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Basic Visualization

Simple Usage

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
normalizeCharge=True Scale colors to full range
showChargeLabels=True Display charge values on atoms

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.