PQViewer

PQViewer opens molecular structures and trajectories from PQ in a local browser, with optional ASE format support. It provides indexed playback, PQ-centred periodic cells, measurements, and reproducible figure export.

Open the web demo · Get started · Jupyter · Viewer guide · Figure guide · Python API

Note

PQViewer is preparing for its first public beta. File and Python interfaces may still change before 1.0.

Quick start

PQViewer requires Python 3.12 or newer.

git clone https://github.com/MolarVerse/PQViewer.git
cd PQViewer
python3 -m venv .venv
source .venv/bin/activate
python -m pip install .
pqviewer examples/water.xyz

The interface is bundled with the Python package. Node.js is not required to install or run the viewer.

Web demo

Interactive SrTiO3 perovskite Drag to rotate. Use Search for Polyhedra.
Open full screen

The fixed-dataset demo keeps edits in the browser. Install PQViewer to open local files, stream trajectories, and run PQAnalysis calculations. See what differs in the web demo.

Trajectory workspace

The timeline provides frame playback and navigation. Selection, measurements, periodic display, and figure export remain in the same workspace.

PQViewer showing a 100-frame UMCM-9 trajectory

UMCM-9 trajectory, frame 1 of 100.

Documentation

Interactive web demo

Use the fixed-dataset viewer and understand its limits.

Web demo
Jupyter

Embed PQViewer in a notebook cell.

Jupyter
Getting started

Installation, optional integrations, and the first trajectory.

Getting started
Viewer guide

Navigation, selection, representations, measurements, and shortcuts.

Viewer guide
Data and conventions

PQ runs, ASE sources, companions, units, and centred periodic cells.

Data sources and periodic conventions
Trajectory analysis

Measurements, tracking, reference frames, and pair analysis.

Trajectory analysis
Figures and recipes

Publication output and reproducible headless rendering.

Figures and recipes
Python API

Open datasets, pass ASE objects, and create an application.

Python API
Troubleshooting

Resolve browser, file, notebook, and figure-rendering problems.

Troubleshooting

Scientific systems

The same viewer and export path cover proteins, isolated molecules, periodic water, crystals, covalent frameworks, and metal-organic frameworks.

Crambin protein shown as a molecular cartoon
Protein — Crambin

PDB 1CRN · 46 residues

Figure recipe

C60 fullerene rendered as a ball-and-stick molecule
Molecule — C60

Isolated fullerene · 60 atoms

Figure recipe

UMCM-9 metal-organic framework
MOF — UMCM-9

Metal-organic framework · 809 atoms

Periodic box containing 27 water molecules
Periodic water

Centred cell · 27 molecules

Figure recipe

Strontium titanate perovskite with complete titanium oxygen octahedra
Crystal — SrTiO3

2 × 2 × 2 perovskite · contained TiO6 octahedra

Figure recipe

Triclinic ACOF covalent organic framework
COF — ACOF

Triclinic covalent organic framework

Gallery images were rendered with PQViewer. Crambin coordinates are from PDB 1CRN. ACOF and UMCM-9 are PQAnalysis examples.