SMILES & MDL Molfile Molecular Graphs (.smi, .smarts, .mol, .sdf)

@modelscript/smiles (languages/smiles) provides zero-regex native WebAssembly GLR parsing, organic valence and Hückel $4n+2$ aromaticity verification, Joback & Reid (1987) group-contribution thermodynamic and critical property estimation, DAEBuilder lowering, and Aspen Plus / Modelica projections for OpenSMILES, SMARTS, and MDL Molfile V2000 / Structure-Data File (.sdf) molecular specifications.

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Supported Extensions & Standards

Extension	Format	Description
.smi, .smiles	OpenSMILES	Line notation encoding molecular graphs, ring closures, branches, stereochemistry (@/@@), and aromatic atoms
.smarts	SMARTS	Substructure query patterns for functional-group matching
.mol, .sdf	MDL V2000 / SDF	2D/3D atomic coordinate tables, bond orders, and associated structure-data property tags (> <Property>)

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Key Capabilities

1. Molecular Graph Topology & Valence Verification

• Constructs typed molecular graphs with implicit/explicit hydrogen counting, ring-closure matching (including %nn two-digit rings), disconnected salts/mixtures (.), formal charges, isotopes, and Kekulé/aromatic conjugation.

2. Joback & Reid Group-Contribution Property Estimator

• Automatically decomposes molecular graphs into functional groups (-CH3, -CH2-, >C=O, -OH, -COOH, -NH2, aromatic ring carbons, halogens) to estimate pure-component physical properties:
  • Normal boiling point $T_b$ and freezing point $T_m$ ($\text{K}$)
  • Critical temperature $T_c$ ($\text{K}$), critical pressure $P_c$ ($\text{bar}$), and critical molar volume $V_c$ (${\text{cm}}^3/\text{mol}$)
  • Standard enthalpy of formation $\mathrm{\Delta }{H}_f^{\circ }$ and Gibbs energy of formation $\mathrm{\Delta }{G}_f^{\circ }$ ($\text{kJ/mol}$)
  • Ideal-gas heat capacity polynomial $C_p^{\circ }(T)=A+BT+C{T}^2+D{T}^3$ and Lee-Kesler acentric factor $\omega$.

3. Aspen Plus, Modelica & DAE Lowering

• Projects estimated critical and thermochemical parameters directly into Aspen Plus pure-component property cards (smilesToAspen), Modelica media records (smilesToModelica), and @modelscript/runtime's DAEBuilder.

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Pre-Flight Diagnostics

10 rules9 error1 warning

Code	Rule	Severity	Message
M9301	unclosed-ring-digit	error	Ring closure digit '<ringId>' in '<moleculeName>' has no matching closing bond.
M9302	unbalanced-branch-parenthesis	error	Branch parenthesis in '<moleculeName>' is unbalanced.
M9303	valence-exceeded	error	Atom '<element>' (index '<atomIndex>') in '<moleculeName>' has bond order sum '<actualValence>' exceeding maximum allowed valence '<maxValence>'.
M9304	invalid-aromatic-kekule-ring	error	Aromatic ring in '<moleculeName>' violates Hückel's 4n+2 pi-electron rule or cannot be Kekulized.
M9305	unknown-chemical-element	error	Atomic symbol '<symbol>' in '<moleculeName>' is not a valid IUPAC element.
M9306	conflicting-ring-bond-order	error	Ring closure '<ringId>' in '<moleculeName>' specifies conflicting bond orders at opening and closing atoms.
M9307	self-loop-bond	error	Bond in '<moleculeName>' connects atom '<atomIndex>' to itself.
M9308	duplicate-atom-bond	error	Multiple bonds declared between identical atom pair ('<atomA>', '<atomB>') in '<moleculeName>'.
M9309	invalid-tetrahedral-chirality	warning	Chiral center '<atomIndex>' in '<moleculeName>' has fewer than 4 distinct substituents.
M9310	empty-molecular-graph	error	Molecule entry '<moleculeName>' contains zero atoms.

Generated from languages/smiles/src/errors.ts. All languages →

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CLI Usage

# Validate ring closures, atomic valences, and Hückel aromaticity
msx lint DrugLibrary.smi

# Parse SMILES or SDF molecular structure files
msx parse Aspirin.smi