geom.gui.structure_gui

Native Qt GUI for creating and visualizing GEOM XYZ structures.

Classes

`ProjectedAtom`
`ProjectedBond`
`GenerationWorker`
`VdwCanvas`
`ViewerStepper`
`ViewerTabBar`	Compact tab bar with drag reordering and wheel navigation.
`StructureWindow`

Functions

`atom_matches_selection`(→ bool)	Evaluate a VMD-like coordinate selection expression for one atom.
`_normalize_selection_expression`(→ str)
`_evaluate_selection_node`(→ bool \| float \| str)
`_compare_selection_values`(→ bool)
`main`(→ int)

Module Contents

geom.gui.structure_gui.missing_dependency[source]

geom.gui.structure_gui.APP_TITLE = 'GEOM Structure Studio'[source]

geom.gui.structure_gui.SUPPORTED_VIEWER_SUFFIXES[source]

geom.gui.structure_gui.CHATGPT_GREEN = '#10A37F'[source]

geom.gui.structure_gui.TEXT = '#202123'[source]

geom.gui.structure_gui.MUTED = '#6E6E80'[source]

geom.gui.structure_gui.SURFACE = '#FFFFFF'[source]

geom.gui.structure_gui.CANVAS = '#F7F7F8'[source]

geom.gui.structure_gui.BORDER = '#D9D9E3'[source]

geom.gui.structure_gui.SIDEBAR = '#ECECF1'[source]

geom.gui.structure_gui.SOFT_BORDER = '#ECECF1'[source]

geom.gui.structure_gui.PANEL = '#FFFFFF'[source]

geom.gui.structure_gui.ACCENT_VIOLET = '#4F00B5'[source]

geom.gui.structure_gui.ACCENT_INDIGO = '#0600A0'[source]

geom.gui.structure_gui.ACCENT_SOFT = '#F4F0FF'[source]

geom.gui.structure_gui.GL_COLOR_BUFFER_BIT = 16384[source]

geom.gui.structure_gui.GL_DEPTH_BUFFER_BIT = 256[source]

geom.gui.structure_gui.GL_TRIANGLE_STRIP = 5[source]

geom.gui.structure_gui.GL_COMPILE = 4864[source]

geom.gui.structure_gui.GL_LEQUAL = 515[source]

geom.gui.structure_gui.GL_FRONT_AND_BACK = 1032[source]

geom.gui.structure_gui.GL_FRONT = 1028[source]

geom.gui.structure_gui.GL_BACK = 1029[source]

geom.gui.structure_gui.GL_CULL_FACE = 2884[source]

geom.gui.structure_gui.GL_DEPTH_TEST = 2929[source]

geom.gui.structure_gui.GL_LIGHTING = 2896[source]

geom.gui.structure_gui.GL_LIGHT0 = 16384[source]

geom.gui.structure_gui.GL_COLOR_MATERIAL = 2903[source]

geom.gui.structure_gui.GL_NORMALIZE = 2977[source]

geom.gui.structure_gui.GL_POLYGON_OFFSET_FILL = 32823[source]

geom.gui.structure_gui.GL_LINE = 6913[source]

geom.gui.structure_gui.GL_FILL = 6914[source]

geom.gui.structure_gui.GL_MODELVIEW = 5888[source]

geom.gui.structure_gui.GL_PROJECTION = 5889[source]

geom.gui.structure_gui.GL_AMBIENT = 4608[source]

geom.gui.structure_gui.GL_DIFFUSE = 4609[source]

geom.gui.structure_gui.GL_POSITION = 4611[source]

geom.gui.structure_gui.GL_SPECULAR = 4610[source]

geom.gui.structure_gui.GL_SHININESS = 5633[source]

geom.gui.structure_gui.GL_AMBIENT_AND_DIFFUSE = 5634[source]

geom.gui.structure_gui.GL_SMOOTH = 7425[source]

geom.gui.structure_gui.VMD_ELEMENT_LABELS = ('X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S',...[source]

geom.gui.structure_gui.VMD_VDW_RADII = (1.5, 1.0, 1.4, 1.82, 2.0, 2.0, 1.7, 1.55, 1.52, 1.47, 1.54, 1.36, 1.18, 2.0, 2.1, 1.8, 1.8,...[source]

