Glossary

Glossary

This page defines drawing, chemistry, file, plugin, and automation terms used throughout the ChemDraft wiki.

Term	Meaning
Atom label	A chemical atom’s visible element or abbreviation label, stored as structure data rather than free text.
CDXML	Chemical Drawing Exchange Markup Language, an XML-based chemical drawing interchange format. Support is feature-specific; see CDXML Support.
CIP	The Cahn–Ingold–Prelog priority system used to describe stereocentres such as R/S and double bonds such as E/Z.
Command	A registered action used by menus, toolbars, shortcuts, plugins, and automation rather than a private UI-only action.
Conformer	One three-dimensional arrangement of a molecule’s atoms. Spin 3D displays a conformer before flattening a selected view back to the page.
Derived interpretation	A clearly identified form of a drawn structure used for a method, such as a neutral or desalted form; it is not silently substituted for the drawing.
Ensemble	A set of related molecular states or conformers considered together by a calculation; always check the method contract for the exact convention.
HOSE fragment	A local atom-environment descriptor used by the NMR predictor’s lookup method.
Interpretation	The named chemical input a calculation describes. The active interpretation is visible and changeable when methods use more than the drawn form.
Method contract	The attached statement of a result’s implementation/version, interpretation, units, conventions, scope, and declining conditions.
MOL / molfile	A connection-table structure format. ChemDraft can copy or export supported structure data as MOL text.
MCP server	A local standard-input/output server that lets a compatible agent call ChemDraft tools. See MCP Server.
Patch	A validated, labelled document change. Plugin and agent document modifications go through patches so they form undoable history.
Permission	A declared capability a plugin must request before it can access sensitive functions such as document writing, native execution, or image reading.
Plugin	An extension package that uses the versioned @chemdraft/plugin-api contract to contribute permitted functionality.
Proposal review	A user review step for a patch based on information the user did not author, notably image recognition.
Radical	An atom or molecule with one or more unpaired electrons; a conversion must preserve it or decline.
SDF	Structure Data File, a record-oriented chemical structure format based on molfile records.
SMILES	A text notation for molecular structures. ChemDraft can use SMILES in clipboard, file, CLI, and agent workflows.
Stereo bond	A wedge, hashed wedge, or other bond display that conveys three-dimensional stereochemical information in a 2D drawing.
Undo entry	One reversible history record. A direct plugin insertion makes one labelled undo entry and selects what it added.

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