Module organic_chemistry 

Organic Chemistry Engine.

Pure-Rust implementations of core organic-chemistry primitives:

• SMILES parsing & molecular graph building
• Molecular formula, exact weight, and isotope-aware mass
• Lipinski Rule-of-Five, Veber, Ghose, Egan drug-likeness filters
• LogP (Crippen–Wildman atomic contributions, 25 atom types)
• TPSA (Ertl 2000 atomic contributions)
• H-bond donors / acceptors, rotatable bonds, aromatic ring count
• Functional group detection (20 groups via SMARTS-inspired pattern matching)
• Chiral centre enumeration
• Morgan circular fingerprint generation
• Thermochemistry: Arrhenius, Gibbs–Helmholtz, van’t Hoff, Henderson–Hasselbalch
• Green chemistry: atom economy, E-factor, PMI, RME, yield-adjusted AE
• pKa estimation (functional-group based)
• SMILES structural validation
• InChI / InChIKey format validation

SHACL constraint name → function: qualia:validateSmiles → validate_smiles() qualia:validateInchi → validate_inchi() qualia:computeMolecularWeight → exact_molecular_weight() qualia:computeLogP → compute_logp() qualia:computeTPSA → compute_tpsa() qualia:evaluateLipinski → evaluate_lipinski() qualia:evaluateVeber → evaluate_veber() qualia:evaluateGhose → evaluate_ghose() qualia:evaluateEgan → evaluate_egan() qualia:detectFunctionalGroups → detect_functional_groups() qualia:computePka → estimate_pka() qualia:computeChiralCenters → count_chiral_centers() qualia:generateCircularFingerprint → circular_fingerprint() qualia:computeArrheniusRate → arrhenius_rate() qualia:computeGibbsEnergy → gibbs_free_energy() qualia:computeEquilibrium → equilibrium_constant() qualia:computeHendersonHasselbalch → henderson_hasselbalch() qualia:computeAtomEconomy → atom_economy() qualia:computeEFactor → e_factor() qualia:computeGreenMetrics → green_metrics()

Structs

Atom

BbbPermeationResult

Bond

EganResult

GhoseResult

GreenMetrics

InchiValidation

IsotopeDistribution

LipinskiResult

MolecularDescriptors

Molecule

PkaEstimate

SmilesValidation

VeberResult

Enums

BondOrder

FunctionalGroup

Constants

R_J_MOL_K

Universal gas constant J / (mol·K)

Functions

arrhenius_rate

Arrhenius rate constant k at temperature T (K). k = A × exp(−Ea / (R × T)) activation_energy_j_mol: Ea in J/mol

arrhenius_ratio

Temperature dependence of k using the Arrhenius equation. Returns (k_t1, k_t2).

atom_economy

Simplified atom economy (Trost): single product vs all reactants.

catalyst_activity

Catalyst activity at time t under first-order deactivation: a(t) = a₀·exp(−k_d·t). Models the degradation that limits sustained yield on small decentralized nodes.

circular_fingerprint

Morgan algorithm: radius-r circular fingerprint as sorted Vec identifiers.

compute_descriptors

Compute all Lipinski/Veber/Ghose descriptors from a parsed molecule.

compute_logp

Per-atom LogP contributions mapped by (element, aromaticity, polar_neighbour). Derived from Wildman & Crippen 1999, Table 1 (25 of 68 atom types).

compute_tpsa

Topological polar surface area in Ų.

conversion_under_variable_temperature

Total fractional conversion of a first-order reaction under a variable temperature profile — e.g. fluctuating off-grid power driving a fluctuating reactor temperature. Integrates dX/dt = k(T)·(1−X) across temp_profile_k (k from the Arrhenius rate, explicit-Euler steps of dt_s), returning the final conversion X ∈ [0,1]. Zero-heap (the profile is a caller slice).

count_chiral_centers

Count sp3 carbon atoms with 4 distinct substituents (simplified: sp3 C with degree 4).

deactivated_reaction_rate

Effective reaction rate accounting for catalyst decay: r_eff = r_base · a(t)/a₀.

detect_functional_groups

Detect functional groups in a molecule. Returns unique set.

e_factor

E-factor (Sheldon): waste_kg / product_kg. Fine chemicals < 50; bulk < 5; pharma 25–100.

equilibrium_constant

Equilibrium constant from ΔG°: K = exp(−ΔG° / (R × T))

estimate_pka

Estimate pKa values from functional group type (literature reference values).

evaluate_egan

evaluate_ghose

evaluate_lipinski

evaluate_veber

exact_molecular_weight

Exact monoisotopic molecular weight (Da).

formula_string

Hill-order formula string (C first, H second, then others alphabetically).

gibbs_free_energy

Gibbs free energy ΔG = ΔH − T × ΔS (all in J/mol or kJ/mol consistently).

gibbs_from_equilibrium

ΔG° from equilibrium constant K: ΔG° = −R × T × ln(K)

gibbs_helmholtz

Gibbs–Helmholtz: ΔG(T2) from ΔG(T1).

green_metrics

henderson_hasselbalch

Henderson–Hasselbalch: pH = pKa + log10([A-] / [HA])

ionisation_fraction

Degree of ionisation α at a given pH for a monoprotic acid.

isotope_mass_distribution

Computes the theoretical M, M+1, M+2 isotopic distribution based on the number of Carbon, Nitrogen, Oxygen, Sulfur, Chlorine, and Bromine atoms.

ligand_efficiency

Computes Ligand Efficiency (LE): pIC50 / Heavy Atom Count (HAC). Standard target is LE >= 0.3.

lipophilic_ligand_efficiency

Computes Lipophilic Ligand Efficiency (LLE): pIC50 - LogP. Standard target is LLE >= 5.0.

molecular_formula

Atom counts by element symbol.

parse_smiles

Parse a SMILES string into a Molecule.

predict_bbb_permeation

Evaluates Blood-Brain Barrier (BBB) permeation probability using Clark’s rules (Molecular Weight, LogP, PSA, HBD).

urea_equilibrium_extent

Equilibrium extent ξ of the Bosch–Meiser urea synthesis 2 NH₃ + CO₂ ⇌ (NH₂)₂CO + H₂O, solved from the equilibrium constant (via the caller-supplied ΔG° at temp_k) and the initial NH₃/CO₂ partial pressures, by bisection on the reaction quotient Q(ξ) = ξ² / ((p_NH₃−2ξ)²·(p_CO₂−ξ)) (strictly increasing in ξ). Returns ξ in the same units as the input pressures. Simplified gas-phase model (industrial urea is liquid-phase/high-P — that shifts the numbers, not the method). Demonstrates Le Chatelier: higher reactant pressure ⇒ higher ξ.

validate_inchi

validate_smiles

vant_hoff_enthalpy

van’t Hoff enthalpy estimate from two equilibrium constants at two temperatures.