geom.gui.structure_gui.VDW_RADII[source]

geom.gui.structure_gui.DEFAULT_VMD_PINK[source]

geom.gui.structure_gui.ELEMENT_COLORS[source]

geom.gui.structure_gui.CPK_COLORS[source]

geom.gui.structure_gui.CPK_DEFAULT[source]

geom.gui.structure_gui.METAL_ELEMENTS[source]

geom.gui.structure_gui.COVALENT_RADII[source]

geom.gui.structure_gui.STRUCTURES[source]

geom.gui.structure_gui.GRAPHENE_VARIANTS[source]

class geom.gui.structure_gui.ProjectedAtom[source]

index: int[source]

element: str[source]

x: float[source]

y: float[source]

z: float[source]

radius: float[source]

depth_radius: float[source]

cpk: bool[source]

ox: float[source]

oy: float[source]

oz: float[source]

class geom.gui.structure_gui.ProjectedBond[source]

first: ProjectedAtom[source]

second: ProjectedAtom[source]

z: float[source]

width: float[source]

geom.gui.structure_gui.atom_matches_selection(atom: geom.gui.structure_generator.AtomRecord, expression: str) → bool[source]: Evaluate a VMD-like coordinate selection expression for one atom.

geom.gui.structure_gui._normalize_selection_expression(expression: str) → str[source]

geom.gui.structure_gui._evaluate_selection_node(node: ast.AST, values: dict[str, float | str]) → bool | float | str[source]

geom.gui.structure_gui._compare_selection_values(left: bool | float | str, operator: ast.cmpop, right: bool | float | str) → bool[source]

class geom.gui.structure_gui.GenerationWorker(command_args: list[str], output_root: pathlib.Path, parent=None)[source]

Bases: PySide6.QtCore.QThread

generated[source]

failed[source]

command_args[source]

output_root[source]

run()[source]

class geom.gui.structure_gui.VdwCanvas(parent=None)[source]

Bases: PySide6.QtOpenGLWidgets.QOpenGLWidget

files_dropped[source]

atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis] = ()[source]

source_atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis] = ()[source]

selection_expression = ''[source]

rotation_x = 0.0[source]

rotation_y = 0.0[source]

zoom = 1.0[source]

pan_x = 0.0[source]

pan_y = 0.0[source]

vdw_scale = 1.45[source]

bond_width_scale = 1.65[source]

render_resolution = 1[source]

translate_mode = False[source]

_is_interacting = False[source]

_last_pos: PySide6.QtCore.QPoint | None = None[source]

_sphere_cache: dict[tuple[str, int, int, bool], PySide6.QtGui.QPixmap][source]

_gl = None[source]

_sphere_list = 0[source]

_sphere_mesh = [][source]

_interaction_timer[source]

set_atoms(atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis])[source]

set_visible_atoms(atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis])[source]

reset_view()[source]

set_vdw_scale(value: float)[source]

set_bond_width_scale(value: float)[source]

set_render_resolution(value: int)[source]

_begin_interaction()[source]

_finish_interaction()[source]

mousePressEvent(event)[source]

mouseMoveEvent(event)[source]

mouseReleaseEvent(event)[source]

wheelEvent(event)[source]

keyPressEvent(event)[source]

_is_reset_view_key(event) → bool[source]

dragEnterEvent(event)[source]

dropEvent(event)[source]

_structure_paths_from_event(event) → list[pathlib.Path][source]

initializeGL()[source]

resizeGL(width: int, height: int)[source]

paintGL()[source]

_make_painter(fine_render: bool) → PySide6.QtGui.QPainter[source]

_paint_axes_overlay()[source]

_paint_background(painter: PySide6.QtGui.QPainter)[source]

_project_atoms() → list[ProjectedAtom][source]

_atom_uses_cpk(element: str) → bool[source]

_scene_has_cpk() → bool[source]

_uses_vdw_opengl(projected: list[ProjectedAtom]) → bool[source]

_uses_mixed_vdw_cpk(projected: list[ProjectedAtom]) → bool[source]

