Index

_

_add_structure_tab() (geom.gui.structure_gui.StructureWindow method) _advance_sample() (desktop_chat_qt.ChatWindow method) _all_canvases() (geom.gui.structure_gui.StructureWindow method) _apply_atom_selection() (geom.gui.structure_gui.StructureWindow method) _apply_styles() (geom.gui.structure_gui.StructureWindow method) _atom_uses_cpk() (geom.gui.structure_gui.VdwCanvas method) _atoms_are_centered() (geom.gui.structure_gui.StructureWindow method) _available_structures_for_material() (geom.gui.structure_gui.StructureWindow method) _begin_interaction() (geom.gui.structure_gui.VdwCanvas method) _build_command_args() (geom.gui.structure_gui.StructureWindow method) _build_sphere_mesh() (geom.gui.structure_gui.VdwCanvas method) _build_ui() (geom.gui.structure_gui.StructureWindow method) _center_to_origin_available() (geom.gui.structure_gui.StructureWindow method) _CODE_FENCE_GENERIC (in module desktop_chat_qt) _compare_selection_values() (in module geom.gui.structure_gui) _configure_dropdown_popups() (geom.gui.structure_gui.StructureWindow method) _configure_parameter_widget() (geom.gui.structure_gui.StructureWindow method) _CONVERSION_LOCK (in module geom.gui.structure_generator) _current_viewer_tab_is_joint() (geom.gui.structure_gui.StructureWindow method) _draw_gnuplot_legend_pillow() (in module geom.functions.rdkit_module) _draw_unit_sphere() (geom.gui.structure_gui.VdwCanvas method) _draw_unit_sphere_mesh() (geom.gui.structure_gui.VdwCanvas method) _evaluate_selection_node() (in module geom.gui.structure_gui) _field_label() (geom.gui.structure_gui.StructureWindow method) _finish_interaction() (geom.gui.structure_gui.VdwCanvas method) _fmt() (geom.gui.structure_gui.StructureWindow method) _GENERATION_LOCK (in module geom.gui.structure_generator) _generation_metadata() (geom.gui.structure_gui.StructureWindow method) _GEOM_LINE (in module desktop_chat_qt) _gl (geom.gui.structure_gui.VdwCanvas attribute) _install_tab_menu() (geom.gui.structure_gui.StructureWindow method) _interaction_timer (geom.gui.structure_gui.VdwCanvas attribute) _is_interacting (geom.gui.structure_gui.VdwCanvas attribute) _is_reset_view_key() (geom.gui.structure_gui.VdwCanvas method) _last_pos (geom.gui.structure_gui.VdwCanvas attribute) _last_user_text (desktop_chat_qt.ChatWindow attribute) _make_canvas() (geom.gui.structure_gui.StructureWindow method) _make_manipulator_spin() (geom.gui.structure_gui.StructureWindow method) _make_option_spin() (geom.gui.structure_gui.StructureWindow method) _make_painter() (geom.gui.structure_gui.VdwCanvas method) _make_viewer_spin() (geom.gui.structure_gui.StructureWindow method) _material_items() (geom.gui.structure_gui.StructureWindow method) _merge_highlights() (in module geom.functions.rdkit_module) _metadata_for_generated_atoms() (geom.gui.structure_gui.StructureWindow method) _minimum_distance() (geom.gui.structure_gui.StructureWindow method) _newest_generated_xyz() (in module geom.gui.structure_generator) _normalize_selection_expression() (in module geom.gui.structure_gui) _ordered_metals() (geom.gui.structure_gui.StructureWindow method) _paint_atom() (geom.gui.structure_gui.VdwCanvas method) _paint_axes() (geom.gui.structure_gui.VdwCanvas method) _paint_axes_overlay() (geom.gui.structure_gui.VdwCanvas method) _paint_background() (geom.gui.structure_gui.VdwCanvas method) _paint_bond() (geom.gui.structure_gui.VdwCanvas method)

