oxirs_core/molecular/

cellular_division.rs

//! Cellular division processes for data partitioning and distribution

use super::dna_structures::DnaDataStructure;
use crate::error::OxirsResult;

/// Cellular division system for data partitioning
#[derive(Debug, Clone)]
pub struct CellularDivision {
    /// Mitotic apparatus for division
    pub mitotic_apparatus: MitoticApparatus,
    /// Checkpoint system for quality control
    pub checkpoint_system: CheckpointSystem,
    /// Division cycle state
    pub cycle_state: CellCycleState,
    /// DNA content
    pub dna_content: Vec<DnaDataStructure>,
}

/// Mitotic apparatus for managing cell division
#[derive(Debug, Clone)]
pub struct MitoticApparatus {
    /// Centrosomes for organizing microtubules
    pub centrosomes: (Centrosome, Centrosome),
    /// Spindle apparatus
    pub spindle_apparatus: SpindleApparatus,
    /// Kinetochores for chromosome attachment
    pub kinetochores: Vec<Kinetochore>,
    /// Division state
    pub division_state: DivisionState,
}

/// Spindle apparatus for chromosome movement
#[derive(Debug, Clone)]
pub struct SpindleApparatus {
    /// Kinetochore microtubules
    pub kinetochore_microtubules: Vec<Microtubule>,
    /// Polar microtubules
    pub polar_microtubules: Vec<Microtubule>,
    /// Astral microtubules
    pub astral_microtubules: Vec<Microtubule>,
    /// Spindle poles
    pub poles: (SpindlePole, SpindlePole),
}

/// Centrosome structure
#[derive(Debug, Clone)]
pub struct Centrosome {
    /// Centrioles
    pub centrioles: (Centriole, Centriole),
    /// Pericentriolar material
    pub pericentriolar_material: PericentriolarMaterial,
    /// Position in cell
    pub position: Position3D,
}

/// Centriole structure
#[derive(Debug, Clone)]
pub struct Centriole {
    /// Barrel structure
    pub barrel: BarrelStructure,
    /// Triplet microtubules
    pub triplets: Vec<TripletMicrotubule>,
    /// Orientation
    pub orientation: Orientation,
}

/// Barrel structure of centriole
#[derive(Debug, Clone)]
pub struct BarrelStructure {
    /// Diameter
    pub diameter: f64,
    /// Length
    pub length: f64,
    /// Wall thickness
    pub wall_thickness: f64,
}

/// Triplet microtubule
#[derive(Debug, Clone)]
pub struct TripletMicrotubule {
    /// A tubule
    pub a_tubule: Microtubule,
    /// B tubule
    pub b_tubule: Microtubule,
    /// C tubule
    pub c_tubule: Microtubule,
}

/// Microtubule structure
#[derive(Debug, Clone)]
pub struct Microtubule {
    /// Protofilaments
    pub protofilaments: Vec<Protofilament>,
    /// Length
    pub length: f64,
    /// Dynamic state
    pub dynamic_state: DynamicState,
    /// Plus end
    pub plus_end: MicrotubuleEnd,
    /// Minus end
    pub minus_end: MicrotubuleEnd,
}

/// Protofilament
#[derive(Debug, Clone)]
pub struct Protofilament {
    /// Tubulin dimers
    pub tubulin_dimers: Vec<TubulinDimer>,
    /// Lateral bonds
    pub lateral_bonds: Vec<LateralBond>,
}

/// Tubulin dimer
#[derive(Debug, Clone)]
pub struct TubulinDimer {
    /// Alpha tubulin
    pub alpha_tubulin: AlphaTubulin,
    /// Beta tubulin
    pub beta_tubulin: BetaTubulin,
    /// GTP/GDP state
    pub nucleotide_state: NucleotideState,
}

/// Alpha tubulin subunit
#[derive(Debug, Clone)]
pub struct AlphaTubulin {
    /// Molecular weight
    pub molecular_weight: f64,
    /// Conformation
    pub conformation: TubulinConformation,
}

