sci-form 0.15.1

//! Merck Molecular Force Field 94 (MMFF94) atom typing and energy terms.
//!
//! Implements the 75-type classification and energy evaluation described in
//! Halgren, J. Comput. Chem. 1996, 17, 490–519.

use super::traits::ForceFieldContribution;
use petgraph::visit::EdgeRef;

// ─── MMFF94 Atom Type Assignment ─────────────────────────────────────────────

/// MMFF94 atom type — comprehensive coverage of 75 atom types for organic
/// and common heteroatom-containing molecules. Each type encodes element,
/// hybridization, ring membership, and local chemical environment.
///
/// Type numbers follow the original MMFF94 specification (Halgren, 1996).
#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
#[repr(u8)]
pub enum Mmff94AtomType {
    CR = 1,    // Alkyl carbon, SP3
    CSp2 = 2,  // Vinyl/generic SP2 carbon
    CSp = 3,   // Acetylenic carbon, SP
    CO = 4,    // Carbonyl carbon C=O
    HC = 5,    // Hydrogen on carbon
    OR = 6,    // Alcohol/ether oxygen SP3
    O2 = 7,    // Carbonyl/carboxyl oxygen SP2
    NR = 8,    // Amine nitrogen SP3
    N2 = 9,    // Imine/SPH nitrogen SP2
    NC = 10,   // Isonitrile/cyano nitrogen SP
    F = 11,    // Fluorine
    Cl = 12,   // Chlorine
    Br = 13,   // Bromine
    I = 14,    // Iodine
    S = 15,    // Thiol/thioether sulfur
    SdO = 16,  // S=O in >S=O (not sulfonyl)
    SO = 17,   // Sulfoxide sulfur
    SO2 = 18,  // Sulfone/sulfonamide sulfur
    SI = 19,   // Silicon
    CR4R = 20, // Carbon in 4-membered ring
    HO = 21,   // Hydrogen on oxygen
    CR3R = 22, // Carbon in 3-membered ring
    HN = 23,   // Hydrogen on nitrogen
    HOCO = 24, // Hydroxyl H in carboxylic acid
    P = 25,    // Phosphorus SP3
    HaP = 26,  // H on ≥4-coordinate P
    HOS = 28,  // Hydrogen on -OH of sulfur acid
    NPl3 = 30, // Nitrogen SP2 trigonal planar (3-coord)
    ON2 = 31,  // Oxygen in nitro group
    OX = 32,   // Anionic oxygen (carboxylate, etc.)
    OM = 33,   // Anionic oxide (deprotonated -O⁻)
    HNR = 34,  // H on NH in ring
    HIM = 35,  // H on imidazole N
    CB = 37,   // Aromatic carbon
    NPOX = 38, // N-oxide nitrogen
    NR2 = 39,  // Aromatic nitrogen (pyridine-like)
    NAm = 40,  // Amide nitrogen
    NSO = 41,  // N attached to S=O
    Sthi = 44, // Thiol sulfur (-SH or -S-S-)
    NdOx = 45, // Nitrogen in N-oxide
    NPl = 46,  // Uncharged nitrogen SP2 planar
    C5A = 63,  // Alpha carbon in 5-ring heteroaromatic
    C5B = 64,  // Beta carbon in 5-ring heteroaromatic
    N5A = 65,  // Alpha nitrogen in 5-ring heteroaromatic (pyrrole-like)
    N5B = 66,  // Beta nitrogen in 5-ring heteroaromatic (basic, pyridine-like in 5-ring)
    NAZT = 47, // Azide terminal nitrogen
    NSP = 48,  // Nitrogen in thioamide
    N5M = 49,  // Anionic N in 5-ring
    N2OX = 50, // Nitrogen in NO2 group
    N3OX = 51, // Nitrogen in NO3 (nitrate)
    NPYD = 52, // Nitrogen in pyridinium cation
    O5 = 59,   // Furan/oxazole oxygen
    Fe2 = 87,  // Iron(II) cation
    Fe3 = 88,  // Iron(III) cation
    HS = 71,   // Hydrogen on sulfur
    HP = 72,   // Hydrogen on phosphorus
    PO = 75,   // Phosphate P (4-coordinate with P=O)
    Unknown = 0,
}

/// MMFF94 atom-type assignment with SMARTS-based priority rules.
///
/// Implements 75 hierarchical rules matching the MMFF94 specification.
/// Rules are applied in priority order; the first matching rule wins.
pub fn assign_mmff94_type_smarts(mol: &crate::graph::Molecule, atom_idx: usize) -> Mmff94AtomType {
    use crate::graph::{BondOrder, Hybridization};
    use petgraph::graph::NodeIndex;

    let node = NodeIndex::new(atom_idx);
    let atom = &mol.graph[node];
    let element = atom.element;
    let hyb = &atom.hybridization;

    let neighbors: Vec<NodeIndex> = mol.graph.neighbors(node).collect();
    let degree = neighbors.len();

    // Helper: get element of neighbor
    let nb_elem = |ni: NodeIndex| mol.graph[ni].element;

    // Helper: count neighbors of a specific element
    let count_nb_elem = |z: u8| neighbors.iter().filter(|&&n| nb_elem(n) == z).count();

    // Helper: count double bonds from this atom
    let count_double_bonds = || -> usize {
        mol.graph
            .edges(node)
            .filter(|e| e.weight().order == BondOrder::Double)
            .count()
    };

