aidsorb.visualize

This module provides helper functions for visualizing molecular point clouds.

Tip

To visualize a molecular point cloud from the CLI:

$ aidsorb visualize path/to/structure

You can also visualize a structure with ase:

from ase.io import read
from ase.visualize import view

atoms = read('path/to/file')
view(atoms)

aidsorb.visualize.draw_pcd(pcd, scheme='cpk', feature_to_color=None, colorscale=None, **kwargs)

Visualize molecular point cloud with Plotly.

Each point pcd[i] is sized based on its atomic number pcd[i, 3].

The color of each point is determined by feature_to_color. If None, the atomic number of each point determines the color. Otherwise, pcd[i, feature_to_color[0]] value determines the color.

Parameters:

• pcd (array of shape (N, 4+C))

• scheme ({'jmol', 'cpk'}, default='jmol') – Takes effect only if feature_to_color=None.

• feature_to_color (tuple of length 2, optional) –

  • feature_to_color[0] == idx, the index of the feature to be colored.

  • feature_to_color[1] == label, the name of the feature for the colorbar.

• colorscale (str, optional) – No effect if feature_to_color=None. For available options, see colorscale.

• **kwargs – Valid keword arguments for plotly.graph_objects.Figure.

Returns:

fig

Return type:

Figure

Examples

>>> pcd = np.random.randint(1, 30, (100, 5))
>>> fig = draw_pcd(pcd, feature_to_color=(0, 'x coord'), colorscale='viridis')

aidsorb.visualize.draw_pcd_from_file(filename, render=True, **kwargs)

Visualize molecular point cloud from a file.

Parameters:

• filename (str) – Absolute or relative path to the file.

• render (bool, default=True) – Render the point cloud with plotly.io.renderers.default.

• **kwargs – Valid keyword arguments for draw_pcd().

Returns:

render

Return type:

Figure if render=False, else None.

aidsorb.visualize.get_atom_colors(atomic_numbers, scheme='cpk')

Convert atomic numbers to colors based on scheme.

Parameters:

• atomic_numbers (array-like of shape (N,))

• scheme ({'jmol', 'cpk'}, default='jmol')

Returns:

colors

Return type:

array of shape (N,)

aidsorb.visualize.get_elements(atomic_numbers)

Convert atomic numbers to element names.

Parameters:

atomic_numbers (array-like of shape (N,))

Returns:

elements

Return type:

array of shape (N,)

Examples

>>> atomic_numbers = np.array([1, 2, 7])
>>> get_elements(atomic_numbers)
array(['Hydrogen', 'Helium', 'Nitrogen'], dtype=object)