liulab-molviz

Draws DNA sequences and plasmids in the browser, from data a caller hands over; later molecules and protein structures in 3D.

Set it up

This repo uses pixi and nothing else — no pip, no conda, no uv. Clone it, then:

pixi install

Use it

The viewer draws in the browser. It is a JavaScript file this package carries, and Python hands it over as text, ready to go inside a <script> element of a page:

from molviz import viewer_script

script = viewer_script()

The viewer's source is TypeScript, in src/viewer/. pixi run build-js builds it into the package. pixi run check and pixi run build run that step for you.

Use it in another pixi project

The package's name on PyPI is liulab-molviz. To draw with it from another pixi project, add it to the dependencies list under [project] in that project's pyproject.toml:

[project]
dependencies = [
    # ...the project's other requirements
    "liulab-molviz>=2026.10",
]

A project whose settings are in pixi.toml adds liulab-molviz = ">=2026.10" under [pypi-dependencies] instead. Either way, pixi install takes molviz and all it needs from PyPI, and pixi.lock pins the exact release it chose.

Then hand molviz.draw a record and write the drawing to a file:

import molviz

record = {
    "name": "pDemo",
    "circular": True,
    "bases": "ACGT" * 500,
    "features": [
        {"name": "GFP", "type": "CDS", "strand": 1, "segments": [{"start": 100, "end": 820}]},
    ],
}
molviz.draw(record).write("pDemo.html")

The file's ending picks what is written. An .html file is a page that opens offline and draws the record in the browser. An .svg, .png or .pdf file holds the drawing itself, made with no browser. The API reference lists every option draw takes, and the test records show what else a record can hold.

Check your work

pixi run check

That runs the linters, the type checker and the tests. It reports every failure at once, so read to the bottom before you fix anything.

Read the docs

The site is at https://liuhlab.github.io/liulab-molviz/. Build it yourself with pixi run docs-build.

Set up your agent

Skills for coding agents live in skills/. Link them into each agent's own folder:

python skills/install.py --target all

If you work on the lab's clusters, add the shared plugin once per machine:

/plugin marketplace add liuhlab/liulab-compute-skills
/plugin install lab-compute@liulab