │ ├── dna_obj.frag │ ├── dna_obj.frag.spv │ ├── dna_obj.rs │ ├── dna_obj.vert │ ├── dna_obj.vert.spv │ ├── dna_obj_fake.frag │ ├── dna_obj_fake.frag.spv │ ├── dna_obj_outline.frag │ ├── dna_obj_outline.frag.spv │ ├── dna_obj_outline.vert │ ├── dna_obj_outline.vert.spv │ ├── drawable.rs │ ├── gltf_drawer.rs │ ├── gltf_obj.frag │ ├── gltf_obj.frag.spv │ ├── gltf_obj.vert │ ├── gltf_obj.vert.spv │ ├── grid │ ├── grid.frag │ ├── grid.frag.spv │ ├── grid.vert │ ├── grid.vert.spv │ ├── mod.rs │ ├── texture.frag │ ├── texture.frag.spv │ ├── texture.rs │ ├── texture.vert │ └── texture.vert.spv │ ├── grid_disc.frag │ ├── grid_disc.frag.spv │ ├── grid_disc.rs │ ├── grid_disc.vert │ ├── grid_disc.vert.spv │ ├── handle_drawer.rs │ ├── instances_drawer.rs │ ├── letter.frag │ ├── letter.frag.spv │ ├── letter.rs │ ├── letter.vert │ ├── letter.vert.spv │ ├── plane.frag │ ├── plane.vert │ ├── plane_drawer.rs │ ├── plane_frag.spv │ ├── plane_vert.spv │ ├── rotation_widget.rs │ ├── sheet_2d.frag │ ├── sheet_2d.frag.spv │ ├── sheet_2d.rs │ ├── sheet_2d.vert │ ├── sheet_2d.vert.spv │ ├── skybox.frag │ ├── skybox.frag.spv │ ├── skybox.vert │ ├── skybox.vert.spv │ └── uniforms.rs ├── ensnano-utils ├── Cargo.toml └── src │ ├── bindgroup_manager.rs │ ├── camera2d.rs │ ├── chars2d │ ├── chars.frag │ ├── chars.frag.spv │ ├── chars.vert │ ├── chars.vert.spv │ ├── mod.rs │ └── text_drawer.rs │ ├── circles2d │ ├── circle.frag │ ├── circle.frag.spv │ ├── circle.vert │ ├── circle.vert.spv │ ├── mod.rs │ ├── rotation_widget.frag │ └── rotation_widget.frag.spv │ ├── full_isometry.rs │ ├── id_generator.rs │ ├── instance.rs │ ├── lib.rs │ ├── light.rs │ ├── mesh.rs │ ├── obj_loader.rs │ ├── text │ └── mod.rs │ └── texture.rs ├── font ├── DejaVuSansMono.ttf ├── Inconsolata-Regular.ttf ├── MaterialIcons-Regular.ttf ├── MaterialIconsOutlined-Regular.otf ├── ensnano.ttf └── ensnano2.ttf ├── icons ├── add_file.png ├── adjust_page.png ├── delete.png ├── direction_cube.png ├── icons │ ├── Build-off.png │ ├── Build-off32.png │ ├── Build-on.png │ ├── Build-on32.png │ ├── Cut-off.png │ ├── Cut-off32.png │ ├── Cut-on.png │ ├── Cut-on32.png │ ├── Grid-off.png │ ├── Grid-off32.png │ ├── Grid-on.png │ ├── Grid-on32.png │ ├── Helix-off.png │ ├── Helix-off32.png │ ├── Helix-on.png │ ├── Helix-on32.png │ ├── Move-off-in32.png │ ├── Move-off.png │ ├── Move-off32.png │ ├── Move-on-in32.png │ ├── Move-on.png │ ├── Move-on32.png │ ├── NewGrid-off.png │ ├── NewGrid-off32.png │ ├── NewGrid-on.png │ ├── NewGrid-on32.png │ ├── NewGridHex-off32.png │ ├── NewGridHex-on32.png │ ├── NewGridTube-off32.png │ ├── NewGridTube-on32.png │ ├── NewHelix-off32.png │ ├── NewHelix-on32.png │ ├── Nucleotide-off.png │ ├── Nucleotide-off32.png │ ├── Nucleotide-on.png │ ├── Nucleotide-on32.png │ ├── RigidBodyEngine-off32.png │ ├── RigidBodyEngine-on32.png │ ├── Roll-off32.png │ ├── Roll-on32.png │ ├── Rotate-off-in32.png │ ├── Rotate-off.png │ ├── Rotate-off32.png │ ├── Rotate-on-in32.png │ ├── Rotate-on.png │ ├── Rotate-on32.png │ ├── Select-off.png │ ├── Select-off32.png │ ├── Select-on.png │ ├── Select-on32.png │ ├── Strand-off.png │ ├── Strand-off32.png │ ├── Strand-on.png │ ├── Strand-on32.png │ ├── SymetryH-on32.png │ ├── SymetryV-on32.png │ ├── TiltLeft-on32.png │ └── TiltRight-on32.png └── save.png ├── img ├── cadnano_del_loop.png ├── ensnano_del_loop.png ├── ensnano_insert_loopout.png ├── ensnano_logo.png ├── made_with_iced_white.svg └── scadnano_insert_loopout.png ├── readme ├── buttons.png ├── cutting_xover.gif ├── helix_creation.gif ├── making_xover.gif └── rotating_helix.gif ├── src ├── app_state.rs ├── app_state │ ├── address_pointer.rs │ ├── design_interactor.rs │ ├── design_interactor │ │ ├── controller.rs │ │ ├── controller │ │ │ ├── clipboard.rs │ │ │ ├── shift_optimization.rs │ │ │ ├── simulations.rs │ │ │ ├── simulations │ │ │ │ ├── revolutions.rs │ │ │ │ ├── revolutions │ │ │ │ │ ├── closed_curves.rs │ │ │ │ │ └── open_curves.rs │ │ │ │ ├── roller.rs │ │ │ │ └── twister.rs │ │ │ └── update_insertion_length.rs │ │ ├── file_parsing.rs │ │ ├── file_parsing │ │ │ ├── cadnano.rs │ │ │ └── junctions.rs │ │ ├── presenter.rs │ │ └── presenter │ │ │ ├── design_content.rs │ │ │ ├── design_content │ │ │ └── xover_suggestions.rs │ │ │ ├── exports.rs │ │ │ ├── impl_main_reader.rs │ │ │ ├── impl_reader2d.rs │ │ │ ├── impl_reader3d.rs │ │ │ └── impl_readergui.rs │ ├── impl_app2d.rs │ ├── impl_app3d.rs │ ├── impl_gui.rs │ ├── impl_gui │ │ └── curve_builders.rs │ └── transitions.rs ├── controller.rs ├── controller │ ├── chanel_reader.rs │ ├── download_intervals.rs │ ├── download_staples.rs │ ├── messages.rs │ ├── normal_state.rs │ ├── quit.rs │ └── set_scaffold_sequence.rs ├── dialog.rs ├── grid_panel.rs ├── keep_proceed.rs ├── main.rs ├── main_tests.rs ├── multiplexer.rs ├── multiplexer │ ├── draw.frag │ ├── draw.frag.spv │ ├── draw.vert │ ├── draw.vert.spv │ └── layout_manager.rs ├── requests.rs ├── requests │ ├── impl_flatscene.rs │ ├── impl_gui.rs │ ├── impl_scene.rs │ └── poll.rs └── scheduler.rs ├── tests ├── loopout_3prime.ens ├── loopout_5prime.ens ├── one_helix.json ├── one_xover.json ├── pastable.json ├── pastable_cyclic.json ├── seq_test.txt ├── test_sequence.json ├── three_neighbour_strands.ens └── two_neighbour_strands.ens └── thirdparties ├── license.html └── lyon └── LICENSE 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