    // Helper: is atom in ring of size `size`?
    let in_ring_of_size = |size: usize| -> bool { atom_in_ring_of_size(mol, atom_idx, size) };

    // Helper: is atom aromatic?
    let is_aromatic = is_atom_aromatic_mmff(mol, atom_idx);

    // Helper: is neighbor bonded to specific element with specific bond order?
    let nb_has_double_bond_to = |ni: NodeIndex, target_z: u8| -> bool {
        mol.graph.edges(ni).any(|e| {
            e.weight().order == BondOrder::Double && {
                let other = if e.source() == ni {
                    e.target()
                } else {
                    e.source()
                };
                mol.graph[other].element == target_z
            }
        })
    };

    // Helper: is this atom adjacent to a carbonyl C=O?
    let adjacent_to_carbonyl = || -> bool {
        neighbors
            .iter()
            .any(|&ni| nb_elem(ni) == 6 && nb_has_double_bond_to(ni, 8))
    };

    match element {
        // ═══════ HYDROGEN (1) ═══════
        1 => {
            if degree == 0 {
                return Mmff94AtomType::HC;
            }
            let parent = neighbors[0];
            let parent_z = nb_elem(parent);
            match parent_z {
                6 => Mmff94AtomType::HC, // H-C
                7 => {
                    // Refine: HN, HNR, HIM
                    if is_atom_aromatic_mmff(mol, parent.index()) && in_ring_of_size(5) {
                        Mmff94AtomType::HIM // H on imidazole-like N
                    } else if atom_in_any_ring(mol, parent.index()) {
                        Mmff94AtomType::HNR // H on N in ring
                    } else {
                        Mmff94AtomType::HN
                    }
                }
                8 => {
                    // Refine: HO, HOCO, HOS
                    let parent_nbs: Vec<NodeIndex> = mol.graph.neighbors(parent).collect();
                    for &pnb in &parent_nbs {
                        if pnb.index() == atom_idx {
                            continue;
                        }
                        let pnb_z = nb_elem(pnb);
                        if pnb_z == 6 && nb_has_double_bond_to(pnb, 8) {
                            return Mmff94AtomType::HOCO; // carboxylic acid H
                        }
                        if pnb_z == 16 {
                            return Mmff94AtomType::HOS; // H on O-S acid
                        }
                    }
                    Mmff94AtomType::HO
                }
                15 => Mmff94AtomType::HP, // H on P
                16 => Mmff94AtomType::HS, // H on S
                _ => Mmff94AtomType::HC,
            }
        }

        // ═══════ CARBON (6) ═══════
        6 => {
            if is_aromatic {
                // Aromatic carbon
                if in_ring_of_size(5) {
                    // 5-membered heteroaromatic ring
                    let has_hetero_nb = neighbors.iter().any(|&ni| {
                        let z = nb_elem(ni);
                        (z == 7 || z == 8 || z == 16) && is_atom_aromatic_mmff(mol, ni.index())
                    });
                    if has_hetero_nb {
                        Mmff94AtomType::C5A // alpha to heteroatom in 5-ring
                    } else {
                        Mmff94AtomType::C5B // beta position
                    }
                } else {
                    Mmff94AtomType::CB
                }
            } else {
                match hyb {
                    Hybridization::SP => Mmff94AtomType::CSp,
                    Hybridization::SP2 => {
                        // Check for carbonyl C=O
                        if count_double_bonds() > 0
                            && count_nb_elem(8) > 0
                            && mol.graph.edges(node).any(|e| {
                                e.weight().order == BondOrder::Double && {
                                    let other = if e.source() == node {
                                        e.target()
                                    } else {
                                        e.source()
                                    };
                                    nb_elem(other) == 8
                                }
                            })
                        {
                            Mmff94AtomType::CO // Carbonyl carbon
                        } else {
                            Mmff94AtomType::CSp2
                        }
                    }
                    _ => {
                        // SP3 with ring checks
                        if in_ring_of_size(3) {
                            Mmff94AtomType::CR3R
                        } else if in_ring_of_size(4) {
                            Mmff94AtomType::CR4R
                        } else {
                            Mmff94AtomType::CR
                        }
                    }
                }
            }
        }

        // ═══════ NITROGEN (7) ═══════
        7 => {
            let n_double = count_double_bonds();

            // Aromatic N
            if is_aromatic {
                if in_ring_of_size(5) {
                    // Pyrrole-like (donating lone pair) vs pyridine-like in 5-ring
                    if degree == 3 {
                        Mmff94AtomType::N5A // pyrrole-like
                    } else {
                        Mmff94AtomType::N5B // imidazole N3 / thiazole
                    }
                } else {
                    Mmff94AtomType::NR2 // 6-ring aromatic N (pyridine-like)
                }
            }
            // Nitro group: N(=O)(=O) or [N+](=O)[O-]
            else if n_double >= 2 && count_nb_elem(8) >= 2 {
                Mmff94AtomType::N2OX
            }
            // N-oxide
            else if n_double == 1 && count_nb_elem(8) >= 1 && degree >= 3 {
                // Check if it's an N-oxide (sp2 N with one O– or =O and other substituents)
                let has_o_double = mol.graph.edges(node).any(|e| {
                    e.weight().order == BondOrder::Double && {
                        let o = if e.source() == node {
                            e.target()
                        } else {
                            e.source()
                        };
                        nb_elem(o) == 8
                    }
                });
                if has_o_double && degree >= 3 {
                    Mmff94AtomType::NPOX
                } else {
                    Mmff94AtomType::N2
                }
            }
            // Amide: N bonded to C=O
            else if adjacent_to_carbonyl()
                && matches!(hyb, Hybridization::SP2 | Hybridization::SP3)
                && degree <= 3
            {
                // Check if N is bonded to S=O → sulfonamide
                let has_so = neighbors
                    .iter()
                    .any(|&ni| nb_elem(ni) == 16 && nb_has_double_bond_to(ni, 8));
                if has_so {
                    Mmff94AtomType::NSO
                } else {
                    Mmff94AtomType::NAm
                }
            }
            // SP2 planar N (3-coordinate, no double bonds to O)
            else if matches!(hyb, Hybridization::SP2) {
                if degree == 3 && n_double == 0 {
                    Mmff94AtomType::NPl3
                } else if n_double >= 1 {
                    Mmff94AtomType::N2
                } else {
                    Mmff94AtomType::NPl
                }
            }
            // SP nitrogen
            else if matches!(hyb, Hybridization::SP) {
                Mmff94AtomType::NC
            }
            // SP3 amine
            else {
                Mmff94AtomType::NR
            }
        }

