ChemDraw CDX and CDXML files

CDXML and CDX

	CDXML	CDX
What it is	ChemDraw's XML format, readable as text	ChemDraw's older binary format
Open in Athanor	✓	✓
Export from Athanor	✓	✓
Checked by the round-trip suite	✓ (6,492 molecules)	Not yet

Which to send? CDXML, unless the person asks for CDX. Every current ChemDraw opens it, and it is the format Athanor checks most.

Athanor also opens ChemDraw templates (.ctp) and style sheets (.cds). A style sheet holds no drawing: add it from the library's + as a document type, to draw in its style.

What the round-trip suite checks

Every build runs 6,492 molecules from PubChem through CDXML, and through SMILES, MOL V3000 and Marvin, and reads each one back. It must keep its formula and every R, S, E and Z it had. A short list of known failures is recorded, and a build fails on any new one, so the list can only shrink.

That covers structures. Whole ChemDraw scheme documents, with arrows, conditions, text and pictures, are read and written too, but no test covers them yet.

What comes in when you open one

Structures, arrows and text open as editable Athanor objects. Anything else is listed when the file opens: "Left out: …. Athanor opens a ChemDraw file's structures, arrows and text." If a file holds only drawings, Athanor says so and offers to bring them in from the library's + as icons.

Converting many files

The command line converts a whole folder to or from CDXML in one go, with the same engine.

See also A file will not open.