ase_notebook.backend.gui module

A module for visualising structures.

The module subclasses ase (v3.18.0) classes, to add additional functionality.

class ase_notebook.backend.gui.AtomGui(config, images=None, element_colors=None)

Bases: ase.gui.gui.GUI

A subclass of the ase GUI, but with additional functionality.

draw(status=True)

Draw all required objects on the canvas.

This is overridden from View, in order to:

• set bond colors, specific to the atom types at each end of the bond.

• add a cross to ‘ghost’ atoms (specified by an array on the atoms)

• add a dash pattern to the unit cell lines

• allow miller index planes to be drawn

move(event)

Handle move event.

release(event)

Handle release event.

set_atoms(atoms)

Set the atoms, unit cell(s) and bonds to draw.

This is overridden from View, in order to

• set bond colors, specific to the atom types at each end of the bond.

• use a modified get_cell_coordinates function, which returns cartesian coordinates, rather than fractional (since they were just converted to cartesian anyway) and can create multiple cells (for each repeat)

• compute miller index planes, by points that intercept with the unit cell

showing_millers()

Return whether to display planes.

class ase_notebook.backend.gui.AtomImages(atoms_list, element_radii=None, radii_scale=0.89)

Bases: ase.gui.images.Images

A subclass of the ase Images, but with additional functionality, for setting radii.

ase_notebook.backend.gui.draw_arc(lbound, diameter, canvas, color, selected, start, extent)

Draw an arc element.

ase_notebook.backend.gui.draw_arrow(canvas, coords, width, scale)

Draw an arrow element.

ase_notebook.backend.gui.draw_axes(canvas, axes, window_size, *, length=15, line_color='black', line_width=1, font_size=14)

Draw the axes element.

ase_notebook.backend.gui.draw_circle(lbound, diameter, canvas, color, selected, tags=(), stroke_width=1)

Draw a circle element, given a lower bound and diameter.

ase_notebook.backend.gui.draw_elements(element_groups, canvas, celldisp, vector_arrays, scale, element_colors, ghost_cross_out=False, movecolor=None, background_color='#ffffff')

Draw elements on a tkinter.Canvas.

Parameters

• element_groups (ase_notebook.draw_elements.DrawGroup) –

• canvas (tkinter.Canvas) –

• celldisp (numpy.array) – cell displacement

• vector_arrays (list) –

• scale (float) – canvas scale (used for drawing vector arrows)

• element_colors (dict) – mapping of element colors (used for partial occupancies)

• ghost_cross_out (bool) – whether to cross out ghost atoms

• movecolor (str or None) – color for moving atom

• background_color (str or None) – color used for coloring partial atom occupancies