rgpycrumbs.geom.fragment_visualization

PyVista-based visualization for molecular fragment analysis.

Renders molecular systems with scalar-coded bond orders using CPK coloring and the batlow colormap from cmcrameri.

Added in version 0.0.6.

Attributes

cmap_name
SCALAR_BAR_ARGS
MIN_DIST_ATM

Functions

visualize_with_pyvista(→ None)

Renders the molecular system with scalar-coded bond orders.

Module Contents

rgpycrumbs.geom.fragment_visualization.cmap_name = 'batlow'

rgpycrumbs.geom.fragment_visualization.SCALAR_BAR_ARGS

rgpycrumbs.geom.fragment_visualization.MIN_DIST_ATM = 0.0001

rgpycrumbs.geom.fragment_visualization.visualize_with_pyvista(atoms: ase.atoms.Atoms, method: rgpycrumbs.geom.fragments.DetectionMethod, bond_data: float | numpy.ndarray, nonbond_cutoff: float = 0.05, bond_threshold: float = 0.8, radius_type: str = 'natural') → None

Renders the molecular system with scalar-coded bond orders.

Added in version 0.0.6.