_paint_bonds_and_atoms() (geom.gui.structure_gui.VdwCanvas method) _paint_mixed_vdw_cpk() (geom.gui.structure_gui.VdwCanvas method) _paint_vdw_depth_buffer() (geom.gui.structure_gui.VdwCanvas method) _paint_vdw_impostors() (geom.gui.structure_gui.VdwCanvas method) _paint_vdw_opengl() (geom.gui.structure_gui.VdwCanvas method) _paint_vdw_surface_buffer() (geom.gui.structure_gui.VdwCanvas method) _project_atoms() (geom.gui.structure_gui.VdwCanvas method) _projected_bonds() (geom.gui.structure_gui.VdwCanvas method) _refresh_manipulator_actions() (geom.gui.structure_gui.StructureWindow method) _refresh_manipulator_sources() (geom.gui.structure_gui.StructureWindow method) _refresh_material_controls() (geom.gui.structure_gui.StructureWindow method) _refresh_option_controls() (geom.gui.structure_gui.StructureWindow method) _refresh_smiles_button_state() (geom.gui.structure_gui.StructureWindow method) _refresh_structure_controls() (geom.gui.structure_gui.StructureWindow method) _rotate_point() (geom.gui.structure_gui.VdwCanvas method) _run_manipulation() (geom.gui.structure_gui.StructureWindow method) _sample_index (desktop_chat_qt.ChatWindow attribute) _samples (desktop_chat_qt.ChatWindow attribute) _save_source_for_canvas() (geom.gui.structure_gui.StructureWindow method) _scene_has_cpk() (geom.gui.structure_gui.VdwCanvas method) _section_label() (geom.gui.structure_gui.StructureWindow method) _selected_manipulator_path() (geom.gui.structure_gui.StructureWindow method) _set_atom_selection_invalid() (geom.gui.structure_gui.StructureWindow method) _set_bond_width_from_input() (geom.gui.structure_gui.StructureWindow method) _set_logo_pixmap() (desktop_chat_qt.ChatWindow method) _set_optional_row_enabled() (geom.gui.structure_gui.StructureWindow method) _set_render_resolution_from_input() (geom.gui.structure_gui.StructureWindow method) _set_vdw_scale_from_input() (geom.gui.structure_gui.StructureWindow method) _short_tab_title() (geom.gui.structure_gui.StructureWindow method) _sphere_cache (geom.gui.structure_gui.VdwCanvas attribute) _sphere_list (geom.gui.structure_gui.VdwCanvas attribute) _sphere_mesh (geom.gui.structure_gui.VdwCanvas attribute) _sphere_pixmap() (geom.gui.structure_gui.VdwCanvas method) _structure_failed() (geom.gui.structure_gui.StructureWindow method) _structure_paths_from_event() (geom.gui.structure_gui.VdwCanvas method) _structure_ready() (geom.gui.structure_gui.StructureWindow method) _sync_atom_selection_input() (geom.gui.structure_gui.StructureWindow method) _sync_current_tab_meta() (geom.gui.structure_gui.StructureWindow method) _toggle_counter (desktop_chat_qt.ChatWindow attribute) _toggles (desktop_chat_qt.ChatWindow attribute) _type_pos (desktop_chat_qt.ChatWindow attribute) _type_timer (desktop_chat_qt.ChatWindow attribute) _typewriter_running (desktop_chat_qt.ChatWindow attribute) _typewriter_tick() (desktop_chat_qt.ChatWindow method) _use_lit_atom_rendering() (geom.gui.structure_gui.VdwCanvas method) _uses_mixed_vdw_cpk() (geom.gui.structure_gui.VdwCanvas method) _uses_vdw_impostors() (geom.gui.structure_gui.VdwCanvas method) _uses_vdw_opengl() (geom.gui.structure_gui.VdwCanvas method) _uses_vdw_surface_buffer() (geom.gui.structure_gui.VdwCanvas method) _vdw_depth_render_scale() (geom.gui.structure_gui.VdwCanvas method) _vdw_surface_render_scale() (geom.gui.structure_gui.VdwCanvas method) _view_light_vector() (geom.gui.structure_gui.VdwCanvas method) _write_xyz() (geom.gui.structure_gui.StructureWindow method) _xyz_snapshot() (in module geom.gui.structure_generator)

A

ACCENT_INDIGO (in module geom.gui.structure_gui) ACCENT_SOFT (in module geom.gui.structure_gui) ACCENT_VIOLET (in module geom.gui.structure_gui) AgentWorker (class in desktop_chat_qt) ai_agents module ai_config module ai_main module ai_runner module ai_validator module alloy (geom.classes.input_class.input_class attribute) alloy_perc (geom.classes.input_class.input_class attribute) alloy_string (geom.classes.input_class.input_class attribute) angle (geom.classes.input_class.input_class attribute) angles (geom.classes.input_class.input_class attribute) angles_input (geom.classes.input_class.input_class attribute)

api_key (in module ai_config) app() (in module test_structure_gui) APP_TITLE (in module desktop_chat_qt) (in module geom.gui.structure_gui) append_chat() (desktop_chat_qt.ChatWindow method) assistant (desktop_chat_qt.AgentWorker attribute) (desktop_chat_qt.ChatWindow attribute) atom_count (geom.gui.structure_generator.StructureResult property) atom_index (geom.classes.input_class.input_class attribute) atom_matches_selection() (in module geom.gui.structure_gui) atomic_arrangement (geom.classes.parameters.parameters attribute), [1] AtomRecord (class in geom.gui.structure_generator) atoms (geom.classes.molecule.molecule attribute), [1] (geom.gui.structure_generator.StructureResult attribute) (geom.gui.structure_gui.VdwCanvas attribute) atomtype (geom.classes.input_class.input_class attribute) atomtype_in (geom.classes.input_class.input_class attribute) atomtype_out (geom.classes.input_class.input_class attribute) atomtypes_alloys (geom.classes.input_class.input_class attribute) atomtypes_core_shell (geom.classes.input_class.input_class attribute) axes (geom.classes.input_class.input_class attribute)

