Create and visualize a molecular point cloud

from plotly.io import show

from aidsorb.utils import pcd_from_file
from aidsorb.visualize import draw_pcd

# sphinx_gallery_thumbnail_number = 2

Create the point cloud

# We add electronegativity as additional feature to atomic number.
name, pcd = pcd_from_file('IRMOF-1.xyz', features=['en_pauling'])

print(f'The name of the point cloud is: {name}')
print(f'The point cloud has shape: {pcd.shape}')

The name of the point cloud is: IRMOF-1
The point cloud has shape: (424, 5)

Visualize it

fig = draw_pcd(pcd, scheme='jmol')
fig.update_layout(margin=dict(b=0, t=0, l=0, r=0))  # Optional.
show(fig)

Tip

You can also use the CLI:

$ aidsorb visualize path/to/structure

# Color it by electronegativity.
fig = draw_pcd(pcd, feature_to_color=(4, 'Electronegativity'), colorscale='viridis')
fig.update_layout(margin=dict(b=0, t=0, l=0, r=0))  # Optional.
show(fig)