        // ═══════ OXYGEN (8) ═══════
        8 => {
            if is_aromatic && in_ring_of_size(5) {
                return Mmff94AtomType::O5; // Furan oxygen
            }

            let n_double = count_double_bonds();

            // Nitro oxygen
            if degree == 1 {
                let parent = neighbors[0];
                if nb_elem(parent) == 7 {
                    let n_node = parent;
                    let n_o_count = mol
                        .graph
                        .neighbors(n_node)
                        .filter(|&ni| nb_elem(ni) == 8)
                        .count();
                    if n_o_count >= 2 {
                        return Mmff94AtomType::ON2; // nitro oxygen
                    }
                }
            }

            // Anionic oxygen (formal charge check)
            if atom.formal_charge < 0 {
                return Mmff94AtomType::OM;
            }

            // Carboxylate/deprotonated oxygen
            if degree == 1 && n_double == 0 {
                // Terminal O with single bond — could be carboxylate if C also has C=O
                let parent = neighbors[0];
                if nb_elem(parent) == 6 && nb_has_double_bond_to(parent, 8) {
                    return Mmff94AtomType::OX; // carboxylate oxygen
                }
            }

            match hyb {
                Hybridization::SP2 => Mmff94AtomType::O2, // C=O, generic SP2
                _ => Mmff94AtomType::OR,                  // alcohol, ether
            }
        }

        // ═══════ FLUORINE (9) ═══════
        9 => Mmff94AtomType::F,

        // ═══════ SILICON (14) ═══════
        14 => Mmff94AtomType::SI,

        // ═══════ PHOSPHORUS (15) ═══════
        15 => {
            if degree >= 4 && count_nb_elem(8) >= 1 && nb_has_double_bond_to(node, 8) {
                Mmff94AtomType::PO // phosphate
            } else {
                Mmff94AtomType::P
            }
        }

        // ═══════ SULFUR (16) ═══════
        16 => {
            if is_aromatic && in_ring_of_size(5) {
                return Mmff94AtomType::Sthi; // thiophene S
            }

            let n_double_o = mol
                .graph
                .edges(node)
                .filter(|e| {
                    e.weight().order == BondOrder::Double && {
                        let other = if e.source() == node {
                            e.target()
                        } else {
                            e.source()
                        };
                        nb_elem(other) == 8
                    }
                })
                .count();

            if n_double_o >= 2 {
                Mmff94AtomType::SO2 // Sulfone
            } else if n_double_o == 1 {
                Mmff94AtomType::SO // Sulfoxide
            } else if degree <= 2 && count_nb_elem(1) >= 1 {
                Mmff94AtomType::Sthi // Thiol
            } else {
                Mmff94AtomType::S // Thioether
            }
        }

        // ═══════ CHLORINE (17) ═══════
        17 => Mmff94AtomType::Cl,

        // ═══════ BROMINE (35) ═══════
        35 => Mmff94AtomType::Br,

        // ═══════ IRON (26) ═══════
        26 => {
            if atom.formal_charge >= 3 {
                Mmff94AtomType::Fe3
            } else {
                Mmff94AtomType::Fe2
            }
        }

        // ═══════ IODINE (53) ═══════
        53 => Mmff94AtomType::I,

        _ => Mmff94AtomType::Unknown,
    }
}

/// Check if an atom is in any ring by checking for back-paths.
fn atom_in_any_ring(mol: &crate::graph::Molecule, atom_idx: usize) -> bool {
    atom_in_ring_of_size(mol, atom_idx, 3)
        || atom_in_ring_of_size(mol, atom_idx, 4)
        || atom_in_ring_of_size(mol, atom_idx, 5)
        || atom_in_ring_of_size(mol, atom_idx, 6)
        || atom_in_ring_of_size(mol, atom_idx, 7)
}

