dol 0.8.1

// =============================================================================
// Biology Spirit - Library Entry Point
// DOL v0.9.0
// =============================================================================

module biology @ 0.9.0

docs {
    Biology Spirit library entry point.

    This module re-exports all public biology modules for convenient access.
    Users can either import the entire biology namespace or specific modules.

    Example usage:
        // Import entire biology library
        use local::biology

        // Or import specific modules
        use local::biology::cells
        use local::biology::genetics
        use local::biology::ecosystems
}

// ---------------------------------------------------------------------------
// Re-exports from submodules
// ---------------------------------------------------------------------------

use local::cells
use local::genetics
use local::ecosystems

// ---------------------------------------------------------------------------
// Biological Constants
// ---------------------------------------------------------------------------

docs {
    Avogadro's number (particles/mol) - for molecular calculations.
}

pub const AVOGADRO: f64 = 6.02214076e23

docs {
    Universal gas constant (J/(mol*K)).
}

pub const GAS_CONSTANT: f64 = 8.314462618

docs {
    Boltzmann constant (J/K).
}

pub const BOLTZMANN: f64 = 1.380649e-23

docs {
    Standard body temperature (K) - human homeostatic temperature.
}

pub const BODY_TEMP_K: f64 = 310.15

docs {
    Standard body temperature (Celsius).
}

pub const BODY_TEMP_C: f64 = 37.0

docs {
    Number of base pairs in human genome (approximate).
}

pub const HUMAN_GENOME_BP: u64 = 3200000000

docs {
    Average cell diameter in micrometers.
}

pub const AVG_CELL_DIAMETER_UM: f64 = 10.0

docs {
    Mitochondrial membrane potential (mV).
}

pub const MITOCHONDRIAL_POTENTIAL_MV: f64 = -180.0

docs {
    ATP hydrolysis free energy under standard conditions (kJ/mol).
}

pub const ATP_HYDROLYSIS_KJ: f64 = -30.5

docs {
    Planck's constant for quantum biology (J*s).
}

pub const PLANCK: f64 = 6.62607015e-34

// ---------------------------------------------------------------------------
// Codon Table Constants
// ---------------------------------------------------------------------------

docs {
    Number of possible codons (4^3).
}

pub const NUM_CODONS: u8 = 64

docs {
    Number of standard amino acids.
}

pub const NUM_AMINO_ACIDS: u8 = 20

docs {
    Stop codons in standard genetic code.
}

pub const STOP_CODONS: Vec<string> = vec!["UAA", "UAG", "UGA"]

docs {
    Start codon (Methionine).
}

pub const START_CODON: string = "AUG"

// ---------------------------------------------------------------------------
// Ecological Constants
// ---------------------------------------------------------------------------

docs {
    Earth's carrying capacity for humans (estimated billions).
}

pub const EARTH_CARRYING_CAPACITY_BILLIONS: f64 = 10.0

docs {
    Average species extinction rate (species per million species per year).
}

pub const BACKGROUND_EXTINCTION_RATE: f64 = 0.1

docs {
    Shannon diversity index for maximum biodiversity in typical ecosystem.
}

pub const MAX_SHANNON_INDEX: f64 = 5.0

// ---------------------------------------------------------------------------
// Utility Types
// ---------------------------------------------------------------------------

docs {
    Result type for biology calculations that may fail.
}

pub gen BiologyResult<T> {
    has value: Option<T>
    has error: Option<string>
    has warning: Option<string>
}

docs {
    Create a successful biology result.
}

pub fun ok<T>(value: T) -> BiologyResult<T> {
    return BiologyResult {
        value: Some(value),
        error: None,
        warning: None
    }
}

docs {
    Create an error biology result.
}

pub fun err<T>(message: string) -> BiologyResult<T> {
    return BiologyResult {
        value: None,
        error: Some(message),
        warning: None
    }
}

docs {
    Check if a biology result is successful.
}

pub fun is_ok<T>(result: BiologyResult<T>) -> bool {
    match result.value {
        Some(_) => true,
        None => false
    }
}

docs {
    3D position for biological structures (micrometers).
}

pub gen Position3D {
    has x: f64
    has y: f64
    has z: f64
}

docs {
    Create a position at origin.
}

pub fun origin() -> Position3D {
    return Position3D { x: 0.0, y: 0.0, z: 0.0 }
}

docs {
    Create a position at given coordinates.
}

pub fun position(x: f64, y: f64, z: f64) -> Position3D {
    return Position3D { x: x, y: y, z: z }
}

docs {
    Calculate distance between two positions.
}

pub fun distance(p1: Position3D, p2: Position3D) -> f64 {
    let dx = p2.x - p1.x
    let dy = p2.y - p1.y
    let dz = p2.z - p1.z
    return (dx * dx + dy * dy + dz * dz)
}