/// Beta tubulin subunit
#[derive(Debug, Clone)]
pub struct BetaTubulin {
    /// Molecular weight
    pub molecular_weight: f64,
    /// Conformation
    pub conformation: TubulinConformation,
    /// GTP binding site
    pub gtp_binding_site: GtpBindingSite,
}

/// Checkpoint system for cell cycle control
#[derive(Debug, Clone)]
pub struct CheckpointSystem {
    /// Spindle checkpoint
    pub spindle_checkpoint: SpindleCheckpoint,
    /// DNA damage checkpoint
    pub dna_damage_checkpoint: DnaDamageCheckpoint,
    /// Replication checkpoint
    pub replication_checkpoint: ReplicationCheckpoint,
}

/// Spindle checkpoint
#[derive(Debug, Clone)]
pub struct SpindleCheckpoint {
    /// Mad proteins
    pub mad_proteins: Vec<MadProtein>,
    /// Bub proteins
    pub bub_proteins: Vec<BubProtein>,
    /// APC/C regulation
    pub apc_c_regulation: ApcCRegulation,
}

/// Mad protein (Mitotic arrest deficient)
#[derive(Debug, Clone)]
pub struct MadProtein {
    /// Protein type
    pub protein_type: MadProteinType,
    /// Activity level
    pub activity_level: f64,
    /// Localization
    pub localization: ProteinLocalization,
}

/// Bub protein (Budding uninhibited by benzimidazoles)
#[derive(Debug, Clone)]
pub struct BubProtein {
    /// Protein type
    pub protein_type: BubProteinType,
    /// Activity level
    pub activity_level: f64,
    /// Kinetochore binding
    pub kinetochore_binding: bool,
}

/// APC/C regulation
#[derive(Debug, Clone)]
pub struct ApcCRegulation {
    /// Cdc20 level
    pub cdc20_level: f64,
    /// Cdh1 level
    pub cdh1_level: f64,
    /// Activity state
    pub activity_state: ApcCActivityState,
}

/// Supporting enums and structs
#[derive(Debug, Clone)]
pub enum CellCycleState {
    G1,
    S,
    G2,
    M(MitosisPhase),
}

#[derive(Debug, Clone)]
pub enum MitosisPhase {
    Prophase,
    Prometaphase,
    Metaphase,
    Anaphase(AnaphaseStage),
    Telophase,
}

#[derive(Debug, Clone)]
pub enum AnaphaseStage {
    A, // Chromosome separation
    B, // Spindle elongation
}

#[derive(Debug, Clone)]
pub enum DivisionState {
    Interphase,
    Mitosis(MitosisPhase),
    Cytokinesis,
}

#[derive(Debug, Clone)]
pub struct Position3D {
    pub x: f64,
    pub y: f64,
    pub z: f64,
}

#[derive(Debug, Clone)]
pub struct Orientation {
    pub angle: f64,
    pub axis: Vec3D,
}

#[derive(Debug, Clone)]
pub struct Vec3D {
    pub x: f64,
    pub y: f64,
    pub z: f64,
}

#[derive(Debug, Clone)]
pub enum DynamicState {
    Growing,
    Shrinking,
    Paused,
}

#[derive(Debug, Clone)]
pub struct MicrotubuleEnd {
    pub cap_structure: CapStructure,
    pub growth_rate: f64,
}

#[derive(Debug, Clone)]
pub enum CapStructure {
    GtpCap,
    GdpCap,
    Frayed,
}

#[derive(Debug, Clone)]
pub struct LateralBond {
    pub strength: f64,
    pub bond_type: BondType,
}

#[derive(Debug, Clone)]
pub enum BondType {
    Hydrogen,
    VanDerWaals,
    Electrostatic,
}

#[derive(Debug, Clone)]
#[allow(clippy::upper_case_acronyms)]
pub enum NucleotideState {
    GTP,
    GDP,
}

#[derive(Debug, Clone)]
pub enum TubulinConformation {
    Straight,
    Curved,
    Intermediate(f64),
}

#[derive(Debug, Clone)]
pub struct GtpBindingSite {
    pub occupied: bool,
    pub binding_affinity: f64,
}