B

base_width (geom.classes.input_class.input_class attribute) bipyramid() (in module geom.functions.create_geom) bipyramid_length (geom.classes.input_class.input_class attribute)

bipyramid_width (geom.classes.input_class.input_class attribute) bond_width_scale (geom.gui.structure_gui.StructureWindow attribute) (geom.gui.structure_gui.VdwCanvas attribute) BORDER (in module geom.gui.structure_gui)

C

calc_min_distance() (in module geom.functions.tools) calculate_normal_and_rhs() (in module geom.functions.tools) CANVAS (in module geom.gui.structure_gui) center_selected_structure() (geom.gui.structure_gui.StructureWindow method) change_atomtype() (geom.classes.molecule.molecule method) change_trans_sense() (geom.classes.input_class.input_class method) chat_frame (desktop_chat_qt.ChatWindow attribute) chat_view (desktop_chat_qt.ChatWindow attribute) CHATGPT_GREEN (in module geom.gui.structure_gui) ChatWindow (class in desktop_chat_qt) check_accepted_parameters() (in module geom.functions.general) check_aromaticity (geom.classes.input_class.input_class attribute) check_dir_axis() (in module geom.functions.general) check_equal_extensions() (in module geom.functions.general) check_FCC() (in module geom.functions.general) check_FCC_or_BCC() (in module geom.functions.general) check_file_exists() (in module geom.functions.general) check_file_extension() (in module geom.functions.general) check_file_extension_rdkit() (in module geom.functions.general) check_input_case() (geom.classes.input_class.input_class method) cleanup_gui_tmp() (in module geom.gui.structure_generator) closeEvent() (geom.gui.structure_gui.StructureWindow method) combo_items() (in module test_structure_gui) command (geom.gui.structure_generator.StructureResult attribute) command_args (geom.gui.structure_gui.GenerationWorker attribute) compare_mesh_files() (in module geom.tests.test_) cone() (in module geom.functions.create_geom)

config_list (in module ai_config) conformers_force_field_optimization() (in module geom.functions.rdkit_module) convergence (geom.classes.parameters.parameters attribute), [1] convergence_step (geom.classes.parameters.parameters attribute), [1] convert_molecule_to_xyz() (in module geom.gui.structure_generator) copy_geometry_file() (in module geom.functions.tools) COVALENT_RADII (in module geom.gui.structure_gui) cpk (geom.gui.structure_gui.ProjectedAtom attribute) CPK_COLORS (in module geom.gui.structure_gui) CPK_DEFAULT (in module geom.gui.structure_gui) create_alloy() (geom.classes.molecule.molecule method) create_ase_bulk (geom.classes.input_class.input_class attribute) create_ase_bulk_graphene() (in module geom.functions.create_geom) create_ase_bulk_metal() (in module geom.functions.create_geom) create_bowtie (geom.classes.input_class.input_class attribute) create_bowtie() (in module geom.functions.tools) create_cuboctahedra() (geom.classes.molecule.molecule method) create_decahedra() (geom.classes.molecule.molecule method) create_dimer (geom.classes.input_class.input_class attribute) create_dimer() (in module geom.functions.tools) create_geom (geom.classes.input_class.input_class attribute) create_geom_assistant() (in module ai_agents) create_icosahedra() (geom.classes.molecule.molecule method) create_results_geom() (in module geom.functions.general) create_structure() (geom.gui.structure_gui.StructureWindow method) create_user_proxy() (in module ai_agents) cto() (in module geom.functions.create_geom) current_result (geom.gui.structure_gui.StructureWindow attribute)

D

DEFAULT_VMD_PINK (in module geom.gui.structure_gui) delete_all_files() (in module geom.functions.tools) delete_geometry_file() (in module geom.functions.tools) delete_structure_tab() (geom.gui.structure_gui.StructureWindow method) depth_radius (geom.gui.structure_gui.ProjectedAtom attribute) desktop_chat_qt module determine_sphere_center() (in module geom.functions.tools)

dimer_distance (geom.classes.input_class.input_class attribute) dir_axis_input (geom.classes.input_class.input_class attribute) dir_factor (geom.classes.input_class.input_class attribute) direction (geom.classes.input_class.input_class attribute) distances (geom.classes.input_class.input_class attribute) distances_input (geom.classes.input_class.input_class attribute) down_button (geom.gui.structure_gui.ViewerStepper attribute) dragEnterEvent() (geom.gui.structure_gui.VdwCanvas method) dropEvent() (geom.gui.structure_gui.VdwCanvas method)

E

element (geom.gui.structure_generator.AtomRecord attribute) (geom.gui.structure_gui.ProjectedAtom attribute) ELEMENT_COLORS (in module geom.gui.structure_gui) elliptic_parabola_a (geom.classes.input_class.input_class attribute) elliptic_parabola_b (geom.classes.input_class.input_class attribute) elliptic_parabola_c (geom.classes.input_class.input_class attribute) embed_3d() (in module geom.functions.rdkit_module) empty_canvas (geom.gui.structure_gui.StructureWindow attribute)

error() (in module geom.functions.output) error_dir_axis() (in module geom.functions.output) escape() (in module desktop_chat_qt) eventFilter() (desktop_chat_qt.ChatWindow method) extract_geom_command() (in module desktop_chat_qt) extract_string_or_list() (in module geom.functions.general) extract_value() (in module geom.functions.general) extract_value_or_default() (in module geom.functions.general)

