Chemistry Guarantees

Chemistry Guarantees

This page explains how ChemDraft preserves chemical meaning, reports uncertainty, and refuses conversions it cannot perform faithfully.

Your drawing remains the source

ChemDraft's chemistry rule applies to drawing, clipboard conversion, files, plugins, and agent tools: an operation that cannot preserve chemical meaning must warn or fail rather than degrade quietly. This is a design and implementation contract, not a promise that every format or engine supports every structure.

Chemical meaning includes:

• Atom identity, bond order, formal charge, isotope labels, and radicals (unpaired electrons).
• Stereochemistry, including encoded tetrahedral configuration and double-bond geometry.
• Superatoms and represented R-group display. A superatom is a labelled group standing for several atoms; an R-group represents a variable substituent.
• Reaction roles and components, coordinates where relevant, and editable mechanism annotations.

Changing colour, line width, style, alignment, or page layout must not change those facts. An attractive depiction is not evidence that a conversion preserved them. See Bonds and Stereochemistry and Charges, Radicals and Dative Bonds for drawing details.

Preservation has limits

Support is specific to an operation. A structure may be analyzable even when a drawing or export route cannot represent it safely.

For example, the headless drawing routes refuse radical or isotope-labelled SMILES that they cannot draw faithfully. The analysis route can retain a radical and report its composition and mass. Removing the radical, isotope, or charge to obtain a successful drawing would answer a different question.

Native document export also checks atom state, including hydrogen and radical information. Comparing two strings after an earlier lossy conversion would be insufficient: both strings could describe the same already-damaged structure. ChemDraft therefore checks the native representation as well as subsequent identity comparisons.

Unknown objects and format-specific features require the same care. File Formats and Compatibility describes supported coverage; it should not be read as universal interchange compatibility.

What a canonical SMILES check proves

SMILES is a text representation of molecular connectivity. A canonical isomeric SMILES is an engine's normalized representation that also retains supported stereochemistry and isotope information.

The CLI checks chemical identity during structure exports, including reading written chemical formats back where implemented. A mismatched canonical identity fails the operation instead of being reported as a successful export. These checks concern represented chemistry; they do not establish that a PDF or image contains editable chemical objects, or that every external reader interprets a file identically.

The naming workflow adds another read-back: a proposed name must parse to the exact drawn structure before ChemDraft shows or inserts it. See Name from Structure.

Interpretations are explicit

Some property methods need a different molecular form from the one drawn. An interpretation is a named form used for a calculation. Derived interpretations carry a transformation ledger: the recorded changes connecting them to the source, with atom correspondence information.

Sodium benzoate must not silently become benzoic acid. Composition, formal charge, and mass describe the supplied salt. A calculation on its largest organic fragment or a neutralized derivative is a separate result with its own interpretation. The source result, including a source-domain refusal, remains available.

The Molecular Inspector shows Computed on: and allows interpretation changes. Inspect that label before copying a number. Atom mappings need particular care for pKa results on rewritten canonical tautomers: the current audit records an unresolved correspondence limitation, so those indices must not be treated as independently verified mappings to the drawing.

A number needs its method

An analysis result carries a method identifier and version, interpretation, units where applicable, conventions, applicability, warnings, and provenance. Engine versions and artifact identity belong to the run. This information distinguishes an exact-mass calculation from an empirical prediction, or a source result from a derived-form result.

Unknown uncertainty stays unknown. An interval validated on one calibration corpus is not automatically validated on a new chemical family. Analysis and Properties explains the status labels and the current pKa limits.

Declining is a feature

unsupported, not-applicable, and failed mean different things. None means zero. A partial result must keep its omissions and warnings; a method never requested must remain distinguishable from one that ran and declined.

Recognition adds an explicit review gate because the user did not author the inferred structure. Deterministic conversion of a user-typed name can instead insert one labelled, undoable patch. Neither route may silently overwrite chemical identity.

These rules apply on macOS and Windows and through the CLI and MCP server. They describe the shared contract, rather than claiming every native workflow has received a hands-on check on both systems.

See also

• Analysis and Properties
• Structure Recognition
• Exporting
• Plugin Permissions