#[derive(Debug, Clone)]
pub struct SpindlePole {
    pub centrosome: Centrosome,
    pub microtubule_nucleation_sites: Vec<NucleationSite>,
}

#[derive(Debug, Clone)]
pub struct NucleationSite {
    pub gamma_tubulin_complex: GammaTubulinComplex,
    pub activity: f64,
}

#[derive(Debug, Clone)]
pub struct GammaTubulinComplex {
    pub gamma_tubulin_count: usize,
    pub associated_proteins: Vec<String>,
}

#[derive(Debug, Clone)]
pub struct Kinetochore {
    pub chromosome_attachment: bool,
    pub microtubule_attachments: Vec<MicrotubuleAttachment>,
    pub tension: f64,
}

#[derive(Debug, Clone)]
pub struct MicrotubuleAttachment {
    pub microtubule_id: String,
    pub attachment_strength: f64,
    pub attachment_type: AttachmentType,
}

#[derive(Debug, Clone)]
pub enum AttachmentType {
    Amphitelic, // Correct bi-orientation
    Syntelic,   // Both sister kinetochores to same pole
    Merotelic,  // One kinetochore to both poles
    Monotelic,  // One kinetochore attached, other free
}

#[derive(Debug, Clone)]
pub struct PericentriolarMaterial {
    pub gamma_tubulin: f64,
    pub pericentrin: f64,
    pub ninein: f64,
}

#[derive(Debug, Clone)]
pub struct DnaDamageCheckpoint {
    pub atm_activity: f64,
    pub atr_activity: f64,
    pub p53_level: f64,
}

#[derive(Debug, Clone)]
pub struct ReplicationCheckpoint {
    pub replication_forks: Vec<ReplicationFork>,
    pub checkpoint_active: bool,
}

#[derive(Debug, Clone)]
pub struct ReplicationFork {
    pub position: usize,
    pub stalled: bool,
    pub proteins: Vec<String>,
}

#[derive(Debug, Clone)]
pub enum MadProteinType {
    Mad1,
    Mad2,
    Mad3,
}

#[derive(Debug, Clone)]
pub enum BubProteinType {
    Bub1,
    Bub3,
    BubR1,
}

#[derive(Debug, Clone)]
pub enum ProteinLocalization {
    Kinetochore,
    SpindlePole,
    Cytoplasm,
    Nucleus,
}

#[derive(Debug, Clone)]
pub enum ApcCActivityState {
    Active,
    Inactive,
    PartiallyActive(f64),
}

impl CellularDivision {
    /// Create new cellular division system
    pub fn new() -> Self {
        Self {
            mitotic_apparatus: MitoticApparatus::new(),
            checkpoint_system: CheckpointSystem::new(),
            cycle_state: CellCycleState::G1,
            dna_content: Vec::new(),
        }
    }

    /// Initiate cell division process
    pub fn initiate_division(&mut self) -> OxirsResult<()> {
        // Progress through cell cycle phases
        self.progress_to_mitosis()?;
        self.execute_mitosis()?;
        self.complete_division()?;
        Ok(())
    }

    /// Progress to mitosis phase
    fn progress_to_mitosis(&mut self) -> OxirsResult<()> {
        match self.cycle_state {
            CellCycleState::G1 => {
                self.cycle_state = CellCycleState::S;
                // Replicate DNA
                self.replicate_dna()?;
                self.cycle_state = CellCycleState::G2;
            }
            CellCycleState::G2 if self.checkpoint_system.check_dna_integrity()? => {
                // Check for DNA damage - passed
                self.cycle_state = CellCycleState::M(MitosisPhase::Prophase);
            }
            _ => {
                // Already in appropriate phase
            }
        }
        Ok(())
    }

