A browser-based visual editor for building Martini 3 coarse-grained molecule mappings.

No installation is required. Open the site in a WebGL-capable browser:

Open CGBuilder

Load an all-atom structure, map beads interactively in a 3D viewer, get automated bead-type predictions, compare SASA values against your AA reference, and export ready-to-use mapping files.

Fork of jbarnoud/cgbuilder, substantially extended with weighted atom assignment, bead-type prediction, SASA comparison, Shaker-format import/export, and more...

Features

• 3D viewer — interactive NGL.js viewport with licorice AA representation and coloured CG bead spheres overlaid in real time.
• Weighted atom assignment — click an atom once to add it to a bead; click again to increase its weight (pulling the bead centre toward that atom); Shift+click to reduce weight or remove.
• Bead-type prediction — inspired by AutoMartini, using RDKit fragment free-energy-of-transfer heuristics. Suggestion chips appear next to each field; applying them is always an explicit click.
• SASA comparison — built-in Shrake-Rupley solver computes per-bead SASA and compares it against the all-atom reference surface rendered by NGL.
• Live validation — multi-residue warnings, capped-heteroatom bond-cutting warnings, atom-overlap detection, and bead-count/size guidelines displayed as you work.
• Shaker-format import — paste an existing mapping to restore beads, types, charges, and atom assignments automatically.
• Export — .gro (CG coordinates), .ndx (atom-index groups), .map (martinize/backward mapping), Shaker Python dict, Bartender mapping, and AA SMILES.

Input formats

Format	Load molecule	Notes
.pdb	✓	Bond orders inferred; explicit H needed for prediction
.gro	✓	GROMACS coordinate file; explicit H needed for prediction

Explicit hydrogens required for bead-type prediction and AA SMILES export. Use a protonation tool before loading if needed.

Export formats

File	Contents
.gro	CG bead coordinates in GROMACS format
.ndx	GROMACS index file — one group per bead, atoms by index
.map	Martini backward/martinize mapping — [ to ]/[ martini ]/[ atoms ] sections
Shaker dict	Shaker-format Python assignment dict — bead names, types, charges, atom lists
Bartender mapping	BEADS section + one line per bead with 1-based atom indices (repeated by weight)
PyCGTOOL mapping	PyCGTOOL .map — [ resname ] section + one line per bead (name type charge atoms…)
AA SMILES	SMILES string for each bead's fragment (requires explicit H)

Running tests

npm test             # single run
npm run test:watch   # watch mode

Tests cover all modules. No browser or DOM dependency is required; the suite runs in Node via Vitest with minimal stubs for NGL and RDKit globals.

---

Dependencies

Library	Purpose
NGL	3D molecular viewer (npm, bundled)
@rdkit/rdkit	SMILES generation and fragment canonicalisation (npm, code-split)
marked	Markdown rendering for in-app docs (npm, bundled)

Development tooling includes TypeScript, ESLint, Prettier, esbuild, Vitest, TypeDoc, Husky, and lint-staged.

Self-deployment

CGBuilder is a static web application. You can build it locally and publish the generated dist/ directory to any static hosting provider or web server.

Node.js 24 is required for building. The repository includes .nvmrc for version managers such as nvm. If you do not use nvm, install Node.js 24 through your preferred method.

git clone https://github.com/Lp0lp/cgbuilder.git
cd cgbuilder
nvm use
npm ci
npm run check

npm run check runs the lint, formatting, test, and production-build checks. After it completes, publish the contents of dist/ to your hosting provider.

Developer workflow

Start the development server with live reload:

npm run dev

Useful commands:

npm run fix           # apply ESLint fixes, then format files
npm run check         # lint, format check, tests, and build
npm test              # run tests once
npm run test:watch    # run tests in watch mode
npm run docs          # generate API documentation

• Code quality is enforced with ESLint.
• Formatting is enforced with Prettier.
• Husky automatically runs lint-staged on staged files before each commit. ESLint runs first, followed by Prettier.
• The GitHub Actions workflow repeats the checks in read-only mode for pull requests and validated builds.

Acknowledgements

• Original CGBuilder by @jbarnoud
• Bead-type prediction approach inspired by AutoMartini (Bereau & Kremer, 2015) and extended for Martini 3 by Szczuka et al., JCTC 2025
• Shrake-Rupley SASA algorithm: Shrake & Rupley, J. Mol. Biol. 1973
• Martini 3 force field