File Formats and Compatibility

File Formats and Compatibility

This page explains which document and interchange formats ChemDraft 1.0.0 can open, save, or export, and where compatibility has deliberate limits.

ChemDraft's working document is its own native model. File formats are boundaries around that model, not substitutes for it. This matters because a drawing can contain chemical information, layout, editable artwork, and page information at once. When a target format cannot faithfully carry something, ChemDraft reports a warning or refuses the operation instead of quietly changing the drawing.

At a glance

Job	Format	What to expect
Continue editing in ChemDraft	.chemdraft	The native save format; use this as the master copy.
Bring in or share an XML drawing	.cdxml	A supported, warning-backed visible subset; see CDXML Support.
Share the appearance of a page	SVG, PDF, PNG, JPEG, BMP, GIF, TIFF	Export formats, not editable chemical interchange formats; see Exporting.
Share a list of structures	SDF or .smi / .smiles	Exports editable native molecules, with scope rules described in Exporting.

The app can also open legacy native JSON payloads. That is a compatibility path, not a recommended format for new work.

Use .chemdraft for active work

A .chemdraft file is an XML CDXML envelope with a ChemDraft-owned native payload. The visible XML layer lets compatible readers see the progressive subset that can be represented there, while the embedded payload preserves the full validated ChemDraft document for a ChemDraft-to-ChemDraft round trip.

The payload records the document's pages, native objects, document state, and compatibility information. It is versioned: the envelope records a codec version and document schema version, and the reader verifies the embedded payload hash and the visible-layer hash before trusting it. ChemDraft currently writes codec chemdraft.cdxml.v2 and can still read the prior v1 codec. The document model also has migration support for older document shapes. A file from a future, unsupported codec or schema version is not opened as though it were current; it produces a compatibility warning instead.

The practical rule is simple: save your editable source as .chemdraft, then make separate exports for submission, sharing, or analysis. Do not treat a graphics export as a backup for an editable drawing.

Opening files

Use File > Open… to choose a document. On desktop builds, ChemDraft can also receive a file opened by the operating system or dropped onto the document window. The Open dialog accepts a native document or CDXML; its parser first identifies whether the contents are a native envelope, legacy JSON, or external CDXML.

Malformed, empty, or unrelated XML is rejected with an explanation rather than partially imported. Binary CDX is not a supported open format. If you have a drawing in that form, obtain CDXML from the source application before opening it here.

Opening external CDXML imports only the supported visible subset and attaches warnings to the result where needed. A molecule imported from visible CDXML does not acquire a derived canonical structure string during import; it remains an editable drawing with its import warnings. Read CDXML Support before relying on a complex import.

Compatibility tiers

Compatibility claims are fixture-driven: ChemDraft claims only behavior represented by its test fixtures, not blanket support for a broad external format.

Tier	Coverage	Result
A — supported	Atoms, bonds, coordinates, charges, isotopes, radicals, wedge bonds, E/Z geometry, superatoms, basic R-groups, text, simple arrows, plus signs, basic brackets, and styles	Intended supported coverage, subject to the documented warning behavior.
B — fixture-dependent	R-group logic, S-groups, polymers, atom lists, mapping, equilibrium arrows, and retrosynthesis arrows	Claim support only when a relevant fixture covers the case.
C — preserve or approximate	Complex graphics, images, unusual fonts, and proprietary style state	Preserved as compatibility data where possible, otherwise approximated or warned about.

An unsupported CDXML object is preserved as an unknown-compatibility-object where feasible. That is useful for carrying information through a ChemDraft document, but it does not turn the object into a fully editable native object. Check the warnings after import and before sending the file onward.

Chemistry is not silently simplified

Formats differ in what they can say about bond display, crossings, isotope and radical information, stereochemistry, annotations, and artwork. ChemDraft's compatibility layer specifically warns for cases including aromatic or unknown bond-order approximation, unsupported bond display metadata, unsupported element or molecule metadata, unpreserved crossing metadata, partial reaction schemes, payload-only mechanism annotations, and unknown imported objects.

That warning is part of the result, not a cosmetic message. If preserving chemical identity matters for your next step, keep the .chemdraft original and inspect the exported or imported structure with the receiving tool. See Chemistry Guarantees for the general preservation policy.

Platform differences

Both platforms can open and save .chemdraft and open CDXML through the app. On macOS, the app may appear as an alternate handler for .cdxml. On Windows, the installer registers only .chemdraft; it intentionally does not take ownership of .cdxml. Use File > Open… or the system's Open With choice for CDXML on Windows.

For safe continuation after an interruption, see Saving Sessions and Recovery.

Next

• CDXML Support
• Exporting
• Saving Sessions and Recovery
• Copy, Paste, and Clipboard