F

failed (geom.gui.structure_gui.GenerationWorker attribute) file_conversion() (in module geom.functions.rdkit_module) file_geom2_translated (geom.classes.input_class.input_class attribute) file_geom_rotated (geom.classes.input_class.input_class attribute) files_dropped (geom.gui.structure_gui.VdwCanvas attribute) filter_xyz_graphene_to_disk() (geom.classes.molecule.molecule method) filter_xyz_graphene_to_ribbon() (geom.classes.molecule.molecule method) filter_xyz_graphene_to_ring() (geom.classes.molecule.molecule method) filter_xyz_graphene_to_triangle() (geom.classes.molecule.molecule method)

filter_xyz_in_cone() (geom.classes.molecule.molecule method) filter_xyz_in_cylinder() (geom.classes.molecule.molecule method) filter_xyz_in_elliptic_paraboloid() (geom.classes.molecule.molecule method) filter_xyz_in_pentagonal_pyramid() (geom.classes.molecule.molecule method) filter_xyz_in_pyramid() (geom.classes.molecule.molecule method) filter_xyz_in_sphere() (geom.classes.molecule.molecule method) find_aromatic_highlights() (in module geom.functions.rdkit_module) finished_with_reply (desktop_chat_qt.AgentWorker attribute) first (geom.gui.structure_gui.ProjectedBond attribute) force_field_optimization() (in module geom.functions.rdkit_module)

G

gen_3d_mesh (geom.classes.input_class.input_class attribute) gen_3d_mesh_rod (geom.classes.input_class.input_class attribute) gen_3d_mesh_sphere (geom.classes.input_class.input_class attribute) gen_bipyramid (geom.classes.input_class.input_class attribute) gen_cone (geom.classes.input_class.input_class attribute) gen_core_shell (geom.classes.input_class.input_class attribute) gen_cto (geom.classes.input_class.input_class attribute) gen_graphene (geom.classes.input_class.input_class attribute) gen_icosahedra (geom.classes.input_class.input_class attribute) gen_idh (geom.classes.input_class.input_class attribute) gen_microscope (geom.classes.input_class.input_class attribute) gen_pencil (geom.classes.input_class.input_class attribute) gen_pentbipyramid (geom.classes.input_class.input_class attribute) gen_pentpyramid (geom.classes.input_class.input_class attribute) gen_pyramid (geom.classes.input_class.input_class attribute) gen_rod (geom.classes.input_class.input_class attribute) gen_rod_core_shell (geom.classes.input_class.input_class attribute) gen_sphere (geom.classes.input_class.input_class attribute) gen_sphere_core_shell (geom.classes.input_class.input_class attribute) gen_tip (geom.classes.input_class.input_class attribute) generate_conformers() (in module geom.functions.rdkit_module) generate_structure() (in module geom.gui.structure_generator) generated (geom.gui.structure_gui.GenerationWorker attribute) GenerationWorker (class in geom.gui.structure_gui) geom module geom.__main__ module geom.classes module geom.classes.input_class module geom.classes.molecule module geom.classes.parameters module geom.functions module geom.functions.create_geom module geom.functions.general module geom.functions.output module geom.functions.rdkit_module module geom.functions.rotate module geom.functions.tools module geom.functions.translate module geom.functions.various module

geom.gui module geom.gui.structure_generator module geom.gui.structure_gui module geom.tests module geom.tests.test_ module geom1_file (geom.classes.input_class.input_class attribute) geom2_file (geom.classes.input_class.input_class attribute) geom_center (geom.classes.input_class.input_class attribute) geom_center() (in module geom.functions.various) geom_file (geom.classes.input_class.input_class attribute) geom_specular (geom.classes.input_class.input_class attribute) geom_specular() (in module geom.functions.various) get_layers() (in module geom.functions.create_geom) get_system_prompt() (in module ai_config) GL_AMBIENT (in module geom.gui.structure_gui) GL_AMBIENT_AND_DIFFUSE (in module geom.gui.structure_gui) GL_BACK (in module geom.gui.structure_gui) GL_COLOR_BUFFER_BIT (in module geom.gui.structure_gui) GL_COLOR_MATERIAL (in module geom.gui.structure_gui) GL_COMPILE (in module geom.gui.structure_gui) GL_CULL_FACE (in module geom.gui.structure_gui) GL_DEPTH_BUFFER_BIT (in module geom.gui.structure_gui) GL_DEPTH_TEST (in module geom.gui.structure_gui) GL_DIFFUSE (in module geom.gui.structure_gui) GL_FILL (in module geom.gui.structure_gui) GL_FRONT (in module geom.gui.structure_gui) GL_FRONT_AND_BACK (in module geom.gui.structure_gui) GL_LEQUAL (in module geom.gui.structure_gui) GL_LIGHT0 (in module geom.gui.structure_gui) GL_LIGHTING (in module geom.gui.structure_gui) GL_LINE (in module geom.gui.structure_gui) GL_MODELVIEW (in module geom.gui.structure_gui) GL_NORMALIZE (in module geom.gui.structure_gui) GL_POLYGON_OFFSET_FILL (in module geom.gui.structure_gui) GL_POSITION (in module geom.gui.structure_gui) GL_PROJECTION (in module geom.gui.structure_gui) GL_SHININESS (in module geom.gui.structure_gui) GL_SMOOTH (in module geom.gui.structure_gui) GL_SPECULAR (in module geom.gui.structure_gui) GL_TRIANGLE_STRIP (in module geom.gui.structure_gui) graphene() (in module geom.functions.create_geom) graphene_edge_type (geom.classes.input_class.input_class attribute) graphene_edge_types (geom.classes.input_class.input_class attribute) graphene_structure (geom.classes.input_class.input_class attribute) graphene_structures (geom.classes.input_class.input_class attribute) GRAPHENE_VARIANTS (in module geom.gui.structure_gui) GUI_TMP_ROOT (in module geom.gui.structure_generator)

