.gitignore
AGENTS.md
README.md
pyproject.toml
pytest.ini
requirements.txt
server.log
.github/workflows/release.yml
agents/README.md
agents/atom_groups_api.md
agents/bond_groups_api.md
agents/compass_api.md
agents/config_api.md
agents/cube_api.md
agents/dash_service.md
agents/ortep_api.md
agents/polyhedron_api.md
agents/scene_api.md
agents/selection_api.md
agents/transforms_api.md
agents/tui_api.md
crystal_viewer/__init__.py
crystal_viewer/__main__.py
crystal_viewer/_version.py
crystal_viewer/cli.py
crystal_viewer/api/__init__.py
crystal_viewer/api/shared.py
crystal_viewer/api/v1_legacy.py
crystal_viewer/api/v2_config.py
crystal_viewer/api/v2_export.py
crystal_viewer/api/v2_intent.py
crystal_viewer/api/v2_overlays.py
crystal_viewer/api/v2_perf.py
crystal_viewer/api/v2_scenes.py
crystal_viewer/api/v2_selection.py
crystal_viewer/api/v2_state.py
crystal_viewer/api/ws.py
crystal_viewer/app/__init__.py
crystal_viewer/app/backend.py
crystal_viewer/app/backend_analysis.py
crystal_viewer/app/backend_camera.py
crystal_viewer/app/backend_core.py
crystal_viewer/app/backend_io.py
crystal_viewer/app/backend_operations.py
crystal_viewer/app/backend_overlays.py
crystal_viewer/app/backend_selection.py
crystal_viewer/app/backend_topology.py
crystal_viewer/app/callbacks_analysis.py
crystal_viewer/app/callbacks_disorder.py
crystal_viewer/app/callbacks_editors.py
crystal_viewer/app/callbacks_operations.py
crystal_viewer/app/callbacks_state.py
crystal_viewer/app/callbacks_view.py
crystal_viewer/app/camera_helpers.py
crystal_viewer/app/dash_impl.py
crystal_viewer/app/editor_operations.py
crystal_viewer/app/editor_tables.py
crystal_viewer/app/editor_transforms.py
crystal_viewer/app/factory.py
crystal_viewer/app/normalizers.py
crystal_viewer/app/render_worker.py
crystal_viewer/app/rightclick.py
crystal_viewer/app/runtime.py
crystal_viewer/app/shared.py
crystal_viewer/app/status_helpers.py
crystal_viewer/app/style_helpers.py
crystal_viewer/atom_groups/__init__.py
crystal_viewer/bond_groups/__init__.py
crystal_viewer/bonds/__init__.py
crystal_viewer/compass/__init__.py
crystal_viewer/compass/annotations.py
crystal_viewer/compass/basis.py
crystal_viewer/compass/core.py
crystal_viewer/compass/projection.py
crystal_viewer/config/__init__.py
crystal_viewer/config/colors.py
crystal_viewer/config/elements.py
crystal_viewer/config/loader.py
crystal_viewer/config/schema.py
crystal_viewer/cube/__init__.py
crystal_viewer/cube/bridge.py
crystal_viewer/cube/core.py
crystal_viewer/cube/export.py
crystal_viewer/cube/io.py
crystal_viewer/cube/meshes.py
crystal_viewer/cube/traces.py
crystal_viewer/depth_sort/__init__.py
crystal_viewer/depth_sort/core.py
crystal_viewer/legacy/__init__.py
crystal_viewer/legacy/crystal_scene.py
crystal_viewer/legacy/plot_crystal.py
crystal_viewer/legacy/publication_view.py
crystal_viewer/loader/__init__.py
crystal_viewer/loader/core.py
crystal_viewer/loader/cube_adapter.py
crystal_viewer/loader/uploads.py
crystal_viewer/math/__init__.py
crystal_viewer/math/camera.py
crystal_viewer/math/ellipsoid.py
crystal_viewer/math/pbc.py
crystal_viewer/math/projection.py
crystal_viewer/math/rotation.py
crystal_viewer/operations/__init__.py
crystal_viewer/operations/disorder.py
crystal_viewer/ortep/__init__.py
crystal_viewer/ortep/billboard.py
crystal_viewer/ortep/core.py
crystal_viewer/ortep/flat_render.py
crystal_viewer/ortep/math.py
crystal_viewer/ortep/mesh.py
crystal_viewer/ortep/traces.py
crystal_viewer/perf/__init__.py
crystal_viewer/perf/bench.py