_paint_mixed_vdw_cpk(projected: list[ProjectedAtom])[source]

_paint_bonds_and_atoms(painter: PySide6.QtGui.QPainter, bond_source: list[ProjectedAtom], atoms: list[ProjectedAtom])[source]

_paint_vdw_opengl(projected: list[ProjectedAtom])[source]

_build_sphere_mesh(stacks: int, slices: int) → list[list[tuple[float, float, float]]][source]

_draw_unit_sphere(gl)[source]

_draw_unit_sphere_mesh(gl)[source]

_uses_vdw_impostors(projected: list[ProjectedAtom]) → bool[source]

_uses_vdw_surface_buffer(projected: list[ProjectedAtom]) → bool[source]

_paint_vdw_surface_buffer(painter: PySide6.QtGui.QPainter, projected: list[ProjectedAtom])[source]

_vdw_surface_render_scale(width: int, height: int, atom_count: int) → float[source]

_paint_vdw_impostors(painter: PySide6.QtGui.QPainter, projected: list[ProjectedAtom])[source]

_sphere_pixmap(atom: ProjectedAtom) → PySide6.QtGui.QPixmap[source]

_paint_vdw_depth_buffer(painter: PySide6.QtGui.QPainter, projected: list[ProjectedAtom])[source]

_vdw_depth_render_scale(width: int, height: int, atom_count: int) → float[source]

_view_light_vector() → tuple[float, float, float][source]

_projected_bonds(projected: list[ProjectedAtom]) → list[ProjectedBond][source]

_paint_bond(painter: PySide6.QtGui.QPainter, bond: ProjectedBond)[source]

_paint_atom(painter: PySide6.QtGui.QPainter, atom: ProjectedAtom)[source]

_use_lit_atom_rendering(atom: ProjectedAtom) → bool[source]

_rotate_point(x: float, y: float, z: float) → tuple[float, float, float][source]

_paint_axes(painter: PySide6.QtGui.QPainter)[source]

class geom.gui.structure_gui.ViewerStepper(value: int, minimum: int, maximum: int, suffix: str, parent=None)[source]

Bases: PySide6.QtWidgets.QWidget

valueChanged[source]

spin[source]

up_button[source]

down_button[source]

setValue(value: int)[source]

value() → int[source]

class geom.gui.structure_gui.ViewerTabBar(parent=None)[source]

Bases: PySide6.QtWidgets.QTabBar

Compact tab bar with drag reordering and wheel navigation.

wheelEvent(event)[source]

class geom.gui.structure_gui.StructureWindow[source]

Bases: PySide6.QtWidgets.QMainWindow

worker: GenerationWorker | None = None[source]

current_result: geom.gui.structure_generator.StructureResult | None = None[source]

output_root: pathlib.Path | None = None[source]

empty_canvas: VdwCanvas | None = None[source]

pending_generation_meta: dict[str, object][source]

vdw_scale = 1.45[source]

bond_width_scale = 1.65[source]

render_resolution = 1[source]

_build_ui()[source]

_field_label(text: str) → PySide6.QtWidgets.QLabel[source]

_configure_dropdown_popups()[source]

_section_label(text: str) → PySide6.QtWidgets.QLabel[source]

_make_canvas() → VdwCanvas[source]

_make_viewer_spin(value: int, minimum: int, maximum: int, suffix: str) → ViewerStepper[source]

reset_current_view()[source]

keyPressEvent(event)[source]

_make_manipulator_spin(value: float, minimum: float, maximum: float, suffix: str) → PySide6.QtWidgets.QDoubleSpinBox[source]

_make_option_spin(value: float, minimum: float, maximum: float) → PySide6.QtWidgets.QDoubleSpinBox[source]

_material_items() → list[str][source]

_refresh_material_controls()[source]

_available_structures_for_material(material: str) → list[str][source]

_refresh_structure_controls()[source]

_configure_parameter_widget(label: PySide6.QtWidgets.QLabel, spin: PySide6.QtWidgets.QDoubleSpinBox, text: str, value: float, minimum: float, maximum: float)[source]

_ordered_metals(metals: list[str]) → list[str][source]