I

icosahedra() (in module geom.functions.create_geom) idh() (in module geom.functions.create_geom) index (geom.gui.structure_gui.ProjectedAtom attribute)

initializeGL() (geom.gui.structure_gui.VdwCanvas method) input_box (desktop_chat_qt.ChatWindow attribute) input_class (class in geom.classes.input_class) input_frame (desktop_chat_qt.ChatWindow attribute)

K

keep_first_conformer() (in module geom.functions.rdkit_module)

keyPressEvent() (geom.gui.structure_gui.StructureWindow method) (geom.gui.structure_gui.VdwCanvas method)

L

lattice_constant (geom.classes.parameters.parameters attribute), [1] load_files() (geom.gui.structure_gui.StructureWindow method) load_files_from_dialog() (geom.gui.structure_gui.StructureWindow method) load_rdkit_file() (in module geom.functions.rdkit_module)

load_smiles_from_input() (geom.gui.structure_gui.StructureWindow method) logfile_close() (in module geom.functions.output) logfile_init() (in module geom.functions.output) logo_label (desktop_chat_qt.ChatWindow attribute)

M

main() (in module ai_main) (in module desktop_chat_qt) (in module geom.__main__) (in module geom.gui.structure_gui) make_acknowledgement() (in module desktop_chat_qt) make_hooked_reply() (in module ai_validator) manipulate_xyz() (in module geom.gui.structure_generator) match_smiles (geom.classes.input_class.input_class attribute) match_substructure() (in module geom.functions.rdkit_module) merge (geom.classes.input_class.input_class attribute) merge_cutoff (geom.classes.input_class.input_class attribute) merge_geoms() (in module geom.functions.tools) (in module geom.functions.various) mesh_output (geom.classes.input_class.input_class attribute) mesh_size (geom.classes.input_class.input_class attribute) messages (desktop_chat_qt.AgentWorker attribute) (desktop_chat_qt.ChatWindow attribute) metal_atomtypes (geom.classes.parameters.parameters attribute), [1] METAL_ELEMENTS (in module geom.gui.structure_gui) microscope() (in module geom.functions.create_geom) min_dist (geom.classes.input_class.input_class attribute) (geom.classes.parameters.parameters attribute), [1] min_dist() (in module geom.functions.various) min_dist_translate (geom.classes.parameters.parameters attribute), [1] mirror_selected_structure() (geom.gui.structure_gui.StructureWindow method) missing_dependency (in module geom.gui.structure_gui) module ai_agents ai_config ai_main ai_runner ai_validator desktop_chat_qt geom geom.__main__ geom.classes geom.classes.input_class geom.classes.molecule geom.classes.parameters geom.functions geom.functions.create_geom geom.functions.general geom.functions.output geom.functions.rdkit_module geom.functions.rotate geom.functions.tools geom.functions.translate geom.functions.various geom.gui geom.gui.structure_generator geom.gui.structure_gui geom.tests geom.tests.test_ test_structure_gui

molecule (class in geom.classes.molecule) mouseMoveEvent() (geom.gui.structure_gui.VdwCanvas method) mousePressEvent() (geom.gui.structure_gui.VdwCanvas method) mouseReleaseEvent() (geom.gui.structure_gui.VdwCanvas method) move_created_geom() (in module geom.tests.test_) move_geom_1_to_000 (geom.classes.input_class.input_class attribute) move_geom_2_to_000 (geom.classes.input_class.input_class attribute) move_geom_to_000 (geom.classes.input_class.input_class attribute) move_input_geom() (in module geom.tests.test_) move_managed_geom() (in module geom.tests.test_) MUTED (in module geom.gui.structure_gui)

N

nAtoms (geom.classes.molecule.molecule attribute), [1]