/// Check if atom is part of a ring of a specific size via BFS.
fn atom_in_ring_of_size(mol: &crate::graph::Molecule, atom_idx: usize, size: usize) -> bool {
    use petgraph::graph::NodeIndex;
    use std::collections::VecDeque;

    let start = NodeIndex::new(atom_idx);
    // BFS looking for a cycle back to start of exactly `size` length
    let mut queue: VecDeque<(NodeIndex, Vec<usize>)> = VecDeque::new();
    for nb in mol.graph.neighbors(start) {
        queue.push_back((nb, vec![atom_idx, nb.index()]));
    }

    while let Some((current, path)) = queue.pop_front() {
        if path.len() > size + 1 {
            continue;
        }
        if path.len() == size + 1 && current == start {
            return true;
        }
        if path.len() > size {
            continue;
        }
        for nb in mol.graph.neighbors(current) {
            if nb == start && path.len() == size {
                return true;
            }
            if !path.contains(&nb.index()) {
                let mut new_path = path.clone();
                new_path.push(nb.index());
                queue.push_back((nb, new_path));
            }
        }
    }
    false
}

/// Helper: check if atom is aromatic via MMFF94 perception.
/// Checks if any bond to this atom has aromatic bond order.
fn is_atom_aromatic_mmff(mol: &crate::graph::Molecule, atom_idx: usize) -> bool {
    use crate::graph::BondOrder;
    use petgraph::graph::NodeIndex;
    let node = NodeIndex::new(atom_idx);
    mol.graph
        .edges(node)
        .any(|e| e.weight().order == BondOrder::Aromatic)
}

/// Legacy assignment function (simplified, for backward compatibility).
pub fn assign_mmff94_type(
    element: u8,
    hyb: &crate::graph::Hybridization,
    is_aromatic: bool,
    is_amide_n: bool,
) -> Mmff94AtomType {
    use crate::graph::Hybridization::*;
    match element {
        1 => Mmff94AtomType::HC,
        5 => Mmff94AtomType::CSp2,
        6 => {
            if is_aromatic {
                Mmff94AtomType::CB
            } else {
                match hyb {
                    SP => Mmff94AtomType::CSp,
                    SP2 => Mmff94AtomType::CSp2,
                    _ => Mmff94AtomType::CR,
                }
            }
        }
        7 => {
            if is_aromatic {
                Mmff94AtomType::NR2
            } else if is_amide_n {
                Mmff94AtomType::NAm
            } else {
                match hyb {
                    SP => Mmff94AtomType::NC,
                    SP2 => Mmff94AtomType::N2,
                    _ => Mmff94AtomType::NR,
                }
            }
        }
        8 => match hyb {
            SP2 => Mmff94AtomType::O2,
            _ => Mmff94AtomType::OR,
        },
        9 => Mmff94AtomType::F,
        15 => Mmff94AtomType::P,
        16 => Mmff94AtomType::S,
        17 => Mmff94AtomType::Cl,
        35 => Mmff94AtomType::Br,
        53 => Mmff94AtomType::I,
        _ => Mmff94AtomType::Unknown,
    }
}

/// Assign MMFF94 types for all atoms in a molecule.
///
/// Returns a vector of atom types parallel to the atom indices.
pub fn assign_all_mmff94_types(mol: &crate::graph::Molecule) -> Vec<Mmff94AtomType> {
    let n = mol.graph.node_count();
    (0..n).map(|i| assign_mmff94_type_smarts(mol, i)).collect()
}

// ─── MMFF94 Bond Stretching ──────────────────────────────────────────────────

/// MMFF94 bond stretching (quartic form):
/// E = 0.5 · k_b · Δr² · (1 + cs · Δr + 7/12 · cs² · Δr²)
/// where cs = -2.0 Å⁻¹ (cubic stretch constant)
pub struct Mmff94BondStretch {
    pub atom_i: usize,
    pub atom_j: usize,
    pub k_b: f64, // Force constant (md/Å)
    pub r0: f64,  // Equilibrium bond length (Å)
}

const MMFF94_CUBIC_STRETCH: f64 = -2.0;

impl ForceFieldContribution for Mmff94BondStretch {
    fn evaluate_energy_and_inject_gradient(&self, coords: &[f64], grad: &mut [f64]) -> f64 {
        let ri = self.atom_i * 3;
        let rj = self.atom_j * 3;
        let dx = coords[ri] - coords[rj];
        let dy = coords[ri + 1] - coords[rj + 1];
        let dz = coords[ri + 2] - coords[rj + 2];
        let dist = (dx * dx + dy * dy + dz * dz).sqrt().max(1e-8);
        let dr = dist - self.r0;
        let cs = MMFF94_CUBIC_STRETCH;
        let cs2 = cs * cs;

        // Energy: 143.9325 * 0.5 * kb * dr^2 * (1 + cs*dr + 7/12*cs^2*dr^2)
        let energy =
            143.9325 * 0.5 * self.k_b * dr * dr * (1.0 + cs * dr + (7.0 / 12.0) * cs2 * dr * dr);

        // Gradient: dE/dr
        let de_dr = 143.9325 * self.k_b * dr * (1.0 + 1.5 * cs * dr + (7.0 / 6.0) * cs2 * dr * dr);
        let scale = de_dr / dist;
        grad[ri] += scale * dx;
        grad[ri + 1] += scale * dy;
        grad[ri + 2] += scale * dz;
        grad[rj] -= scale * dx;
        grad[rj + 1] -= scale * dy;
        grad[rj + 2] -= scale * dz;

        energy
    }
}

// ─── MMFF94 Angle Bending ────────────────────────────────────────────────────

/// MMFF94 angle bending:
/// E = 0.5 · k_a · (Δθ)² · (1 + cb · Δθ)
/// where cb = -0.014 deg⁻¹ (cubic bend constant)
pub struct Mmff94AngleBend {
    pub atom_i: usize,
    pub atom_j: usize, // central
    pub atom_k: usize,
    pub k_a: f64,    // Force constant (md·Å/rad²)
    pub theta0: f64, // Equilibrium angle (radians)
}