_refresh_option_controls()[source]

_set_optional_row_enabled(widgets, enabled: bool)[source]

_apply_atom_selection(*_args)[source]

_sync_atom_selection_input()[source]

_set_atom_selection_invalid(invalid: bool)[source]

_set_vdw_scale_from_input(value: int)[source]

_set_render_resolution_from_input(value: int)[source]

_set_bond_width_from_input(value: int)[source]

_refresh_smiles_button_state()[source]

_all_canvases() → list[VdwCanvas][source]

_apply_styles()[source]

create_structure()[source]

load_files_from_dialog()[source]

load_files(paths: list[pathlib.Path])[source]

load_smiles_from_input()[source]

_add_structure_tab(title: str, atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis], path: pathlib.Path | None = None, metadata: dict[str, object] | None = None)[source]

_install_tab_menu(tab_index: int, canvas: VdwCanvas)[source]

save_structure(canvas: VdwCanvas)[source]

_save_source_for_canvas(canvas: VdwCanvas) → pathlib.Path | None | bool[source]

_write_xyz(path: pathlib.Path, atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis])[source]

delete_structure_tab(canvas: VdwCanvas)[source]

_refresh_manipulator_sources(sync_to_current_tab: bool = False)[source]

_refresh_manipulator_actions(*_args)[source]

_center_to_origin_available() → bool[source]

_current_viewer_tab_is_joint() → bool[source]

_atoms_are_centered(atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis], tolerance: float = 1e-06) → bool[source]

_selected_manipulator_path() → pathlib.Path[source]

_run_manipulation(command_builder)[source]

center_selected_structure()[source]

mirror_selected_structure()[source]

rotate_selected_structure()[source]

translate_selected_structure()[source]

translate_pair_selected_structures()[source]

_minimum_distance(first: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis], second: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis]) → float[source]

_short_tab_title(title: str) → str[source]

_sync_current_tab_meta()[source]

_generation_metadata() → dict[str, object][source]

_metadata_for_generated_atoms(atoms: tuple[geom.gui.structure_generator.AtomRecord, Ellipsis]) → dict[str, object][source]

_build_command_args() → list[str][source]

_fmt(value: float) → str[source]

_structure_ready(result: geom.gui.structure_generator.StructureResult)[source]

_structure_failed(details: str)[source]

closeEvent(event)[source]

geom.gui.structure_gui.main() → int[source]

`missing_dependency`
`APP_TITLE`
`SUPPORTED_VIEWER_SUFFIXES`
`CHATGPT_GREEN`
`TEXT`
`MUTED`
`SURFACE`
`CANVAS`
`BORDER`
`SIDEBAR`
`SOFT_BORDER`
`PANEL`
`ACCENT_VIOLET`
`ACCENT_INDIGO`
`ACCENT_SOFT`
`GL_COLOR_BUFFER_BIT`
`GL_DEPTH_BUFFER_BIT`
`GL_TRIANGLE_STRIP`
`GL_COMPILE`
`GL_LEQUAL`
`GL_FRONT_AND_BACK`
`GL_FRONT`
`GL_BACK`
`GL_CULL_FACE`
`GL_DEPTH_TEST`
`GL_LIGHTING`
`GL_LIGHT0`
`GL_COLOR_MATERIAL`
`GL_NORMALIZE`
`GL_POLYGON_OFFSET_FILL`
`GL_LINE`
`GL_FILL`
`GL_MODELVIEW`
`GL_PROJECTION`
`GL_AMBIENT`
`GL_DIFFUSE`
`GL_POSITION`
`GL_SPECULAR`
`GL_SHININESS`
`GL_AMBIENT_AND_DIFFUSE`
`GL_SMOOTH`
`VMD_ELEMENT_LABELS`
`VMD_VDW_RADII`
`VDW_RADII`
`DEFAULT_VMD_PINK`
`ELEMENT_COLORS`
`CPK_COLORS`
`CPK_DEFAULT`
`METAL_ELEMENTS`
`COVALENT_RADII`
`STRUCTURES`
`GRAPHENE_VARIANTS`

geom.gui.structure_gui

Attributes

Classes

Functions

Module Contents