MolVis renders molecules, simulation boxes, and trajectories straight in the browser, with one engine shared across a web viewer, a VSCode editor, and a Jupyter widget. It reads the common chemistry formats (PDB, XYZ, LAMMPS, Zarr), plays back dynamics frame-by-frame, and lets you select, edit, measure, and annotate structures interactively.

Under active development. Public APIs may change between minor releases.

Vision

Molecular visualization tools have long made you choose: a powerful desktop application that is hard to install and impossible to share, or a lightweight web viewer that cannot keep up once your work gets serious. MolVis exists to erase that trade-off — a single rendering engine that runs anywhere a browser does, with no compromise on what you can see or do.

We want looking at a structure to be frictionless. Drag a file onto a page, open it in your editor next to its input deck, or display it inline in a notebook cell — the viewport, the modes, and the shortcuts are identical everywhere, so the muscle memory you build transfers across every context you work in.

And we want visualization to be more than a picture. MolVis treats editing, measurement, pipeline transforms, and analysis as first-class, fully reversible operations on live molecular data — so the viewer becomes a place where you actually do the work, not just admire the result.

Capabilities

Subsystem	Capability
@molcrafts/molvis-core	Engine library — Babylon.js rendering, commands, modes, pipeline, RPC bridge
Rendering & artist	Ten global molecular representations, adaptive 2-D outlines, surface/cloud shaders, MolVis themes, labels
Interaction modes	View, Select, Edit, Manipulate, Measure — switchable without losing context
Command system	Every operation is a reversible do()/undo() command with full history
Modifier pipeline	Composable, reorderable transforms — slice, expression-select, color, wrap PBC, hide
Analysis	RDF, clustering, MSD, ring detection, topology analysis
I/O	Read/write PDB, XYZ, LAMMPS data & dump, Zarr trajectories
Overlays	Arrows, text labels, vector fields, atom markers anchored to the scene
page	React 19 web app — the single frontend bundle that drives every host
molvis (npm)	VSCode extension — custom editor for .pdb/.xyz/.data/.dump/.lammpstrj
molcrafts-molvis (PyPI)	Python package — drives the page bundle over a local WebSocket, with bidirectional events

Install

npm install @molcrafts/molvis-core

Requires Node.js 22+. The Python package (pip install molcrafts-molvis) needs Python 3.10+; the VSCode extension installs from the Marketplace.

Quick start

import { mountMolvis } from "@molcrafts/molvis-core";
import { readFrames } from "@molcrafts/molvis-core/io";

const container = document.getElementById("viewer");
if (!container) throw new Error("viewer container not found");

const app = mountMolvis(container);
await app.start();

const pdbText = await (await fetch("/structure.pdb")).text();
const [frame] = readFrames(pdbText, "structure.pdb");
app.renderFrame(frame);

See the documentation for the web viewer, the VSCode extension, the Python API, and how to extend the engine.

Documentation

• Tutorial — learn frames, camera, representations, selection, pipeline, trajectories, and export
• Interfaces — Web/TypeScript, Python/Jupyter, and VS Code guides
• Development — embed MolVis and write custom modifiers and commands
• API Reference — TypeScript library and Python package

MolCrafts ecosystem

Project	Role
molpy	Python toolkit — the shared molecular data model & workflow layer
molrs	Rust core — molecular data structures & compute kernels (native + WASM)
molpack	Packmol-grade molecular packing (Rust + Python)
molvis — this repo	WebGL molecular visualization & editing
molexp	Workflow & experiment-management platform
molnex	Molecular machine-learning framework
molq	Unified job queue — local / SLURM / PBS / LSF
molcfg	Layered configuration library
mollog	Structured logging, stdlib-compatible
molhub	Molecular dataset hub
molmcp	MCP server for the ecosystem
molrec	Atomistic record specification

Contributing

Contributions are welcome — see CONTRIBUTING.md or the development guide.

License

BSD-3-Clause — see LICENSE.

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