crystal_viewer/perf/bench_pipeline.py
crystal_viewer/perf/oracle.py
crystal_viewer/perf/profile_app.py
crystal_viewer/perf_log/__init__.py
crystal_viewer/perf_log/core.py
crystal_viewer/presets/__init__.py
crystal_viewer/presets/core.py
crystal_viewer/render/__init__.py
crystal_viewer/render/api.py
crystal_viewer/render/assembly.py
crystal_viewer/render/boundary_replicas.py
crystal_viewer/render/cache.py
crystal_viewer/render/common.py
crystal_viewer/render/compass.py
crystal_viewer/render/display_modes.py
crystal_viewer/render/figures.py
crystal_viewer/render/meshes.py
crystal_viewer/render/morphology.py
crystal_viewer/render/scene_traces.py
crystal_viewer/render/selection.py
crystal_viewer/render/serialize.py
crystal_viewer/render/style.py
crystal_viewer/render/topology.py
crystal_viewer/render/traces_atoms.py
crystal_viewer/render/traces_isosurface.py
crystal_viewer/render/traces_overlays.py
crystal_viewer/render/viewport.py
crystal_viewer/render/cube/__init__.py
crystal_viewer/render/cube/core.py
crystal_viewer/render/cube/export.py
crystal_viewer/render/cube/io.py
crystal_viewer/render/cube/meshes.py
crystal_viewer/render/cube/traces.py
crystal_viewer/render/ortep/__init__.py
crystal_viewer/render/ortep/billboard.py
crystal_viewer/render/ortep/core.py
crystal_viewer/render/ortep/math.py
crystal_viewer/render/ortep/mesh.py
crystal_viewer/render/ortep/traces.py
crystal_viewer/render/overlay/__init__.py
crystal_viewer/render/overlay/compass.py
crystal_viewer/render/overlay/labels.py
crystal_viewer/render/overlay/manual.py
crystal_viewer/render/style/__init__.py
crystal_viewer/render/style/atom_groups.py
crystal_viewer/render/style/bond_groups.py
crystal_viewer/render/style/core.py
crystal_viewer/render/style/disorder.py
crystal_viewer/render/style/palette.py
crystal_viewer/renderer/__init__.py
crystal_viewer/scene/__init__.py
crystal_viewer/scene/core.py
crystal_viewer/scene/serialize.py
crystal_viewer/scene/state.py
crystal_viewer/scene/store.py
crystal_viewer/scene/style.py
crystal_viewer/scene/types.py
crystal_viewer/scenes/__init__.py
crystal_viewer/scenes/core.py
crystal_viewer/structure/__init__.py
crystal_viewer/structure/bonds.py
crystal_viewer/structure/cif_parse.py
crystal_viewer/structure/disorder_index.py
crystal_viewer/structure/formula_unit.py
crystal_viewer/structure/geometry.py
crystal_viewer/structure/molcrys_bridge.py
crystal_viewer/structure/snapshot.py
crystal_viewer/style/__init__.py
crystal_viewer/style/atom_groups.py
crystal_viewer/style/bond_groups.py
crystal_viewer/style/disorder.py
crystal_viewer/style/palette.py
crystal_viewer/topology/__init__.py
crystal_viewer/topology/analysis.py
crystal_viewer/transforms/__init__.py
crystal_viewer/transforms/core.py
crystal_viewer/transforms/pipeline.py
crystal_viewer/tui/__init__.py
crystal_viewer/tui/_hull2d.py
crystal_viewer/tui/app.py
crystal_viewer/tui/braille.py
crystal_viewer/tui/compositor.py
crystal_viewer/tui/controller.py
crystal_viewer/tui/crystal_ir.py
crystal_viewer/tui/inspection.py
crystal_viewer/tui/loader_adapter.py
crystal_viewer/tui/observation.py
crystal_viewer/tui/renderer.py
crystal_viewer/tui/serializer.py
crystal_viewer/tui/state.py
crystal_viewer/tui/summary.py
crystal_viewer/tui/text.py
crystal_viewer/utils/__init__.py
crystal_viewer/utils/json_safe.py
crystal_viewer/viewpoint/__init__.py
crystal_viewer/viewpoint/core.py
docs/README.md
docs/build_images.py
docs/cli.md
docs/dev-notes.md
docs/perf.md
docs/postmortems.md
