STEMKit

Browser tools for computational chemistry, plus stemkit-core, the tested library underneath them.

All computation is client-side. No uploads, no accounts, no install. Tools work offline once the page loads.

Live: https://stemkit.net

Quick start

Serve the site (static, no build step):

git clone https://github.com/LD-Shell/stemkit.git
cd stemkit
python3 -m http.server 8000     # then open http://localhost:8000/

Opening the HTML files over file:// will not work. Seventeen tools load ES modules, which browsers block outside HTTP.

Use the library, from npm (Node 18 or later, no dependencies):

npm install stemkit-core

import { readFileSync } from 'node:fs';
import { parseXvg, extractColumn, columnStats } from 'stemkit-core';

const { matrix } = parseXvg(readFileSync('rmsd.xvg', 'utf8'));
console.log(columnStats(extractColumn(matrix, 1)));

Run the tests, from a clone:

npm install
npm test                        # 4989 tests, 44 modules
node tests/smoke.mjs            # end-to-end against a real install

npm scripts

Script	Does
npm test	Jest, 4989 tests
npm run test:coverage	coverage report (see docs/COVERAGE.md)
npm run check:links	internal and external link check
npm run check:links:internal	internal only, no network
npm run check:chrome	shared header, theme script, tool names, footer version and CSP agree across pages
npm run build:csp, check:csp	write or check each page's Content-Security-Policy (run build:csp after editing an inline script)
npm run build:css	rebuild Tailwind after editing src/tailwind/input.css
npm run watch:css	same, on change
npm run build:sitemap	regenerate sitemap.xml from the pages
npm run check:sitemap	fail if sitemap.xml misses a page or dates one before its last commit
npm run check:gromacs, check:ndx	compare the .mdp checker and index groups with an installed GROMACS (GMX_BIN)
npm run check:plumed	compare the PLUMED input reader with installed PLUMED versions (PLUMED_BINS)
npm run check:lammps, check:lammps-data, check:lammps-workflow	compare the LAMMPS input checker, data-file reader and workflow builder with an installed LAMMPS (LMP_BIN)
npm run build:lammps-docs	regenerate the LAMMPS reference tables from a LAMMPS source tree

What is here

18 research tools:

Area	Tools
Data and statistics	plot digitiser, data cleaner, statistics calculator, error-bar generator, outlier detector, curve fitter, plot builder
Molecular simulation	XVG visualiser, structure inspector, coordinate manipulator, MD workflow generator (GROMACS, LAMMPS, PLUMED)
Writing and citations	BibTeX sanitiser, BibTeX deduplicator, DOI to BibTeX, journal abbreviator (ISO 4), visual LaTeX tables, equation formatter
Units	scientific converter: energy, length, time, force, pressure, dipole, charge, polarizability, spectroscopy, temperature, heat capacity

Three further pages are workflow helpers, not research tools, and are not part of the scholarly contribution: Pomodoro timer, decision matrix, kinetics sandbox.

Every research tool has a narrated video tutorial, shown on the tool's page (the MD workflow generator has one for each engine) and collected in the STEMKit Tutorials playlist on YouTube. The player loads from YouTube only when play is pressed.

stemkit-core holds the computation: 42 DOM-free domain modules, plus an aggregate export (index.js), a Node entry (node.js), a dependency-injection layer (vendor.js) and the release version (version.js). API reference in src/core/README.md.

Who it is for

Researchers in computational chemistry and the experimental sciences who need a correct answer without installing anything or uploading their data: checking a trajectory, comparing replicates, fitting a model, digitising a figure, setting up and checking GROMACS, LAMMPS and PLUMED inputs, and preparing figures, tables and references. Every tool writes, or is backed by, code that repeats its result, so what was done in the browser can be reproduced.

Why the computation is a separate library

Client-side tools are good for privacy and bad for reproducibility: a figure produced by clicking is hard to regenerate six months later. Moving the computation into an importable library makes the same code path scriptable, version-pinnable and testable.

Docs

File	Covers
src/core/README.md	library API
docs/SETUP.md	layout, deployment, gotchas
docs/COVERAGE.md	reading the coverage report
docs/CSS.md	stylesheets and where rules belong
docs/FIGURES.md	the shared plot area and Python script on every plotting page
CHANGELOG.md	changes, including output-affecting fixes
CONTRIBUTING.md	contributing, and where code belongs
THIRD_PARTY_LICENSES.md	licences of vendored libraries and of the GROMACS, PLUMED and LAMMPS reference data
paper/	the JOSS paper (paper.md) and the preprint (preprint.tex, preprint.md, preprint.pdf)

Contributing and support

Report a bug or ask a question in the issue tracker. Contributions are welcome: CONTRIBUTING.md explains where code belongs, how to run the tests and what a pull request should contain, and CODE_OF_CONDUCT.md applies to every space of the project.

Citing

10.5281/zenodo.21543112

Resolves to the current release. Machine-readable metadata in CITATION.cff.

Licence

MIT, see LICENSE. Vendored libraries under js/dependencies/ keep their own licences: THIRD_PARTY_LICENSES.md.