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

H_{2} O

CO_2

C O_{2}

C_6H_12O_6

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

2 H_{2} O

3H_2

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

Ca {(O H)}_{2}

(NH_4)_2SO_4

{(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]^4-`)
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. The complex’s charge sits outside the brackets.

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[Fe(CN)_6]^4-

Install the asciichem gem to see this rendered.

[Co(NH_3)_6]^3+

Install the asciichem gem to see this rendered.

These are parsed as Group(bracket: :square, nodes: [...]) followed by an Atom with the charge. (In v1, the charge attaches to the last atom; v2 may promote it to a complex-level attribute.)

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