docs/scores.md
docs/derivations/README.md
docs/derivations/camera.md
docs/derivations/display_modes.md
docs/derivations/lattice.md
docs/derivations/ortep.md
docs/derivations/transforms.md
docs/images/banner.png
docs/images/feature_coordination.png
docs/images/feature_histogram.png
docs/images/feature_publication.png
docs/images/feature_three_modes.png
docs/images/feature_unit_cell.png
docs/redesign/README.md
docs/redesign/caches.md
docs/redesign/callbacks.md
docs/redesign/migration.md
docs/redesign/operations.md
docs/redesign/rendering.md
docs/redesign/state.md
frontend/README.md
frontend/assets/diagnostic.js
frontend/assets/mattervis.js
frontend/assets/native_upload.js
frontend/assets/panel_resize.css
frontend/assets/panel_resize.js
frontend/assets/right_click_menu.css
frontend/assets/view_tools.css
matter_vis.egg-info/PKG-INFO
matter_vis.egg-info/SOURCES.txt
matter_vis.egg-info/dependency_links.txt
matter_vis.egg-info/entry_points.txt
matter_vis.egg-info/requires.txt
matter_vis.egg-info/scm_file_list.json
matter_vis.egg-info/scm_version.json
matter_vis.egg-info/top_level.txt
scripts/01_quick_render.py
scripts/02_coordination_analysis.py
scripts/03_display_modes_panel.py
scripts/04_static_publication.py
scripts/05_app_and_api.py
scripts/06_cp2k_cube_orbital.py
scripts/07_scene_tabs.py
scripts/08_ortep_interactive.py
scripts/09_ortep_publication.py
scripts/10_periodic_cube_isosurface.py
scripts/10_tui_controller_visuals.py
scripts/11_bond_scale_benchmark.py
scripts/README.md
scripts/data/DAP-4.cif
scripts/data/README.md
skills/visualize-materials/SKILL.md
skills/visualize-materials/references/camera.md
skills/visualize-materials/references/diagnose-and-select.md
skills/visualize-materials/references/install.md
skills/visualize-materials/references/matplotlib-flat-ortep.md
skills/visualize-materials/references/molecule-highlight.md
skills/visualize-materials/references/plotly-render.md
skills/visualize-materials/references/polyhedra.md
skills/visualize-materials/references/publication-layout.md
skills/visualize-materials/references/trajectory-animation.md
skills/visualize-materials/references/tui.md
skills/visualize-materials/references/verification.md
tests/_layout_helpers.py
tests/conftest.py
tests/test_cli_camera.py
tests/test_cli_identity.py
tests/test_disorder_isolated_atoms.py
tests/test_module_organization.py
tests/test_public_import_contracts.py
tests/app/test_app_state.py
tests/app/test_bfdh_analysis.py
tests/app/test_callback_dispatch_regression.py
tests/app/test_camera_capture_no_poll_echo.py
tests/app/test_camera_persistence_per_tab.py
tests/app/test_editor_builders.py
tests/app/test_frontend_scene_tab_routing.py
tests/app/test_inline_edit_emits_state.py
tests/app/test_layout_refresh_reflects_state.py
tests/app/test_minor_opacity_disable.py
tests/app/test_phase3_ui_layout.py
tests/app/test_preset_security.py
tests/app/test_scene_store_recovery.py
tests/app/test_scene_tabs_dispatcher.py
tests/app/test_status_banner.py
tests/app/test_surface_editor_error.py
tests/app/test_upload_security.py
tests/app/test_view_camera_callbacks.py
tests/app/test_visual_control_regressions.py
tests/config/test_config_loader.py
tests/config/test_config_mck_overrides_passthrough.py
tests/config/test_config_rest.py
tests/config/test_element_tables.py
tests/cube/test_cube_bond_scale.py
tests/cube/test_periodic_isosurface.py
tests/loader/test_disorder_fast_path.py
tests/operations/test_resolve_disorder.py
tests/ortep/test_adp_propagation.py