O

on_agent_reply() (desktop_chat_qt.ChatWindow method) on_anchor_clicked() (desktop_chat_qt.ChatWindow method) origin_CM (geom.classes.input_class.input_class attribute) origin_CM_1 (geom.classes.input_class.input_class attribute) origin_CM_2 (geom.classes.input_class.input_class attribute)

output_root (geom.gui.structure_gui.GenerationWorker attribute) (geom.gui.structure_gui.StructureWindow attribute) ox (geom.gui.structure_gui.ProjectedAtom attribute) oy (geom.gui.structure_gui.ProjectedAtom attribute) oz (geom.gui.structure_gui.ProjectedAtom attribute)

P

paintGL() (geom.gui.structure_gui.VdwCanvas method) pan_x (geom.gui.structure_gui.VdwCanvas attribute) pan_y (geom.gui.structure_gui.VdwCanvas attribute) PANEL (in module geom.gui.structure_gui) param (in module geom.functions.translate) parameters (class in geom.classes.parameters) parse_alloy_arguments() (in module geom.functions.general) parse_bowtie_argument() (in module geom.functions.general) parse_center() (in module geom.functions.general) parse_create() (in module geom.functions.general) parse_dimer_argument() (in module geom.functions.general) parse_merge() (in module geom.functions.general) parse_min() (in module geom.functions.general) parse_mirror() (in module geom.functions.general) parse_rdkit() (in module geom.functions.general) parse_rotation() (in module geom.functions.general) parse_translation() (in module geom.functions.general) pencil() (in module geom.functions.create_geom)

pending_generation_meta (geom.gui.structure_gui.StructureWindow attribute) pentbipyramid() (in module geom.functions.create_geom) pentbipyramid_type (geom.classes.input_class.input_class attribute) pentpyramid() (in module geom.functions.create_geom) plot_2d_molecule() (in module geom.functions.rdkit_module) plot_3d_molecule() (in module geom.functions.rdkit_module) print_computed_distance() (in module geom.functions.output) print_convergence_achieved() (in module geom.functions.output) print_geom() (in module geom.functions.output) print_geom_center() (in module geom.functions.output) print_help() (in module geom.functions.general) print_min_dist() (in module geom.functions.output) print_normal_termination() (in module geom.functions.output) print_optimization_starts() (in module geom.functions.output) print_optimizing_distance() (in module geom.functions.output) ProjectedAtom (class in geom.gui.structure_gui) ProjectedBond (class in geom.gui.structure_gui) pyramid() (in module geom.functions.create_geom)

R

radius (geom.classes.input_class.input_class attribute) (geom.gui.structure_gui.ProjectedAtom attribute) radius_in (geom.classes.input_class.input_class attribute) radius_out (geom.classes.input_class.input_class attribute) rdkit (geom.classes.input_class.input_class attribute) rdkit_abbreviations (geom.classes.input_class.input_class attribute) rdkit_bw (geom.classes.input_class.input_class attribute) rdkit_conformers (geom.classes.input_class.input_class attribute) rdkit_confs (geom.classes.input_class.input_class attribute) rdkit_confs_ext (geom.classes.input_class.input_class attribute) rdkit_confs_prune_rms (geom.classes.input_class.input_class attribute) rdkit_file_conversion (geom.classes.input_class.input_class attribute) rdkit_file_extensions (geom.classes.parameters.parameters attribute) rdkit_file_extensions_confs (geom.classes.parameters.parameters attribute) rdkit_file_extensions_opt (geom.classes.parameters.parameters attribute) rdkit_force_field (geom.classes.input_class.input_class attribute) rdkit_force_fields (geom.classes.parameters.parameters attribute) rdkit_match (geom.classes.input_class.input_class attribute) rdkit_max_iters (geom.classes.input_class.input_class attribute) rdkit_mol_file (geom.classes.input_class.input_class attribute) rdkit_mol_file_extension (geom.classes.input_class.input_class attribute) rdkit_opt (geom.classes.input_class.input_class attribute) rdkit_output_file (geom.classes.input_class.input_class attribute) rdkit_visualize (geom.classes.input_class.input_class attribute) rdkit_visualize_2d (geom.classes.input_class.input_class attribute) rdkit_visualize_3d (geom.classes.input_class.input_class attribute) read_command_line() (in module geom.functions.general) read_geom() (geom.classes.molecule.molecule method) read_input() (geom.classes.input_class.input_class method) read_xyz() (in module geom.gui.structure_generator)

