Polyhedron & Ring Highlight

Two visualization features for structural analysis:

Polyhedron — render coordination polyhedra around atoms in solid-state structures
Ring Highlight — fill aromatic and aliphatic rings in molecules with a semi-transparent color

Polyhedron Visualization

Live Demo: CaSiO₃ (Tetragonal Perovskite)

SiO₄ tetrahedra and CaO₈ polyhedra in CaSiO₃ (2×2×2 supercell, space group I4/mcm):

How It Works

For each atom with coordination number (CN) ≥ 4, a convex hull polyhedron is drawn around its bonded neighbors. The face color is the average CPK color of the three corner atoms for each triangular face.

The bond detection uses scaled covalent radii (controlled by bondThreshold); the polyhedra follow exactly the same neighbor list.

Optionally, thin edge lines (THREE.EdgesGeometry) can be overlaid on each face to make the geometry more legible.

Code Example

NaCl (bulk)From CIF

from ase.build import bulk
from aseview import MolecularViewer

# NaCl rocksalt — Na & Cl are octahedrally coordinated (CN=6)
atoms = bulk("NaCl", "rocksalt", a=5.64) * (2, 2, 2)

viewer = MolecularViewer(
    atoms,
    showPolyhedron=True,       # enable polyhedra
    polyhedronOpacity=0.25,    # face transparency 0.0–1.0
    showPolyhedronEdge=True,   # dark wireframe edges
    polyhedronEdgeOpacity=0.7, # edge visibility 0.0–1.0
)
viewer.show()

from ase.io import read
from aseview import MolecularViewer

atoms = read("structure.cif") * (2, 2, 2)

viewer = MolecularViewer(
    atoms,
    style="default",
    showCell=True,
    showPolyhedron=True,
    polyhedronOpacity=0.25,
    bondThreshold=1.1,
)
viewer.show()

Parameters

Parameter	Type	Default	Description
`showPolyhedron`	`bool`	`False`	Enable polyhedron rendering
`polyhedronOpacity`	`float`	`0.25`	Face transparency (0 = invisible, 1 = solid)
`showPolyhedronEdge`	`bool`	`True`	Show wireframe edge lines on each face
`polyhedronEdgeOpacity`	`float`	`0.70`	Edge line opacity (0 = invisible, 1 = opaque)

Coordination threshold

Only atoms with CN ≥ 4 generate polyhedra. Atoms with fewer bonds (e.g., terminal O in a chain) are skipped.

Edge line width

WebGL does not support linewidth > 1. Edges are always 1 px wide; adjust polyhedronEdgeOpacity to make them more or less prominent.

UI Controls

When Polyhedron is toggled ON in Display Settings, the following controls appear:

Control	Description
Polyhedron Opacity slider	Adjust face transparency
Polyhedron Edge toggle	Show / hide wireframe edges
Edge Opacity slider	Adjust edge line visibility
Exclude Elements chips	Click a chip to remove that element's polyhedra from the view; click again to restore

Ring Highlight

Live Demo: Carbazole

Tricyclic aromatic system: two benzene rings fused to a pyrrole ring (C₁₂H₉N core):

How It Works

A BFS-based ring detection algorithm finds all smallest rings of 4–8 atoms in the molecular bond graph. For each ring, a fan-triangulated face is drawn using the CPK color of the most common element in that ring.

Code Example

BenzeneNaphthaleneFrom XYZ

from ase.build import molecule
from aseview import MolecularViewer

benzene = molecule("C6H6")

viewer = MolecularViewer(
    benzene,
    showRings=True,
    ringOpacity=0.4,
)
viewer.show()

from ase.build import molecule
from aseview import MolecularViewer

naphthalene = molecule("C10H8")

viewer = MolecularViewer(
    naphthalene,
    style="cartoon",
    showRings=True,
    ringOpacity=0.4,
)
viewer.show()

from ase.io import read
from aseview import MolecularViewer

atoms = read("carbazole.xyz")

viewer = MolecularViewer(
    atoms,
    style="cartoon",
    showRings=True,
    ringOpacity=0.35,
    bondThreshold=1.15,
)
viewer.show()

Parameters

Parameter	Type	Default	Description
`showRings`	`bool`	`False`	Enable ring face rendering
`ringOpacity`	`float`	`0.30`	Face transparency (0 = invisible, 1 = solid)

Ring size range

Rings of 4–8 atoms are detected. Larger macrocycles (crown ethers, porphyrins > 8 atoms) are not highlighted.

UI Controls

In the sidebar → Display Settings:

Ring Highlight toggle — show/hide ring faces
Ring Opacity slider — adjust transparency in real time

Combining Both Features

Both features can be enabled simultaneously:

from ase.io import read
from aseview import MolecularViewer

atoms = read("your_structure.cif")

viewer = MolecularViewer(
    atoms,
    showPolyhedron=True,
    polyhedronOpacity=0.2,
    showPolyhedronEdge=True,
    polyhedronEdgeOpacity=0.7,
    showRings=True,
    ringOpacity=0.35,
    showCell=True,
)
viewer.show()