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//! Rasayan — Biochemistry Engine
//!
//! **Rasayan** (Sanskrit: रसायन — alchemy, chemistry of life) provides
//! computational models of biochemistry for the AGNOS ecosystem. Enzyme
//! kinetics, metabolic pathways, signal transduction, protein structure,
//! membrane transport, and bioenergetics.
//!
//! # Architecture
//!
//! Twenty-five core modules (plus optional `logging`, `mcp`, `ai`):
//!
//! - [`enzyme`] — Michaelis-Menten kinetics, competitive/uncompetitive/mixed
//! inhibition, substrate inhibition, allosteric regulation (Hill equation),
//! reversible reactions (Haldane), multi-substrate kinetics (ping-pong,
//! sequential), temperature dependence (Arrhenius, Q10), linearization
//! transforms (Lineweaver-Burk, Eadie-Hofstee), enzyme database.
//! - [`metabolism`] — Metabolic state: ATP/ADP balance, energy charge,
//! aerobic/anaerobic yield, oxygen-dependent ATP regeneration, metabolic rate.
//! - [`signal`] — Signal transduction: ligand-receptor binding, dose-response
//! (Hill function), second messengers (cAMP, Ca2+, IP3), Gs/Gq/Gi pathway
//! activation, messenger decay.
//! - [`protein`] — Protein analysis: 20 amino acid properties (molecular
//! weight, hydrophobicity, pKa), sequence molecular weight, composition,
//! isoelectric point (pI), extinction coefficient (280nm), Chou-Fasman
//! secondary structure prediction.
//! - [`alignment`] — Sequence alignment scoring: BLOSUM62/PAM250 substitution
//! matrices, pairwise alignment scoring, Needleman-Wunsch global alignment.
//! - [`ptm`] — Post-translational modification site prediction: N-glycosylation,
//! phosphorylation (Ser/Thr/Tyr), PKA/CK2 sites, disulfide bonds, myristoylation.
//! - [`domain`] — Protein domain classification: zinc finger (C2H2), leucine
//! zipper, EF-hand, Walker A/P-loop, RGD, DEAD-box, NLS, KDEL motifs.
//! - [`neurotransmitter`] — Neurotransmitter synthesis: serotonin (TPH),
//! dopamine (TH), norepinephrine (DBH), GABA (GAD), glutamate, ACh (ChAT),
//! endorphins (POMC). Bridge functions for mastishk/bhava.
//! - [`hormonal`] — Hormonal pathways: HPA axis cortisol (CRH→ACTH→cortisol,
//! negative feedback), melatonin (serotonin→melatonin, light suppression),
//! oxytocin, BDNF. Bridge functions for bhava.
//! - [`pathway`] — Metabolic network: unified simulation connecting all
//! pathways with shared cofactor pools, steady-state flux analysis,
//! respiratory quotient.
//! - [`membrane`] — Membrane transport: Nernst potential, Goldman-Hodgkin-Katz
//! equation, Fick's first law diffusion, ionic state.
//! - [`glycolysis`] — 10-step glycolytic pathway with individual enzyme kinetics,
//! regulatory checkpoints (hexokinase, PFK, pyruvate kinase), configurable
//! parameters, and per-tick ATP/NADH flux accounting.
//! - [`tca`] — TCA (Krebs) cycle: pyruvate dehydrogenase + 8 cycle steps,
//! regulatory checkpoints (citrate synthase, isocitrate DH, α-KG DH),
//! NADH/FADH2/GTP/CO2 flux output.
//! - [`etc`] — Electron transport chain: complexes I-IV, ATP synthase, proton
//! motive force, respiratory control, ubiquinone and cytochrome c carrier pools.
//! - [`amino_catabolism`] — Amino acid catabolism: transamination,
//! oxidative deamination (GDH), carbon skeleton routing to TCA entry
//! points, NH4+ clearance.
//! - [`beta_oxidation`] — Fatty acid beta-oxidation: acyl-CoA activation,
//! CPT-I malonyl-CoA regulation, spiral producing acetyl-CoA/NADH/FADH2.
//! - [`energy`] — Bioenergetics: ATP hydrolysis, phosphocreatine system,
//! anaerobic/aerobic thresholds, metabolic equivalent (MET).
//! - [`constants`] — Shared physical constants (gas constant, Faraday constant).
//! - [`mcp`] — MCP tool definitions via bote (feature-gated: `mcp`): 8 tools
//! for enzyme kinetics, metabolism, signaling, protein, membrane, alignment,
//! PTM, and domain analysis.
//! - [`ai`] — Hoosh client for LLM-powered biochemistry queries (feature-gated:
//! `ai`): `BiochemClient` with enzyme, pathway, and protein query helpers.
//!
//! # Relationship to Other Crates
//!
//! ```text
//! rasayan (this) — enzyme kinetics, metabolism, signal transduction
//! | metabolic state feeds into
//! mastishk — neuroscience (neurotransmitter synthesis depends on precursors)
//! | neurotransmitter levels feed into
//! bhava — emotion/personality
//! also:
//! kimiya — general chemistry (rasayan uses reaction kinetics from kimiya)
//! jivanu — microbiology (microbial metabolism, pharmacokinetics)
//! sharira — physiology (muscle bioenergetics, fatigue)
//! ```
pub use RasayanError;