    /// Execute mitosis
    fn execute_mitosis(&mut self) -> OxirsResult<()> {
        // Extract the current phase to avoid borrowing conflicts
        let current_phase = if let CellCycleState::M(ref phase) = self.cycle_state {
            phase.clone()
        } else {
            return Ok(());
        };

        let new_phase = match current_phase {
            MitosisPhase::Prophase => {
                self.mitotic_apparatus.prepare_spindle()?;
                MitosisPhase::Prometaphase
            }
            MitosisPhase::Prometaphase => {
                self.mitotic_apparatus.attach_chromosomes()?;
                MitosisPhase::Metaphase
            }
            MitosisPhase::Metaphase => {
                if self
                    .checkpoint_system
                    .spindle_checkpoint
                    .check_alignment()?
                {
                    MitosisPhase::Anaphase(AnaphaseStage::A)
                } else {
                    MitosisPhase::Metaphase
                }
            }
            MitosisPhase::Anaphase(stage) => match stage {
                AnaphaseStage::A => {
                    self.separate_chromosomes()?;
                    MitosisPhase::Anaphase(AnaphaseStage::B)
                }
                AnaphaseStage::B => {
                    self.elongate_spindle()?;
                    MitosisPhase::Telophase
                }
            },
            MitosisPhase::Telophase => {
                self.reform_nuclei()?;
                self.cycle_state = CellCycleState::G1;
                return Ok(());
            }
        };

        // Update the phase
        if let CellCycleState::M(ref mut phase) = self.cycle_state {
            *phase = new_phase;
        }

        Ok(())
    }

    /// Complete division process
    fn complete_division(&mut self) -> OxirsResult<()> {
        // Reset mitotic apparatus
        self.mitotic_apparatus.reset()?;

        // Distribute DNA content to daughter cells
        let (daughter1, _daughter2) = self.distribute_dna_content()?;

        // For simulation, we keep one daughter cell's content
        self.dna_content = daughter1;

        Ok(())
    }

    /// Replicate DNA content
    fn replicate_dna(&mut self) -> OxirsResult<()> {
        let mut replicated = Vec::new();

        for dna in &self.dna_content {
            let mut copy = dna.clone();
            // Trigger replication machinery
            copy.replication_machinery
                .replicate_strand(&dna.primary_strand)?;
            replicated.push(copy);
        }

        self.dna_content.extend(replicated);
        Ok(())
    }

    /// Separate chromosomes during anaphase A
    fn separate_chromosomes(&mut self) -> OxirsResult<()> {
        // Simulate chromosome separation
        for kinetochore in &mut self.mitotic_apparatus.kinetochores {
            kinetochore.tension = 0.0; // Release tension

            // Degrade cohesin proteins (simulated)
            for attachment in &mut kinetochore.microtubule_attachments {
                if matches!(attachment.attachment_type, AttachmentType::Amphitelic) {
                    attachment.attachment_strength *= 0.5; // Reduce strength
                }
            }
        }
        Ok(())
    }

    /// Elongate spindle during anaphase B
    fn elongate_spindle(&mut self) -> OxirsResult<()> {
        // Extend polar microtubules
        for microtubule in &mut self.mitotic_apparatus.spindle_apparatus.polar_microtubules {
            microtubule.length *= 1.5; // Elongate
            microtubule.dynamic_state = DynamicState::Growing;
        }
        Ok(())
    }

    /// Reform nuclei during telophase
    fn reform_nuclei(&mut self) -> OxirsResult<()> {
        // Nuclear envelope reformation (simulated)
        // Chromosome decondensation (simulated)
        Ok(())
    }

    /// Distribute DNA content to daughter cells
    fn distribute_dna_content(
        &self,
    ) -> OxirsResult<(Vec<DnaDataStructure>, Vec<DnaDataStructure>)> {
        let midpoint = self.dna_content.len() / 2;
        let daughter1 = self.dna_content[..midpoint].to_vec();
        let daughter2 = self.dna_content[midpoint..].to_vec();
        Ok((daughter1, daughter2))
    }

    /// Add DNA content for division
    pub fn add_dna_content(&mut self, dna: DnaDataStructure) {
        self.dna_content.push(dna);
    }

    /// Get current cell cycle state
    pub fn current_state(&self) -> &CellCycleState {
        &self.cycle_state
    }
}

impl Default for MitoticApparatus {
    fn default() -> Self {
        Self::new()
    }
}

impl MitoticApparatus {
    /// Create new mitotic apparatus
    pub fn new() -> Self {
        Self {
            centrosomes: (Centrosome::new(), Centrosome::new()),
            spindle_apparatus: SpindleApparatus::new(),
            kinetochores: Vec::new(),
            division_state: DivisionState::Interphase,
        }
    }

