hofmann 0.15.0

A modern Python reimagining of the XBS ball-and-stick crystal structure viewer

hofmann

A modern Python reimagining of Methfessel's XBS ball-and-stick viewer (1995), named after August Wilhelm von Hofmann who built the first ball-and-stick molecular models in 1865.

hofmann renders crystal and molecular structures as depth-sorted ball-and-stick images with static, publication-quality vector output (SVG, PDF) via matplotlib.

Features

• Static publication-quality output (SVG, PDF, PNG) via matplotlib
• XBS .bs and .mv (trajectory) file formats
• Optional ASE Atoms and pymatgen Structure interoperability
• Periodic boundary conditions with automatic image expansion
• Coordination polyhedra with configurable shading and slab clipping
• Unit cell wireframe rendering
• Interactive viewer with mouse rotation, zoom, and keyboard controls
• Orthographic and perspective projection

Installation

pip install hofmann

For ASE interoperability:

pip install "hofmann[ase]"

For pymatgen interoperability:

pip install "hofmann[pymatgen]"

Requirements

• Python 3.11+
• numpy >= 1.24
• matplotlib >= 3.7
• scipy >= 1.10
• ase >= 3.22 (optional)
• pymatgen >= 2024.1.1 (optional)

Quick start

From an XBS file

from hofmann import StructureScene

scene = StructureScene.from_xbs("structure.bs")
scene.render_mpl("output.svg")

From ASE Atoms

from ase.build import bulk
from hofmann import StructureScene, BondSpec

atoms = bulk("Si", "diamond", a=5.43)
bonds = [BondSpec(species=("Si", "Si"), max_length=2.8)]
scene = StructureScene.from_ase(atoms, bonds)
scene.render_mpl("si.pdf")

From a pymatgen Structure

from pymatgen.core import Lattice, Structure
from hofmann import StructureScene, BondSpec

lattice = Lattice.cubic(5.43)
structure = Structure(
    lattice, ["Si"] * 8,
    [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0],
     [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
     [0.25, 0.25, 0.25], [0.75, 0.75, 0.25],
     [0.75, 0.25, 0.75], [0.25, 0.75, 0.75]],
)

bonds = [BondSpec(species=("Si", "Si"), max_length=2.8)]
scene = StructureScene.from_pymatgen(structure, bonds)
scene.render_mpl("si.pdf")

Controlling the view

scene.view.look_along([1, 1, 0])   # View along [110]
scene.view.zoom = 1.5              # Zoom in
scene.view.perspective = 0.3       # Mild perspective
scene.render_mpl("rotated.svg")

Interactive viewer

view, style = scene.render_mpl_interactive()

# Reuse the adjusted view for static output:
scene.view = view
scene.render_mpl("final.svg", style=style)

Documentation

Full documentation is available at hofmann.readthedocs.io, covering:

• Getting started -- installation and first renders
• Scenes and structures -- scenes, frames, bonds, polyhedra
• Rendering -- views, render styles, unit cells, axes
• Colouring -- per-atom data colouring, custom functions, multiple layers
• Interactive viewer -- mouse and keyboard controls
• XBS file format -- .bs and .mv format reference
• API reference -- full autodoc API

Citing hofmann

If you use hofmann in published work, please cite it:

B. J. Morgan, hofmann, https://github.com/bjmorgan/hofmann

A machine-readable citation is available in CITATION.cff.

Licence

MIT. See LICENSE for details.