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                        # 4371 tests, 44 modules
node tests/smoke.mjs            # end-to-end against a real install

npm scripts

| Script | Does | |---|---| | npm test | Jest, 4371 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 and tool names agree across pages | | 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| | npm run build:sitemap | regenerate sitemap.xml from the pages | | npm run check:sitemap | fail if sitemap.xml is out of date | | npm run check:gromacs, check:ndx | compare the .mdp checker and index groups with an installed GROMACS (GMX_BIN) | | npm run check:plumed | compare the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.

stemkit-core holds the computation: 43 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.

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/ | manuscript, LaTeX and Markdown |

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.