Atoms and Labels

Atoms and Labels

This page explains skeletal atoms, explicit typed labels, abbreviations, and how ChemDraft avoids guessing their chemistry.

Use the Atom Label Tool to click an atom and edit its label. Use the Text Tool for prose, conditions, or a label that should stay a text object. A Text-tool click directly on an atom opens that atom’s label editor. The explicit Convert Text to Atom Label command can convert selected text near an atom; it reaches one bond length.

Skeletal atoms and literal labels

An atom made with the ordinary drawing tools follows skeletal conventions: carbon is normally not printed and its implicit hydrogens are calculated from its bonds. An element hotkey applied to an atom likewise makes an ordinary skeletal atom.

Text committed as exactly one element symbol becomes a real one-atom molecule at that point. For example, fe is canonicalized to Fe; it can be bonded, targeted by hover actions, and valence-checked. This converted text is a literal label: it draws exactly as typed and has no implicit hydrogens. A lone literal N therefore remains marked as hypovalent until real bonds supply its valence. A literal OH2 is understood as a one-heavy-atom condensed label with its stated hydrogens, so it represents water.

This distinction prevents a quiet chemistry change. Typing a label never silently turns it into an unstated-hydrogen skeletal atom. Conversely, applying an element hotkey to a literal atom clears its literal status and returns to ordinary skeletal behavior.

Labels on existing atoms

When you type a one-bond label onto a ring or chain atom, ChemDraft decides whether it is a relabel or a substituent attachment. An element label and suitable multi-bond labels relabel the existing atom. A one-bond substituent label is attached as a new atom while preserving the original atom and graph. The preview matches the eventual placement, and a deliberate commit selects the new atom. If the original atom has no available valence, ChemDraft falls back to relabelling and states the reason.

Escape restores the original graph. The editor uses one labelled undo entry, and the close decision is also respected by saving, exporting, and autosave while editing is active.

Abbreviations and attachment direction

ChemDraft’s label grammar is case-sensitive for abbreviations. OMe has its abbreviation meaning; a different spelling that is not recognized stays literal text rather than becoming a guessed group. Elements take priority in ordinary reading, but bonded labels that chemists use as groups have deliberate context rules. In particular, a bonded Ac, Pr, or Ts can be read as an abbreviation, while an unbonded one remains the element symbol.

Group labels are anchored at the atom they chemically attach through, not at the visual centre of the letters. With one bond, a label can turn so the attachment faces the bond; at a ring vertex it turns outward when the geometry identifies a side. The stored label and chemistry do not change when this display anchoring changes.

Direction can matter. CN is recognized as cyano only when the carbon faces its bond. If the bond is on the other side, it remains a formula label rather than being silently interpreted as the wrong isomer.

Valence feedback

ChemDraft shares one label grammar and valence calculation across labels, formulas, badges, and drawing actions. A group or spelled label is assessed by its available attachment valence; an element label is assessed as that element. Generic placeholders such as R, bare formulas, and unrecognized text are not given invented valence. If a tool cannot preserve the intended chemical meaning, it reports or refuses the action rather than changing it.

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• Templates and Abbreviations
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