    /// Prepare spindle apparatus
    pub fn prepare_spindle(&mut self) -> OxirsResult<()> {
        self.division_state = DivisionState::Mitosis(MitosisPhase::Prophase);

        // Separate centrosomes
        self.centrosomes.0.position = Position3D {
            x: -10.0,
            y: 0.0,
            z: 0.0,
        };
        self.centrosomes.1.position = Position3D {
            x: 10.0,
            y: 0.0,
            z: 0.0,
        };

        // Nucleate microtubules
        self.spindle_apparatus.nucleate_microtubules()?;

        Ok(())
    }

    /// Attach chromosomes to spindle
    pub fn attach_chromosomes(&mut self) -> OxirsResult<()> {
        // Create kinetochores for chromosome attachment
        for i in 0..10 {
            // Simulate 10 chromosomes
            let kinetochore = Kinetochore {
                chromosome_attachment: true,
                microtubule_attachments: vec![MicrotubuleAttachment {
                    microtubule_id: format!("mt_{i}"),
                    attachment_strength: 1.0,
                    attachment_type: AttachmentType::Amphitelic,
                }],
                tension: 0.5,
            };
            self.kinetochores.push(kinetochore);
        }
        Ok(())
    }

    /// Reset apparatus after division
    pub fn reset(&mut self) -> OxirsResult<()> {
        self.division_state = DivisionState::Interphase;
        self.kinetochores.clear();
        self.spindle_apparatus = SpindleApparatus::new();
        Ok(())
    }
}

impl Default for SpindleApparatus {
    fn default() -> Self {
        Self::new()
    }
}

impl SpindleApparatus {
    /// Create new spindle apparatus
    pub fn new() -> Self {
        Self {
            kinetochore_microtubules: Vec::new(),
            polar_microtubules: Vec::new(),
            astral_microtubules: Vec::new(),
            poles: (SpindlePole::new(), SpindlePole::new()),
        }
    }

    /// Nucleate microtubules from centrosomes
    pub fn nucleate_microtubules(&mut self) -> OxirsResult<()> {
        // Create different types of microtubules
        for i in 0..20 {
            let microtubule = Microtubule::new(format!("kt_mt_{i}"));
            self.kinetochore_microtubules.push(microtubule);
        }

        for i in 0..10 {
            let microtubule = Microtubule::new(format!("polar_mt_{i}"));
            self.polar_microtubules.push(microtubule);
        }

        for i in 0..15 {
            let microtubule = Microtubule::new(format!("astral_mt_{i}"));
            self.astral_microtubules.push(microtubule);
        }

        Ok(())
    }
}

impl Default for CheckpointSystem {
    fn default() -> Self {
        Self::new()
    }
}

impl CheckpointSystem {
    /// Create new checkpoint system
    pub fn new() -> Self {
        Self {
            spindle_checkpoint: SpindleCheckpoint::new(),
            dna_damage_checkpoint: DnaDamageCheckpoint::new(),
            replication_checkpoint: ReplicationCheckpoint::new(),
        }
    }

    /// Check DNA integrity
    pub fn check_dna_integrity(&self) -> OxirsResult<bool> {
        let damage_level =
            self.dna_damage_checkpoint.atm_activity + self.dna_damage_checkpoint.atr_activity;
        Ok(damage_level < 0.1) // Low damage threshold
    }
}

impl Default for SpindleCheckpoint {
    fn default() -> Self {
        Self::new()
    }
}

