Stereochemistry

AsciiChem captures configuration stereochemistry via prefix markers on the molecule. Stereo bonds (wedge / hash) are documented in Bonds.

The five markers

Marker	Source form	Use
R	`(R)-`	Rectus configuration (CIP)
S	`(S)-`	Sinister configuration (CIP)
E	`(E)-`	Entgegen (trans alkene, CIP)
Z	`(Z)-`	Zusammen (cis alkene, CIP)
α / alpha	`(α)-`/`(a)-`/`(alpha)-`	Alpha anomer (sugars)
β / beta	`(β)-`/`(b)-`/`(beta)-`	Beta anomer (sugars)

Three spellings are accepted for the Greek letters: typed alpha / beta (AsciiMath-style), short a / b, and Unicode α / β. The Text formatter canonicalises to Unicode on output.

Worked examples

Amino acids (R/S)

(R)-CH(OH)COOH

(R)- C H (O H) C O O H

(S)-CH(OH)COOH

(S)- C H (O H) C O O H

Lactic acid’s two enantiomers.

Sugar anomers (alpha/beta)

(alpha)-C

(alpha)- C

(beta)-C

(beta)- C

(α)-C

(alpha)- C

(β)-C

(beta)- C

Geometric isomers (E/Z)

(E)-CH=CH

(E)- C H = C H

(Z)-CH=CH

(Z)- C H = C H

How it binds

The stereo prefix attaches to the molecule, not to a specific atom. The chemist reads (R)-CH(OH)COOH and knows which carbon the R refers to; AsciiChem stores it as metadata on the molecule.

mol = AsciiChem.parse("(R)-CH(OH)COOH").nodes.first
mol.stereo         # => :R
mol.stereo_letter  # => "R"

Disambiguation

(OH) is a parenthesised group, not a stereo prefix. The grammar distinguishes via the closed letter set: R/S/E/Z and the alpha/beta spellings are the only valid stereo letters. Anything else inside the parens falls through to the regular group parse.

Ca(OH)_2

Ca {(O H)}_{2}

Parses as Atom(Ca) followed by Group(OH) with multiplicity 2. No stereo is set.

Round-trip

AsciiChem.parse("(R)-CH_3").to_text      # => "(R)-CH_3"
AsciiChem.parse("(alpha)-CH_3").to_text  # => "(α)-CH_3"  (canonical)
AsciiChem.parse("(a)-CH_3").to_text      # => "(α)-CH_3"  (canonical)

The Text formatter emits the Unicode form for alpha/beta. The ASCII spellings are accepted on input but not emitted on output — this is the canonicaliser’s job.