tests/ortep/test_ortep_billboard.py
tests/ortep/test_ortep_integration.py
tests/ortep/test_ortep_math.py
tests/ortep/test_ortep_mesh.py
tests/ortep/test_ortep_mixed_modes.py
tests/ortep/test_ortep_traces.py
tests/perf/test_dap_o4_oracle.py
tests/perf/test_near_zero_latency.py
tests/perf/test_pipeline_oracle.py
tests/perf/test_topology_compute_offthread.py
tests/perf/test_update_view_under_50ms.py
tests/perf/oracles/pipeline_v1.json
tests/render/test_atom_groups_extra_selectors.py
tests/render/test_atom_groups_renderer.py
tests/render/test_bond_effective_opacity.py
tests/render/test_bond_groups.py
tests/render/test_boundary_replicas.py
tests/render/test_camera_aspect_persistence.py
tests/render/test_camera_projection.py
tests/render/test_canonical_boundary_bonds.py
tests/render/test_cif_symmetry_expansion.py
tests/render/test_compass_basis.py
tests/render/test_depth_sort.py
tests/render/test_disorder_modifiers.py
tests/render/test_disorder_preview_trace.py
tests/render/test_figure_cache_perf.py
tests/render/test_flat_projected_scale.py
tests/render/test_legacy_aliases.py
tests/render/test_ordered_structure_bond_opacity.py
tests/render/test_partial_occupancy_render_identity.py
tests/render/test_payload_size.py
tests/render/test_polyhedron_enabled_toggle_perf.py
tests/render/test_render_dispatch.py
tests/render/test_selection_outline_trace.py
tests/render/test_style_schema.py
tests/render/test_topology_with_styles.py
tests/render/test_unit_cell_box_aspectratio.py
tests/render/test_unwrap_modes.py
tests/render/test_view_alignment.py
tests/scenes/test_atom_groups_api.py
tests/scenes/test_atom_groups_backend.py
tests/scenes/test_healthz_api.py
tests/scenes/test_legacy_alias_v1.py
tests/scenes/test_monochrome_migration.py
tests/scenes/test_per_tab_close.py
tests/scenes/test_perf_log.py
tests/scenes/test_scenes_api.py
tests/scenes/test_scenes_resolver.py
tests/scenes/test_scenes_store.py
tests/scenes/test_v1_state_deprecation.py
tests/scenes/test_view_alignment_api.py
tests/scenes/test_ws_set_state_scene_id.py
tests/selection/test_box_select_projection.py
tests/selection/test_selection_dispatcher.py
tests/selection/test_selection_rest.py
tests/selection/test_selection_state_schema.py
tests/state_machine/test_no_lost_events.py
tests/state_machine/test_reducer_order.py
tests/structure/test_bonds_pbc_reference.py
tests/structure/test_disorder_index.py
tests/topology/test_disorder_bonds.py
tests/topology/test_loader_mol_indices.py
tests/topology/test_phase4_api.py
tests/topology/test_polyhedron_instance_overrides.py
tests/topology/test_polyhedron_specs_api.py
tests/topology/test_polyhedron_specs_backend.py
tests/topology/test_polyhedron_specs_mck04.py
tests/topology/test_polyhedron_specs_renderer.py
tests/topology/test_shape_classification.py
tests/topology/test_topology.py
tests/topology/test_topology_api_errors.py
tests/topology/test_transforms.py
tests/tui/test_tui_camera_controls.py
tests/tui/test_tui_command_mode.py
tests/tui/test_tui_controller.py
tests/tui/test_tui_focus_and_inspection.py
tests/tui/test_tui_local_geometry.py
tests/tui/test_tui_usability.py
tests/tui/fixtures/dirty_geometry.vasp
verification_screens/tui_controller/01_initial_mono.txt
verification_screens/tui_controller/02_orbit_mono.txt
verification_screens/tui_controller/03_focus_mono.txt
verification_screens/tui_controller/04_molecule_minor_mono.txt
verification_screens/tui_controller/05_molecule_minor_color.txt
verification_screens/tui_controller/README.md