remove_dangling_atoms_metals() (geom.classes.molecule.molecule method) remove_dangling_bonds_graphene() (geom.classes.molecule.molecule method) remove_duplicate_xyz() (geom.classes.molecule.molecule method) remove_H (geom.classes.input_class.input_class attribute) render_msg() (in module desktop_chat_qt) render_resolution (geom.gui.structure_gui.StructureWindow attribute) (geom.gui.structure_gui.VdwCanvas attribute) reset_current_view() (geom.gui.structure_gui.StructureWindow method) reset_view() (geom.gui.structure_gui.VdwCanvas method) resizeGL() (geom.gui.structure_gui.VdwCanvas method) rod() (in module geom.functions.create_geom) rod_3d_mesh() (in module geom.functions.create_geom) rod_core_shell() (in module geom.functions.create_geom) rod_length (geom.classes.input_class.input_class attribute) rod_length_in (geom.classes.input_class.input_class attribute) rod_length_out (geom.classes.input_class.input_class attribute) rod_width (geom.classes.input_class.input_class attribute) rod_width_in (geom.classes.input_class.input_class attribute) rod_width_out (geom.classes.input_class.input_class attribute) rotate (geom.classes.input_class.input_class attribute) rotate() (in module geom.functions.tools) rotate_1 (geom.classes.input_class.input_class attribute) rotate_1() (in module geom.functions.rotate) rotate_angles (geom.classes.input_class.input_class attribute) rotate_angles() (in module geom.functions.rotate) rotate_selected_structure() (geom.gui.structure_gui.StructureWindow method) rotation_x (geom.gui.structure_gui.VdwCanvas attribute) rotation_y (geom.gui.structure_gui.VdwCanvas attribute) run() (desktop_chat_qt.AgentWorker method) (geom.gui.structure_gui.GenerationWorker method) run_geom_command() (in module ai_runner)

S

save_distance_opt() (in module geom.functions.output) save_rdkit_conformers() (in module geom.functions.rdkit_module) save_rdkit_file() (in module geom.functions.rdkit_module) save_structure() (geom.gui.structure_gui.StructureWindow method) second (geom.gui.structure_gui.ProjectedBond attribute) select_case() (in module geom.functions.create_geom) (in module geom.functions.rdkit_module) (in module geom.functions.rotate) (in module geom.functions.translate) (in module geom.functions.various) selection_expression (geom.gui.structure_gui.VdwCanvas attribute) send_btn (desktop_chat_qt.ChatWindow attribute) send_message() (desktop_chat_qt.ChatWindow method) set_atoms() (geom.gui.structure_gui.VdwCanvas method) set_bond_width_scale() (geom.gui.structure_gui.VdwCanvas method) set_render_resolution() (geom.gui.structure_gui.VdwCanvas method) set_vdw_scale() (geom.gui.structure_gui.VdwCanvas method) set_visible_atoms() (geom.gui.structure_gui.VdwCanvas method) setValue() (geom.gui.structure_gui.ViewerStepper method) side_length (geom.classes.input_class.input_class attribute) SIDEBAR (in module geom.gui.structure_gui)

slice_xyz_by_z_threshold() (geom.classes.molecule.molecule method) small_tasks (geom.classes.input_class.input_class attribute) smiles_to_xyz() (in module geom.gui.structure_generator) SOFT_BORDER (in module geom.gui.structure_gui) source_atoms (geom.gui.structure_gui.VdwCanvas attribute) sphere() (in module geom.functions.create_geom) sphere_3d_mesh() (in module geom.functions.create_geom) sphere_center (geom.classes.input_class.input_class attribute) sphere_core_shell() (in module geom.functions.create_geom) spin (geom.gui.structure_gui.ViewerStepper attribute) stereo_annotations (geom.classes.input_class.input_class attribute) strip_terminate_tokens() (in module desktop_chat_qt) StructureResult (class in geom.gui.structure_generator) STRUCTURES (in module geom.gui.structure_gui) StructureWindow (class in geom.gui.structure_gui) subtract_geoms() (in module geom.functions.tools) supported_atomistic_metals() (in module geom.gui.structure_generator) supported_fcc_metals() (in module geom.gui.structure_generator) supported_metals() (in module geom.gui.structure_generator) SUPPORTED_VIEWER_SUFFIXES (in module geom.gui.structure_gui) SURFACE (in module geom.gui.structure_gui) system_prompt (desktop_chat_qt.ChatWindow attribute)

T

test_atom_selection_is_stored_per_tab() (in module test_structure_gui) test_atom_selection_supports_negative_comparisons() (in module test_structure_gui) test_center_to_origin_button_depends_on_selected_structure_center() (in module test_structure_gui) test_center_to_origin_disabled_for_joint_visualization() (in module test_structure_gui) test_controlled_distance() (in module geom.tests.test_) test_controlled_rotation() (in module geom.tests.test_) test_core_shell_generation_reports_au_ag_counts() (in module test_structure_gui) test_create_bowtie() (in module geom.tests.test_) test_create_cone() (in module geom.tests.test_) test_create_cuboctahedra() (in module geom.tests.test_) test_create_decahedra() (in module geom.tests.test_) test_create_dimer() (in module geom.tests.test_) test_create_graphene_disk() (in module geom.tests.test_) test_create_graphene_ribbon() (in module geom.tests.test_) test_create_graphene_ring() (in module geom.tests.test_) test_create_graphene_triangle_armchair() (in module geom.tests.test_) test_create_graphene_triangle_zigzag() (in module geom.tests.test_) test_create_icosahedra() (in module geom.tests.test_) test_create_microscope() (in module geom.tests.test_) test_create_pyramid() (in module geom.tests.test_) test_create_rod() (in module geom.tests.test_) test_create_rod_core_shell() (in module geom.tests.test_) test_create_sphere() (in module geom.tests.test_) test_create_sphere_core_shell() (in module geom.tests.test_) test_create_tip() (in module geom.tests.test_) test_folder_path (in module geom.tests.test_) test_generator_builds_core_shell_and_microscope_commands() (in module test_structure_gui) test_generator_keeps_expected_metal_and_graphene_options() (in module test_structure_gui) test_gui_window_smoke_loads_main_sections() (in module test_structure_gui)

