ChemDoodle

ChemDoodle is a family of chemical graphics and cheminformatics software produced by iChemLabs, active since 2007. It spans a desktop drawing/publishing application (ChemDoodle 2D), a molecular modeling package (ChemDoodle 3D), and, most relevant here, ChemDoodle Web Components (CWC) — a pure-JavaScript, HTML5 library for rendering and editing chemical structures, reactions, and spectra in the browser. CWC was documented in a 2015 Journal of Cheminformatics paper and is dual-licensed under GPL v3 and a proprietary commercial license.

Internally, CWC represents chemistry with a molecular graph: atom, bond, and ring objects held in arrays, carrying element, charge, stereochemistry, and query-notation attributes. Its native serialization is ChemDoodle JSON, a lightweight object notation that round-trips the full library data model. Two-dimensional depictions are drawn on the HTML5 <canvas> element, while 3D scenes (ball-and-stick, wireframe, ribbon and pipe-and-plank protein views, and crystal cells) are rendered with WebGL for hardware acceleration. A configurable 2D sketcher — offered in simplified, full, and query variants — lets users draw structures and export them.

In the graph-data and format-conversion landscape, CWC is a client-side reader/writer for common molecular formats rather than a general graph converter. It natively parses MDL Molfiles (format:molfile, V2000 and V3000), MDL RXN reaction files, format:cml, format:xyz, format:pdb, JCAMP-DX spectra, and CIF crystallographic files; it natively writes Molfile, RXN, and CML. Line notations and richer conversions are offloaded to iChemLabs cloud services: format:smiles parsing, format:inchi, format:cdxml/CDX ChemDraw files, IUPAC name-to-structure, spectrum simulation, and property calculation. This split means offline deployments are limited to the natively supported set.

Typical uses are interactive structure viewers, drawing widgets embedded in journals, databases, and teaching sites, and 3D visualization of proteins and crystals — often alongside toolkits such as tool:rdkit or tool:openbabel for the heavier cheminformatics that CWC deliberately delegates. Its main limitations are the cloud dependency for advanced format handling and computation, the GPL/commercial licensing split that constrains proprietary reuse, and a molecule-centric scope: it targets chemical structures, not the arbitrary node-link graphs handled by tools like tool:cytoscape or tool:graphviz.