Basic Visualization

Simple Usage

PythonCLI

from ase.io import read
from aseview import MolecularViewer

atoms = read("molecule.xyz")
viewer = MolecularViewer(atoms, style="cartoon")
viewer.show()

aseview molecule.xyz --style cartoon

Available Styles

Style	Description
`cartoon`	Cartoon style with black bonds (default)
`default`	Standard CPK coloring
`neon`	Glowing neon effect
`glossy`	Shiny reflective surface
`metallic`	Metallic appearance
`rowan`	Rowan-inspired style
`bubble`	Bubble-like appearance
`grey`	Greyscale rendering

Neon Style Example

viewer = MolecularViewer(atoms, style="neon", backgroundColor="#000000")
viewer.show()

Partial Charge Visualization

Visualize partial charges using colorBy="Charge". Colors: red (negative) → white (neutral) → blue (positive).

import numpy as np
from ase.io import read
from aseview import MolecularViewer

atoms = read("molecule.xyz")
atoms.arrays['charges'] = np.array([...])  # partial charges

viewer = MolecularViewer(atoms, colorBy="Charge")
viewer.show()

Charge Options

Option	Description
`colorBy="Charge"`	Enable charge coloring
`normalizeCharges=True`	Scale colors to full range
`showChargeLabels=True`	Display charge values on atoms

Constraint Visualization

Highlight fixed atoms with showConstraint=True. Fixed atoms from FixAtoms appear with a semi-transparent yellow overlay while keeping their normal element color. The option is only shown when constraints are present.

from ase.constraints import FixAtoms
from aseview import MolecularViewer

atoms.set_constraint(FixAtoms(indices=[0, 1, 2]))
viewer = MolecularViewer(atoms, showConstraint=True)
viewer.show()

See the Solid-State examples for a full surface slab demo.

Customization

viewer = MolecularViewer(
    atoms,
    style="metallic",
    atomSize=0.5,           # Atom radius scale
    bondThickness=0.15,     # Bond radius
    bondThreshold=1.2,      # Bond detection threshold
    backgroundColor="#1a1a2e"
)
viewer.show()

Saving to HTML

viewer = MolecularViewer(atoms)
viewer.save_html("molecule.html")

Creates a standalone HTML file viewable in any browser without Python.