pymatgen.vis.structure_vtk module

This module contains classes to wrap Python VTK to make nice molecular plots.

class MultiStructuresInteractorStyle(parent)

Bases: StructureInteractorStyle

Interactor for MultiStructureVis.

Parameters:

() (parent) –

keyPressEvent(obj, event)

Parameters:

• () (event) –

• () –

class MultiStructuresVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=False, poly_radii_tol_factor=0.5, excluded_bonding_elements=None, animated_movie_options={'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0})

Bases: StructureVis

Visualization for multiple structures.

Parameters:

• element_color_mapping – Optional color mapping for the elements, as a dict of {symbol: rgb tuple}. For example, {“Fe”: (255, 123,0), ….} If None is specified, a default based on Jmol’s color scheme is used.

• show_unit_cell – Set to False to not show the unit cell boundaries. Defaults to True.

• show_bonds – Set to True to show bonds. Defaults to True.

• show_polyhedron – Set to True to show polyhedrons. Defaults to False.

• poly_radii_tol_factor – The polyhedron and bonding code uses the ionic radii of the elements or species to determine if two atoms are bonded. This specifies a tolerance scaling factor such that atoms which are (1 + poly_radii_tol_factor) * sum of ionic radii apart are still considered as bonded.

• excluded_bonding_elements – List of atom types to exclude from bonding determination. Defaults to an empty list. Useful when trying to visualize a certain atom type in the framework (e.g., Li in a Li-ion battery cathode material).

• () (animated_movie_options) – Used for moving.

DEFAULT_ANIMATED_MOVIE_OPTIONS = {'looping_type': 'restart', 'number_of_loops': 1, 'time_between_frames': 0.1, 'time_between_loops': 1.0}

apply_tags()

Apply tags.

display_help()

Display the help for various keyboard shortcuts.

display_info(info)

Parameters:

info (str) – Information.

display_warning(warning)

Parameters:

warning (str) – Warning

erase_info()

Erase all info.

erase_warning()

Remove warnings.

set_animated_movie_options(animated_movie_options=None)

Parameters:

() (animated_movie_options) –

set_structure(structure: Structure, reset_camera=True, to_unit_cell=False)

Add a structure to the visualizer.

Parameters:

• structure – structure to visualize

• reset_camera – Set to True to reset the camera to a default determined based on the structure.

• to_unit_cell – Whether or not to fall back sites into the unit cell.

set_structures(structures: Sequence[Structure], tags=None)

Add list of structures to the visualizer.

Parameters:

• structures (list[Structures]) – structures to be visualized.

• () (tags) – List of tags.

class StructureInteractorStyle(parent)

Bases: object

A custom interactor style for visualizing structures.

Parameters:

() (parent) –

keyPressEvent(obj, event)

Parameters:

• () (event) –

• () –

leftButtonPressEvent(obj, event)

Parameters:

• () (event) –

• () –

leftButtonReleaseEvent(obj, event)

Parameters:

• () (event) –

• () –

mouseMoveEvent(obj, event)

Parameters:

• () (event) –

• () –

class StructureVis(element_color_mapping=None, show_unit_cell=True, show_bonds=False, show_polyhedron=True, poly_radii_tol_factor=0.5, excluded_bonding_elements=None)

Bases: object

Provides Structure object visualization using VTK.

Constructs a Structure Visualization.

Parameters:

• element_color_mapping – Optional color mapping for the elements, as a dict of {symbol: rgb tuple}. For example, {“Fe”: (255, 123,0), ….} If None is specified, a default based on Jmol’s color scheme is used.

• show_unit_cell – Set to False to not show the unit cell boundaries. Defaults to True.

• show_bonds – Set to True to show bonds. Defaults to True.

• show_polyhedron – Set to True to show polyhedrons. Defaults to False.

• poly_radii_tol_factor – The polyhedron and bonding code uses the ionic radii of the elements or species to determine if two atoms are bonded. This specifies a tolerance scaling factor such that atoms which are (1 + poly_radii_tol_factor) * sum of ionic radii apart are still considered as bonded.

• excluded_bonding_elements – List of atom types to exclude from bonding determination. Defaults to an empty list. Useful when trying to visualize a certain atom type in the framework (e.g., Li in a Li-ion battery cathode material).

Useful keyboard shortcuts implemented.

h : Show help A/a : Increase/decrease cell by one unit vector in a-direction B/b : Increase/decrease cell by one unit vector in b-direction C/c : Increase/decrease cell by one unit vector in c-direction # : Toggle showing of polyhedrons - : Toggle showing of bonds [ : Decrease poly_radii_tol_factor by 0.05 ] : Increase poly_radii_tol_factor by 0.05 r : Reset camera direction o : Orthogonalize structure Up/Down : Rotate view along Up direction by 90 clock/anticlockwise Left/right : Rotate view along camera direction by 90 clock/anticlockwise

add_bonds(neighbors, center, color=None, opacity=None, radius=0.1)

Adds bonds for a site.