impl SpindleCheckpoint {
    /// Create new spindle checkpoint
    pub fn new() -> Self {
        Self {
            mad_proteins: vec![
                MadProtein {
                    protein_type: MadProteinType::Mad1,
                    activity_level: 1.0,
                    localization: ProteinLocalization::Kinetochore,
                },
                MadProtein {
                    protein_type: MadProteinType::Mad2,
                    activity_level: 1.0,
                    localization: ProteinLocalization::Kinetochore,
                },
            ],
            bub_proteins: vec![
                BubProtein {
                    protein_type: BubProteinType::Bub1,
                    activity_level: 1.0,
                    kinetochore_binding: true,
                },
                BubProtein {
                    protein_type: BubProteinType::Bub3,
                    activity_level: 1.0,
                    kinetochore_binding: true,
                },
            ],
            apc_c_regulation: ApcCRegulation {
                cdc20_level: 0.5,
                cdh1_level: 0.1,
                activity_state: ApcCActivityState::Inactive,
            },
        }
    }

    /// Check chromosome alignment
    pub fn check_alignment(&self) -> OxirsResult<bool> {
        // Simplified check - all Mad proteins should have low activity
        let mad_activity: f64 = self.mad_proteins.iter().map(|p| p.activity_level).sum();
        Ok(mad_activity < 0.5)
    }
}

// Implementation stubs for other components
impl Default for Centrosome {
    fn default() -> Self {
        Self::new()
    }
}

impl Centrosome {
    pub fn new() -> Self {
        Self {
            centrioles: (Centriole::new(), Centriole::new()),
            pericentriolar_material: PericentriolarMaterial {
                gamma_tubulin: 1.0,
                pericentrin: 1.0,
                ninein: 1.0,
            },
            position: Position3D {
                x: 0.0,
                y: 0.0,
                z: 0.0,
            },
        }
    }
}

impl Default for Centriole {
    fn default() -> Self {
        Self::new()
    }
}

impl Centriole {
    pub fn new() -> Self {
        Self {
            barrel: BarrelStructure {
                diameter: 0.2,
                length: 0.5,
                wall_thickness: 0.02,
            },
            triplets: Vec::new(),
            orientation: Orientation {
                angle: 0.0,
                axis: Vec3D {
                    x: 0.0,
                    y: 0.0,
                    z: 1.0,
                },
            },
        }
    }
}

impl Microtubule {
    pub fn new(_id: String) -> Self {
        Self {
            protofilaments: Vec::new(),
            length: 10.0,
            dynamic_state: DynamicState::Growing,
            plus_end: MicrotubuleEnd {
                cap_structure: CapStructure::GtpCap,
                growth_rate: 1.0,
            },
            minus_end: MicrotubuleEnd {
                cap_structure: CapStructure::GdpCap,
                growth_rate: 0.0,
            },
        }
    }
}

impl Default for SpindlePole {
    fn default() -> Self {
        Self::new()
    }
}

impl SpindlePole {
    pub fn new() -> Self {
        Self {
            centrosome: Centrosome::new(),
            microtubule_nucleation_sites: Vec::new(),
        }
    }
}

impl Default for DnaDamageCheckpoint {
    fn default() -> Self {
        Self::new()
    }
}

impl DnaDamageCheckpoint {
    pub fn new() -> Self {
        Self {
            atm_activity: 0.0,
            atr_activity: 0.0,
            p53_level: 0.1,
        }
    }
}

impl Default for ReplicationCheckpoint {
    fn default() -> Self {
        Self::new()
    }
}

impl ReplicationCheckpoint {
    pub fn new() -> Self {
        Self {
            replication_forks: Vec::new(),
            checkpoint_active: false,
        }
    }
}

impl Default for CellularDivision {
    fn default() -> Self {
        Self::new()
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_cellular_division_creation() {
        let division = CellularDivision::new();
        assert!(matches!(division.cycle_state, CellCycleState::G1));
        assert_eq!(division.dna_content.len(), 0);
    }

    #[test]
    fn test_mitotic_apparatus() {
        let apparatus = MitoticApparatus::new();
        assert!(matches!(
            apparatus.division_state,
            DivisionState::Interphase
        ));
        assert_eq!(apparatus.kinetochores.len(), 0);
    }

    #[test]
    fn test_checkpoint_system() {
        let checkpoint = CheckpointSystem::new();
        assert!(checkpoint
            .check_dna_integrity()
            .expect("operation should succeed"));
    }
}