MatterVis: Crystal Structure Visualization Toolkit

Overview

MatterVis is a Python toolkit for interactive and publication-quality visualization of crystal structures. Built on Dash and Plotly, it provides a browser-based 3D viewer, coordination-topology analysis, ORTEP-style Matplotlib export, and a REST + WebSocket API for agent-driven automation.

Key Features

• Headless CLI — Three subcommands (render, serve, tui) cover the full workflow: CIF → publication-quality figure, interactive 3D viewer, or terminal-based inspection. Ideal for batch processing, CI pipelines, and remote servers
• Browser Viewer — Drag-and-drop CIF upload, interactive 3D display with Mesh3d atoms and bonds, and a fast Scatter3d fallback for large cells. The viewer uses the built-in element palette by default
• Coordination Topology — Automatic coordination-number detection via the nearest-neighbour gap, continuous shape measure (CShM) classification against 12 ideal polyhedra (CN 4–12), planarity RMS, and prism/antiprism twist analysis
• Publication Export — Vendored ORTEP-style Matplotlib renderer with correct depth ordering, two-colour bonds, smart label placement, and configurable presets
• Multi-Panel Figures — uniform_viewport(scenes) stamps a shared world-cube on any list of scenes so every build_figure call emits at the same physical length per pixel
• Automation API — REST + WebSocket endpoints on the same Flask server; drive the viewer from notebooks, agents, or subprocesses
• Zero Catalog Required — Ships with a bundled DAP-4.cif so mat-vis serve works out of the box

Unit Cell — DAP-4 unit cell (flat ORTEP with element colours)

Coordination Shell — A-site coordination with convex hull overlay (CN=9, tricapped trigonal prism)

Three Display Modes — Formula unit, unit cell, and coordination shell side by side

Publication-Quality Export — Colour ORTEP-style Matplotlib renderer with labels

Asymmetric Unit — Diagnostic crystallographic view with atom labels and unit-cell context

Installation

From PyPI (recommended)

pip install matter-vis

From source (development)

git clone https://github.com/SchrodingersCattt/MatterVis.git
cd MatterVis
pip install -e .

All dependencies are declared in pyproject.toml. requires-python = ">=3.10". The available extras are:

molcrys_kit is an optional runtime dependency. When available, the per-fragment A/B/X heuristic uses its classifier; otherwise crystal_viewer uses built-in element/size heuristics.

Quick Start

CLI — one-liner from CIF to figure

Install MatterVis, then render a crystal structure with a single command:

# PNG with default ball-and-stick style
mat-vis render structure.cif -o figure.png

# PDF, full unit cell, ORTEP hatch shading in greyscale
mat-vis render structure.cif -o figure.pdf \
  --view unit_cell --style ortep --ortep-mode ortep_hatch --monochrome

# Interactive HTML for supplementary information
mat-vis render structure.cif -o si_figure.html \
  --show-hydrogen --show-labels

# Launch the interactive browser viewer
mat-vis serve --cif structure.cif

See docs/cli.md for the full flag reference and common recipes.

Python API — programmatic control

from crystal_viewer.loader import build_bundle_scene, build_loaded_crystal
from crystal_viewer.renderer import build_figure
from crystal_viewer.scene import scene_style

bundle = build_loaded_crystal(name="DAP-4", cif_path="scripts/data/DAP-4.cif")
scene  = build_bundle_scene(bundle, display_mode="unit_cell")
style  = scene_style(scene, {"show_unit_cell": True})

fig = build_figure(scene, style)
fig.write_image("dap4.png", width=900, height=720, scale=2)
fig.write_html("dap4.html", include_plotlyjs="cdn")

Command Line Interface

Installing MatterVis also installs the mat-vis command. The CLI is self-documenting; use --help at any level to see the exact arguments:

mat-vis --help
mat-vis render --help
mat-vis serve --help
mat-vis tui --help

The three subcommands cover:

• mat-vis render ... — render atomistic structures and trajectories from CIF, Cube, VASP, XYZ, ASE, and LAMMPS inputs to PNG/PDF/SVG/HTML/GIF/MP4
• mat-vis serve ... — launch the interactive Dash browser viewer with drag-and-drop CIF upload, topology analysis, and REST + WebSocket API
• mat-vis tui ... — terminal-based crystal structure viewer for headless servers and SSH sessions

Documentation

crystal_viewer/ — source code · scripts/ — runnable demo scripts · docs/ — full documentation

License

This project is licensed under the MIT License — see the LICENSE file for details.