CDXML

CDXML (ChemDraw XML) is the XML-based native document format of ChemDraw, the widely used chemical structure drawing application originally developed by CambridgeSoft, later acquired by PerkinElmer (2011) and now maintained by Revvity Signals Software. It is the text-based counterpart to ChemDraw's older binary CDX format: CDXML is a straightforward XML encoding of the same object model, and documents can be converted losslessly between CDX and CDXML in both directions. Everything storable in CDX can be stored in CDXML, differing only in serialization details.

Structurally, a CDXML file begins with an XML declaration and a DOCTYPE referencing the cdxml.dtd, with a root element that contains one or more Page objects representing drawing spaces. Chemistry is captured inside Fragment elements, which hold Node elements (typically atoms, though nodes serve broader roles) and Bond elements connecting pairs of nodes. Most chemical detail (element, position, charge, bond order, stereochemistry, color) lives in XML attributes rather than nested elements. Objects carry optional id attributes, and cross-references between objects (for example a bond naming its two node ids) are expressed by referencing those id values. Beyond molecules, a document also encodes reactions, arrows, text labels, brackets, and arbitrary vector graphics, since CDXML is fundamentally a page-layout format for chemical documents rather than a pure connection table.

Within the format-conversion landscape, CDXML functions as a rich but drawing-centric interchange format for 2D chemistry. It sits alongside line notations such as SMILES and InChI and connection-table formats like Molfile and SDF, and is commonly converted to or from those for cheminformatics use. Toolkits including Open Babel and RDKit can read CDXML (with varying completeness), and web renderers such as ChemDoodle handle it; ChemAxon's Marvin stack also supports CDX/CDXML sketch files. It carries far more presentational information than graph-oriented chemical formats like CML.

Its principal strength is fidelity to what a chemist drew, including layout, annotations, and reaction schemes, making it the de facto standard for authoring chemical figures in publications and electronic lab notebooks. Its main limitations are practical: the official specification (hundreds of attributes and dozens of elements) is acknowledged as incomplete, so robust support often requires reverse engineering; the mixture of chemical semantics with free-form graphics complicates reliable extraction of clean molecular graphs; and the format is effectively tied to a single commercial vendor's ecosystem.