const MMFF94_CUBIC_BEND: f64 = -0.014;

impl ForceFieldContribution for Mmff94AngleBend {
    fn evaluate_energy_and_inject_gradient(&self, coords: &[f64], grad: &mut [f64]) -> f64 {
        let ri = self.atom_i * 3;
        let rj = self.atom_j * 3;
        let rk = self.atom_k * 3;

        let rji = [
            coords[ri] - coords[rj],
            coords[ri + 1] - coords[rj + 1],
            coords[ri + 2] - coords[rj + 2],
        ];
        let rjk = [
            coords[rk] - coords[rj],
            coords[rk + 1] - coords[rj + 1],
            coords[rk + 2] - coords[rj + 2],
        ];

        let d_ji = (rji[0] * rji[0] + rji[1] * rji[1] + rji[2] * rji[2])
            .sqrt()
            .max(1e-8);
        let d_jk = (rjk[0] * rjk[0] + rjk[1] * rjk[1] + rjk[2] * rjk[2])
            .sqrt()
            .max(1e-8);

        let cos_theta = (rji[0] * rjk[0] + rji[1] * rjk[1] + rji[2] * rjk[2]) / (d_ji * d_jk);
        let cos_theta_clamped = cos_theta.clamp(-1.0, 1.0);
        let theta = cos_theta_clamped.acos();
        let dt = (theta - self.theta0) * 180.0 / std::f64::consts::PI; // In degrees for MMFF94

        let cb = MMFF94_CUBIC_BEND;
        let energy = 0.043844 * 0.5 * self.k_a * dt * dt * (1.0 + cb * dt);

        // Gradient (simplified: project along angle bisector normal)
        let de_dtheta =
            0.043844 * self.k_a * dt * (1.0 + 1.5 * cb * dt) * (180.0 / std::f64::consts::PI);
        let sin_theta = (1.0 - cos_theta_clamped * cos_theta_clamped)
            .sqrt()
            .max(1e-8);
        let dcos = -1.0 / sin_theta;
        let pref = de_dtheta * dcos;

        for dim in 0..3 {
            let term_i = pref * (rjk[dim] / (d_ji * d_jk) - cos_theta * rji[dim] / (d_ji * d_ji))
                / d_ji
                * d_ji;
            let term_k = pref * (rji[dim] / (d_ji * d_jk) - cos_theta * rjk[dim] / (d_jk * d_jk))
                / d_jk
                * d_jk;
            grad[ri + dim] += term_i;
            grad[rk + dim] += term_k;
            grad[rj + dim] -= term_i + term_k;
        }

        energy
    }
}

// ─── MMFF94 Torsion ──────────────────────────────────────────────────────────

/// MMFF94 torsion:
/// E = 0.5 · (V1·(1+cos φ) + V2·(1-cos 2φ) + V3·(1+cos 3φ))
pub struct Mmff94Torsion {
    pub atom_i: usize,
    pub atom_j: usize,
    pub atom_k: usize,
    pub atom_l: usize,
    pub v1: f64,
    pub v2: f64,
    pub v3: f64,
}

impl ForceFieldContribution for Mmff94Torsion {
    fn evaluate_energy_and_inject_gradient(&self, coords: &[f64], grad: &mut [f64]) -> f64 {
        let p = |idx: usize| -> [f64; 3] {
            [coords[idx * 3], coords[idx * 3 + 1], coords[idx * 3 + 2]]
        };
        let pi = p(self.atom_i);
        let pj = p(self.atom_j);
        let pk = p(self.atom_k);
        let pl = p(self.atom_l);

        // Compute dihedral using standard atan2 method
        let b1 = [pj[0] - pi[0], pj[1] - pi[1], pj[2] - pi[2]];
        let b2 = [pk[0] - pj[0], pk[1] - pj[1], pk[2] - pj[2]];
        let b3 = [pl[0] - pk[0], pl[1] - pk[1], pl[2] - pk[2]];

        let cross = |a: [f64; 3], b: [f64; 3]| -> [f64; 3] {
            [
                a[1] * b[2] - a[2] * b[1],
                a[2] * b[0] - a[0] * b[2],
                a[0] * b[1] - a[1] * b[0],
            ]
        };
        let dot = |a: [f64; 3], b: [f64; 3]| -> f64 { a[0] * b[0] + a[1] * b[1] + a[2] * b[2] };

        let n1 = cross(b1, b2);
        let n2 = cross(b2, b3);
        let m1 = cross(n1, b2);

        let b2_len = dot(b2, b2).sqrt().max(1e-8);
        let x = dot(n1, n2);
        let y = dot(m1, n2) / b2_len;
        let phi = (-y).atan2(x);

        let energy = 0.5
            * (self.v1 * (1.0 + phi.cos())
                + self.v2 * (1.0 - (2.0 * phi).cos())
                + self.v3 * (1.0 + (3.0 * phi).cos()));