Parameters:

• neighbors – Neighbors of the site.

• center – The site in the center for all bonds.

• color – Color of the tubes representing the bonds

• opacity – Opacity of the tubes representing the bonds

• radius – Radius of tube s representing the bonds

add_edges(edges, type='line', linewidth=2, color=(0.0, 0.0, 0.0))

Parameters:

• () (linewidth) – List of edges

• () –

• () – Width of line

• color (nd.array/tuple) – RGB color.

add_faces(faces, color, opacity=0.35)

Adding face of polygon.

Parameters:

• () (color) – Coordinates of the faces.

• () – Color.

• opacity (float) – Opacity

add_line(start, end, color=(0.5, 0.5, 0.5), width=1)

Adds a line.

Parameters:

• start – Starting coordinates for line.

• end – Ending coordinates for line.

• color – Color for text as RGB. Defaults to grey.

• width – Width of line. Defaults to 1.

add_partial_sphere(coords, radius, color, start=0, end=360, opacity=1.0)

Adding a partial sphere (to display partial occupancies.

Parameters:

• coords (nd.array) – Coordinates

• radius (float) – Radius of sphere

• () (color) – Color of sphere.

• start (float) – Starting angle.

• end (float) – Ending angle.

• opacity (float) – Opacity.

add_picker()

Create a cell picker.

add_picker_fixed()

Create a cell picker.Returns:

add_polyhedron(neighbors, center, color, opacity=1.0, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)

Adds a polyhedron.

Parameters:

• neighbors – Neighbors of the polyhedron (the vertices).

• center – The atom in the center of the polyhedron.

• color – Color for text as RGB.

• opacity – Opacity of the polyhedron

• draw_edges – If set to True, the a line will be drawn at each edge

• edges_color – Color of the line for the edges

• edges_linewidth – Width of the line drawn for the edges

add_site(site)

Add a site to the render window. The site is displayed as a sphere, the color of which is determined based on the element. Partially occupied sites are displayed as a single element color, though the site info still shows the partial occupancy.

Parameters:

site – Site to add.

add_text(coords, text, color=(0, 0, 0))

Add text at a coordinate.

Parameters:

• coords – Coordinates to add text at.

• text – Text to place.

• color – Color for text as RGB. Defaults to black.

add_triangle(neighbors, color, center=None, opacity=0.4, draw_edges=False, edges_color=(0.0, 0.0, 0.0), edges_linewidth=2)

Adds a triangular surface between three atoms.

Parameters:

• neighbors – Atoms between which a triangle will be drawn.

• color – Color for triangle as RGB.

• center – The “central atom” of the triangle

• opacity – opacity of the triangle

• draw_edges – If set to True, the a line will be drawn at each edge

• edges_color – Color of the line for the edges

• edges_linewidth – Width of the line drawn for the edges

display_help()

Display the help for various keyboard shortcuts.

orthongonalize_structure()

Orthogonalize the structure.

redraw(reset_camera=False)

Redraw the render window.

Parameters:

reset_camera – Set to True to reset the camera to a pre-determined default for each structure. Defaults to False.

rotate_view(axis_ind=0, angle=0)

Rotate the camera view.

Parameters:

• axis_ind – Index of axis to rotate. Defaults to 0, i.e., a-axis.

• angle – Angle to rotate by. Defaults to 0.

set_structure(structure: Structure, reset_camera=True, to_unit_cell=True)

Add a structure to the visualizer.

Parameters:

• structure – structure to visualize

• reset_camera – Set to True to reset the camera to a default determined based on the structure.

• to_unit_cell – Whether or not to fall back sites into the unit cell.

show()

Display the visualizer.

write_image(filename='image.png', magnification=1, image_format='png')

Save render window to an image.

Parameters:

• filename – file to save to. Defaults to image.png.

• magnification – Use it to render high res images.

• image_format – choose between jpeg, png. Defaults to ‘png’.

zoom(factor)

Zoom the camera view by a factor.

make_movie(structures, output_filename='movie.mp4', zoom=1.0, fps=20, bitrate='10000k', quality=1, **kwargs)

Generate a movie from a sequence of structures using vtk and ffmpeg.

Parameters:

• structures ([Structure]) – sequence of structures

• output_filename (str) – filename for structure output. defaults to movie.mp4

• zoom (float) – A zoom to be applied to the visualizer. Defaults to 1.0.

• fps (int) – Frames per second for the movie. Defaults to 20.

• bitrate (str) – Video bitate. Defaults to “10000k” (fairly high quality).

• quality (int) – A quality scale. Defaults to 1.

• kwargs – Any kwargs supported by StructureVis to modify the images generated.