Molecule annotations

Molecule annotations attach CML metadata to a molecule using the @key("value") suffix. Multiple annotations can be chained.

Names

Source Rendered

H_2O @name("Water")

${\mathrm{H}}_2\mathrm{O}$

Maps to CML <name>Water</name>.

Identifiers

Known identifier types (inchi, smiles, cas, iupac, cid, chebi) map to CML <identifier convention="...">:

Source Rendered

C @inchi("InChI=1/C")

$\mathrm{C}$

C @smiles("C")

$\mathrm{C}$

C @cas("74-82-8")

$\mathrm{C}$

Title

Source Rendered

H_2O @title("water molecule")

${\mathrm{H}}_2\mathrm{O}$

Sets the CML title attribute on <molecule>.

Formula

Source Rendered

H_2O @formula("H 2 O 1")

${\mathrm{H}}_2\mathrm{O}$

Maps to CML <formula concise="H 2 O 1"/>.

Labels

Source Rendered

H_2O @label("solvent")

${\mathrm{H}}_2\mathrm{O}$

Maps to CML <label value="solvent"/>.

Properties

Any annotation key that isn’t a known type (name, title, formula, label, or identifier convention) becomes a CML property:

Source Rendered

H_2O @mw("18.015")

${\mathrm{H}}_2\mathrm{O}$

H_2O @density("0.997")

${\mathrm{H}}_2\mathrm{O}$

H_2O @logP("-0.5")

Install the asciichem gem to see this rendered.

Maps to CML <property title="mw"><scalar>18.015</scalar></property>.

Metadata

Key-value metadata pairs using @meta("key","value"):

Source Rendered

H_2O @meta("creator","asciichem")

${\mathrm{H}}_2\mathrm{O}$

H_2O @meta("source","NIST")@meta("year","2024")

${\mathrm{H}}_2\mathrm{O}$

Multiple annotations

Chain annotations without spaces between them:

Source Rendered

H_2O @name("Water")@inchi("InChI=1/H2O/h1H2")@cas("7732-18-5")

${\mathrm{H}}_2\mathrm{O}$

Round-trip

All annotations survive AsciiChem → CML → AsciiChem round-trip without loss. Names, identifiers, title, formulas, labels, and properties use native CML elements. Metadata and AsciiChem-specific fields ride via the aci: extension namespace.