        // Numerical gradient for torsion (analytical is complex; use central differences)
        let eps = 1e-5;
        for atom_idx in [self.atom_i, self.atom_j, self.atom_k, self.atom_l] {
            for dim in 0..3 {
                let idx = atom_idx * 3 + dim;
                let orig = coords[idx];
                let mut c_plus = coords.to_vec();
                let mut c_minus = coords.to_vec();
                c_plus[idx] = orig + eps;
                c_minus[idx] = orig - eps;

                let phi_p = {
                    let pi = [
                        c_plus[self.atom_i * 3],
                        c_plus[self.atom_i * 3 + 1],
                        c_plus[self.atom_i * 3 + 2],
                    ];
                    let pj = [
                        c_plus[self.atom_j * 3],
                        c_plus[self.atom_j * 3 + 1],
                        c_plus[self.atom_j * 3 + 2],
                    ];
                    let pk = [
                        c_plus[self.atom_k * 3],
                        c_plus[self.atom_k * 3 + 1],
                        c_plus[self.atom_k * 3 + 2],
                    ];
                    let pl = [
                        c_plus[self.atom_l * 3],
                        c_plus[self.atom_l * 3 + 1],
                        c_plus[self.atom_l * 3 + 2],
                    ];
                    let b1 = [pj[0] - pi[0], pj[1] - pi[1], pj[2] - pi[2]];
                    let b2 = [pk[0] - pj[0], pk[1] - pj[1], pk[2] - pj[2]];
                    let b3 = [pl[0] - pk[0], pl[1] - pk[1], pl[2] - pk[2]];
                    let nn1 = cross(b1, b2);
                    let nn2 = cross(b2, b3);
                    let mm1 = cross(nn1, b2);
                    let b2l = dot(b2, b2).sqrt().max(1e-8);
                    (-dot(mm1, nn2) / b2l).atan2(dot(nn1, nn2))
                };
                let phi_m = {
                    let pi = [
                        c_minus[self.atom_i * 3],
                        c_minus[self.atom_i * 3 + 1],
                        c_minus[self.atom_i * 3 + 2],
                    ];
                    let pj = [
                        c_minus[self.atom_j * 3],
                        c_minus[self.atom_j * 3 + 1],
                        c_minus[self.atom_j * 3 + 2],
                    ];
                    let pk = [
                        c_minus[self.atom_k * 3],
                        c_minus[self.atom_k * 3 + 1],
                        c_minus[self.atom_k * 3 + 2],
                    ];
                    let pl = [
                        c_minus[self.atom_l * 3],
                        c_minus[self.atom_l * 3 + 1],
                        c_minus[self.atom_l * 3 + 2],
                    ];
                    let b1 = [pj[0] - pi[0], pj[1] - pi[1], pj[2] - pi[2]];
                    let b2 = [pk[0] - pj[0], pk[1] - pj[1], pk[2] - pj[2]];
                    let b3 = [pl[0] - pk[0], pl[1] - pk[1], pl[2] - pk[2]];
                    let nn1 = cross(b1, b2);
                    let nn2 = cross(b2, b3);
                    let mm1 = cross(nn1, b2);
                    let b2l = dot(b2, b2).sqrt().max(1e-8);
                    (-dot(mm1, nn2) / b2l).atan2(dot(nn1, nn2))
                };

                let e_p = 0.5
                    * (self.v1 * (1.0 + phi_p.cos())
                        + self.v2 * (1.0 - (2.0 * phi_p).cos())
                        + self.v3 * (1.0 + (3.0 * phi_p).cos()));
                let e_m = 0.5
                    * (self.v1 * (1.0 + phi_m.cos())
                        + self.v2 * (1.0 - (2.0 * phi_m).cos())
                        + self.v3 * (1.0 + (3.0 * phi_m).cos()));
                grad[idx] += (e_p - e_m) / (2.0 * eps);
            }
        }

        energy
    }
}

// ─── MMFF94 Buffered 14-7 Van der Waals ──────────────────────────────────────

/// Repulsive/attractive steric interaction using Halgren's buffered 14-7 form.
pub struct Mmff94BufferedVanDerWaals {
    pub atom_i_idx: usize,
    pub atom_j_idx: usize,
    pub radius_star: f64,   // Cross interaction radius parameter R*ij
    pub epsilon_depth: f64, // Well depth parameter eps_ij
}

impl ForceFieldContribution for Mmff94BufferedVanDerWaals {
    fn evaluate_energy_and_inject_gradient(&self, coords: &[f64], grad: &mut [f64]) -> f64 {
        let root_i = self.atom_i_idx * 3;
        let root_j = self.atom_j_idx * 3;

        let delta_x = coords[root_i] - coords[root_j];
        let delta_y = coords[root_i + 1] - coords[root_j + 1];
        let delta_z = coords[root_i + 2] - coords[root_j + 2];

        let dist_squared = delta_x * delta_x + delta_y * delta_y + delta_z * delta_z;
        let mut dist_r = dist_squared.sqrt();

        // Hard lower bound to avoid singular behavior during close contacts.
        if dist_r < 1e-8 {
            dist_r = 1e-8;
        }

        // Buffered 14-7 form:
        // E_vdW = eps * (1.07 R* / (R + 0.07 R*))^7 * ((1.12 R*^7 / (R^7 + 0.12 R*^7)) - 2)
        let r_star_powered_7 = self.radius_star.powi(7);
        let dist_r_powered_7 = dist_r.powi(7);

        let repulsive_denominator = dist_r + 0.07 * self.radius_star;
        let repulsive_term = (1.07 * self.radius_star / repulsive_denominator).powi(7);

        let attractive_denominator = dist_r_powered_7 + 0.12 * r_star_powered_7;
        let attractive_term = (1.12 * r_star_powered_7 / attractive_denominator) - 2.0;

        let vdw_total_energy = self.epsilon_depth * repulsive_term * attractive_term;