test_install_and_uninstall_scripts_parse() (in module test_structure_gui) test_manipulator_enantiomer_generates_mirrored_xyz() (in module test_structure_gui) test_manipulator_enantiomer_uses_selected_structure_then_centers() (in module test_structure_gui) test_manipulator_source_tracks_selected_viewer_tab() (in module test_structure_gui) test_mixed_metal_cpk_scene_uses_mixed_render_path() (in module test_structure_gui) test_rdkit_optimization() (in module geom.tests.test_) test_remove_duplicate_xyz_preserves_first_atom_labels() (in module geom.tests.test_) test_smiles_tab_uses_typed_title() (in module test_structure_gui) test_specular_geometry() (in module geom.tests.test_) test_structure_gui module test_viewer_atom_selection_filters_current_structure() (in module test_structure_gui) TEXT (in module geom.gui.structure_gui) tip() (in module geom.functions.create_geom) title_label (desktop_chat_qt.ChatWindow attribute) tmp_folder (geom.classes.input_class.input_class attribute) trans_geom_center_to_000() (geom.classes.molecule.molecule method) translate (geom.classes.input_class.input_class attribute) translate_1 (geom.classes.input_class.input_class attribute) translate_1() (in module geom.functions.translate) translate_center (geom.classes.input_class.input_class attribute) translate_center() (in module geom.functions.translate) translate_controlled_distance (geom.classes.input_class.input_class attribute) translate_controlled_distance() (in module geom.functions.translate) translate_geom() (geom.classes.molecule.molecule method) translate_mode (geom.gui.structure_gui.VdwCanvas attribute) translate_pair_controlled_distance() (in module geom.gui.structure_generator) translate_pair_selected_structures() (geom.gui.structure_gui.StructureWindow method) translate_selected_structure() (geom.gui.structure_gui.StructureWindow method) type_label (desktop_chat_qt.ChatWindow attribute)

U

up_button (geom.gui.structure_gui.ViewerStepper attribute)

V

value() (geom.gui.structure_gui.ViewerStepper method) valueChanged (geom.gui.structure_gui.ViewerStepper attribute) VDW_RADII (in module geom.gui.structure_gui) vdw_scale (geom.gui.structure_gui.StructureWindow attribute) (geom.gui.structure_gui.VdwCanvas attribute) VdwCanvas (class in geom.gui.structure_gui)

verbose (geom.classes.input_class.input_class attribute) verbose_inp (geom.classes.input_class.input_class attribute) ViewerStepper (class in geom.gui.structure_gui) ViewerTabBar (class in geom.gui.structure_gui) visualize() (in module geom.functions.rdkit_module) VMD_ELEMENT_LABELS (in module geom.gui.structure_gui) VMD_VDW_RADII (in module geom.gui.structure_gui)

W

warn() (in module geom.functions.output) wheelEvent() (geom.gui.structure_gui.VdwCanvas method) (geom.gui.structure_gui.ViewerTabBar method)

width (geom.gui.structure_gui.ProjectedBond attribute) window() (in module test_structure_gui) worker (geom.gui.structure_gui.StructureWindow attribute)

X

x (geom.gui.structure_generator.AtomRecord attribute) (geom.gui.structure_gui.ProjectedAtom attribute) X_length (geom.classes.input_class.input_class attribute) xyz (geom.classes.molecule.molecule attribute) xyz_center (geom.classes.molecule.molecule attribute), [1]

xyz_max (geom.classes.molecule.molecule attribute), [1] xyz_min (geom.classes.molecule.molecule attribute), [1] xyz_output (geom.classes.input_class.input_class attribute) xyz_path (geom.gui.structure_generator.StructureResult attribute) xyz_to_pdb() (in module geom.functions.rdkit_module)

Y

y (geom.gui.structure_generator.AtomRecord attribute) (geom.gui.structure_gui.ProjectedAtom attribute)

Y_length (geom.classes.input_class.input_class attribute)

Z

z (geom.gui.structure_generator.AtomRecord attribute) (geom.gui.structure_gui.ProjectedAtom attribute) (geom.gui.structure_gui.ProjectedBond attribute) z_max (geom.classes.input_class.input_class attribute)

z_max_paraboloid (geom.classes.input_class.input_class attribute) z_max_pyramid (geom.classes.input_class.input_class attribute) z_min (geom.classes.input_class.input_class attribute) zoom (geom.gui.structure_gui.VdwCanvas attribute)