Molecules

A molecule is an ordered sequence of atoms and groups, with an optional leading stoichiometric coefficient, optional stereo prefix, and optional CML annotations.

Simple molecules

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H_2O
CO_2
C_6H_12O_6

H_{2} O C O_{2} C_{6} H_{12} O_{6}

Each atom carries its own subscript. The model is Molecule(nodes: [Atom, Atom, ...]).

CML annotations

Molecules can carry CML metadata via the @key("value") suffix:

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H_2O @name("Water")@inchi("InChI=1/H2O/h1H2")

H_{2} O

Supported annotations:

@name("...") — molecule name
@inchi("..."), @smiles("..."), @cas("...") — identifiers
@title("...") — molecule title
@formula("H 2 O 1") — concise formula
@label("solvent") — label
@mw("18.015") — any custom property
@meta("key","value") — metadata key-value pair

See Annotations for details.

Stoichiometric coefficients

Leading digits on a molecule are its coefficient:

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2H_2O
3H_2

2 H_{2} O 3 H_{2}

The Molecule#coefficient field holds the string. The MathML renderer emits it as an <mn> before the atoms.

Groups

Parenthesised sub-formulas are groups. A group can carry an outer multiplicity.

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Ca(OH)_2
(NH_4)_2SO_4

Ca {(O H)}_{2} {(N H_{4})}_{2} S O_{4}

For Ca(OH)_2:

Atom Ca
Group OH with multiplicity 2, bracket :paren

For (NH_4)_2SO_4:

Group NH_4 with multiplicity 2
Atoms S, O with subscripts 4

Bracket variants

AsciiChem supports three bracket kinds:

Bracket	Open / Close	Use
Paren	`(` `)`	Generic grouping (`Ca(OH)_2`)
Square	`[` `]`	Coordination complexes (`[Fe(CN)_6]`)
Brace	`{` `}`	Optional / rare

The bracket kind is preserved through round-trip — (OH)_2 stays as (OH)_2, not [OH]_2.

Coordination complexes

Square brackets wrap coordination complexes, and a subscript can apply to the bracketed group:

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[Fe(CN)_6]
[OH]_2
[Fe(CN)_6]_3

[Fe {(C N)}_{6}] {[O H]}_{2} {[Fe {(C N)}_{6}]}_{3}

These are parsed as Group(bracket: :square, nodes: [...]) with the subscript as the group multiplicity.

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