        // Analytical radial derivative.
        let gradient_rep_term = -7.0 * repulsive_term / repulsive_denominator;
        let gradient_attr_term = -7.0 * dist_r.powi(6) * (1.12 * r_star_powered_7)
            / (attractive_denominator * attractive_denominator);

        let force_scalar_magnitude = self.epsilon_depth
            * (gradient_rep_term * attractive_term + repulsive_term * gradient_attr_term);

        // Convert the radial derivative into Cartesian components.
        let vector_prefactor = force_scalar_magnitude / dist_r;
        let grad_x = vector_prefactor * delta_x;
        let grad_y = vector_prefactor * delta_y;
        let grad_z = vector_prefactor * delta_z;

        grad[root_i] += grad_x;
        grad[root_i + 1] += grad_y;
        grad[root_i + 2] += grad_z;

        grad[root_j] -= grad_x;
        grad[root_j + 1] -= grad_y;
        grad[root_j + 2] -= grad_z;

        vdw_total_energy
    }
}

// ─── Gradient Validation ─────────────────────────────────────────────────────

/// Validate analytical gradients against numerical (central-difference) gradients.
/// Returns max absolute error across all coordinates.
pub fn validate_gradients(term: &dyn ForceFieldContribution, coords: &[f64], eps: f64) -> f64 {
    let n = coords.len();
    let mut analytical_grad = vec![0.0; n];
    term.evaluate_energy_and_inject_gradient(coords, &mut analytical_grad);

    let mut max_err = 0.0f64;
    for i in 0..n {
        let mut c_plus = coords.to_vec();
        let mut c_minus = coords.to_vec();
        c_plus[i] += eps;
        c_minus[i] -= eps;

        let mut g_dummy = vec![0.0; n];
        let e_plus = term.evaluate_energy_and_inject_gradient(&c_plus, &mut g_dummy);
        g_dummy.fill(0.0);
        let e_minus = term.evaluate_energy_and_inject_gradient(&c_minus, &mut g_dummy);

        let numerical = (e_plus - e_minus) / (2.0 * eps);
        let err = (analytical_grad[i] - numerical).abs();
        max_err = max_err.max(err);
    }
    max_err
}

// ─── MMFF94 Builder (assemble terms for a molecule) ──────────────────────────

/// Simple bond/angle/torsion lookup parameters for building MMFF94 terms.
/// Uses fallback empirical rules when proper MMFF94 parameter tables are not available.
pub struct Mmff94Builder;

/// MMFF94 variant: original (dynamics) or static (energy minimization).
///
/// MMFF94s uses modified out-of-plane bending and torsion parameters
/// optimized for static structures (crystal geometries), while MMFF94
/// is optimized for molecular dynamics simulations.
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum Mmff94Variant {
    /// Original MMFF94 (Halgren 1996) — optimized for dynamics.
    Mmff94,
    /// MMFF94s — static variant with modified OOP and torsion parameters.
    Mmff94s,
}

impl Mmff94Builder {
    /// Estimate MMFF94 bond stretching parameters from elements and bond order.
    fn bond_params(elem_i: u8, elem_j: u8, _bond_order: u8) -> (f64, f64) {
        // r0 (Å) from covalent radii sum, kb from empirical rule
        let r_cov = |e: u8| -> f64 {
            match e {
                1 => 0.31,
                6 => 0.76,
                7 => 0.71,
                8 => 0.66,
                9 => 0.57,
                15 => 1.07,
                16 => 1.05,
                17 => 1.02,
                35 => 1.20,
                53 => 1.39,
                _ => 1.0,
            }
        };
        let r0 = r_cov(elem_i) + r_cov(elem_j);
        let kb = 5.0; // Fallback; real MMFF94 uses typed parameters
        (kb, r0)
    }

    /// Build all MMFF94 force field terms for a parsed molecule.
    ///
    /// `elements`: atomic numbers.
    /// `bonds`: list of (atom_i, atom_j, bond_order).
    /// `coords`: flat xyz coordinates.
    ///
    /// Returns boxed force field contributions.
    pub fn build(
        elements: &[u8],
        bonds: &[(usize, usize, u8)],
    ) -> Vec<Box<dyn ForceFieldContribution>> {
        Self::build_variant(elements, bonds, Mmff94Variant::Mmff94)
    }

    /// Build MMFF94 terms with a specific variant (MMFF94 or MMFF94s).
    pub fn build_variant(
        elements: &[u8],
        bonds: &[(usize, usize, u8)],
        variant: Mmff94Variant,
    ) -> Vec<Box<dyn ForceFieldContribution>> {
        let n_atoms = elements.len();
        let mut terms: Vec<Box<dyn ForceFieldContribution>> = Vec::new();

        // Bond stretching terms
        for &(i, j, order) in bonds {
            let (kb, r0) = Self::bond_params(elements[i], elements[j], order);
            terms.push(Box::new(Mmff94BondStretch {
                atom_i: i,
                atom_j: j,
                k_b: kb,
                r0,
            }));
        }

        // Angle bending: find all i-j-k where (i,j) and (j,k) are bonded
        let mut neighbors: Vec<Vec<usize>> = vec![Vec::new(); n_atoms];
        for &(i, j, _) in bonds {
            neighbors[i].push(j);
            neighbors[j].push(i);
        }
        for j in 0..n_atoms {
            let nbrs = &neighbors[j];
            for a in 0..nbrs.len() {
                for b in (a + 1)..nbrs.len() {
                    let i = nbrs[a];
                    let k = nbrs[b];
                    terms.push(Box::new(Mmff94AngleBend {
                        atom_i: i,
                        atom_j: j,
                        atom_k: k,
                        k_a: 0.5,                       // Fallback force constant
                        theta0: 109.5_f64.to_radians(), // SP3 default
                    }));
                }
            }
        }

        // Torsion terms: find all i-j-k-l where (i,j), (j,k), (k,l) are bonded
        for &(j, k, _) in bonds {
            for &i in &neighbors[j] {
                if i == k {
                    continue;
                }
                for &l in &neighbors[k] {
                    if l == j || l == i {
                        continue;
                    }
                    // MMFF94s uses stiffer torsion barriers for planar groups
                    let (v1, v2, v3) = match variant {
                        Mmff94Variant::Mmff94s => (0.0, 1.5, 0.0),
                        Mmff94Variant::Mmff94 => (0.0, 1.0, 0.0),
                    };
                    terms.push(Box::new(Mmff94Torsion {
                        atom_i: i,
                        atom_j: j,
                        atom_k: k,
                        atom_l: l,
                        v1,
                        v2,
                        v3,
                    }));
                }
            }
        }

        // 1-4 vdW terms (atoms separated by 3 bonds)
        for &(j, k, _) in bonds {
            for &i in &neighbors[j] {
                if i == k {
                    continue;
                }
                for &l in &neighbors[k] {
                    if l == j || l == i {
                        continue;
                    }
                    let r_star = 3.5; // Generic
                    let eps = 0.05;
                    terms.push(Box::new(Mmff94BufferedVanDerWaals {
                        atom_i_idx: i,
                        atom_j_idx: l,
                        radius_star: r_star,
                        epsilon_depth: eps,
                    }));
                }
            }
        }

        terms
    }

    /// Compute total energy from all MMFF94 terms.
    pub fn total_energy(
        terms: &[Box<dyn ForceFieldContribution>],
        coords: &[f64],
    ) -> (f64, Vec<f64>) {
        let n = coords.len();
        let mut grad = vec![0.0; n];
        let mut total = 0.0;
        for term in terms {
            total += term.evaluate_energy_and_inject_gradient(coords, &mut grad);
        }
        (total, grad)
    }
}

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

    #[test]
    fn test_mmff94_vdw_energy() {
        let term = Mmff94BufferedVanDerWaals {
            atom_i_idx: 0,
            atom_j_idx: 1,
            radius_star: 3.6,
            epsilon_depth: 0.1,
        };
        let coords = vec![0.0, 0.0, 0.0, 3.6, 0.0, 0.0];
        let mut grad = vec![0.0; 6];
        let e = term.evaluate_energy_and_inject_gradient(&coords, &mut grad);
        // At equilibrium distance, energy should be near -epsilon
        assert!(e < 0.0 && e > -0.2, "vdW energy at R*: {e}");
    }

    #[test]
    fn test_mmff94_vdw_gradient_validation() {
        let term = Mmff94BufferedVanDerWaals {
            atom_i_idx: 0,
            atom_j_idx: 1,
            radius_star: 3.6,
            epsilon_depth: 0.1,
        };
        let coords = vec![0.0, 0.0, 0.0, 4.0, 0.0, 0.0];
        let max_err = validate_gradients(&term, &coords, 1e-5);
        assert!(max_err < 1e-4, "vdW gradient error: {max_err}");
    }

    #[test]
    fn test_mmff94_bond_stretch() {
        let term = Mmff94BondStretch {
            atom_i: 0,
            atom_j: 1,
            k_b: 5.0,
            r0: 1.5,
        };
        // At equilibrium: energy ≈ 0
        let coords_eq = vec![0.0, 0.0, 0.0, 1.5, 0.0, 0.0];
        let mut grad = vec![0.0; 6];
        let e_eq = term.evaluate_energy_and_inject_gradient(&coords_eq, &mut grad);
        assert!(e_eq.abs() < 1e-10, "bond stretch at r0: {e_eq}");

        // Stretched: energy > 0
        let coords_stretch = vec![0.0, 0.0, 0.0, 2.0, 0.0, 0.0];
        grad.fill(0.0);
        let e_str = term.evaluate_energy_and_inject_gradient(&coords_stretch, &mut grad);
        assert!(
            e_str > 0.0,
            "bond stretch energy should be positive: {e_str}"
        );
    }

    #[test]
    fn test_mmff94_bond_stretch_gradient_validation() {
        let term = Mmff94BondStretch {
            atom_i: 0,
            atom_j: 1,
            k_b: 5.0,
            r0: 1.5,
        };
        let coords = vec![0.0, 0.0, 0.0, 2.0, 0.1, 0.0];
        let max_err = validate_gradients(&term, &coords, 1e-5);
        assert!(max_err < 1e-3, "bond stretch gradient error: {max_err}");
    }

    #[test]
    fn test_mmff94_torsion_energy() {
        let term = Mmff94Torsion {
            atom_i: 0,
            atom_j: 1,
            atom_k: 2,
            atom_l: 3,
            v1: 0.0,
            v2: 5.0,
            v3: 0.0,
        };
        // Planar trans: phi ≈ 180°
        let coords = vec![-1.5, 1.0, 0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 3.0, 1.0, 0.0];
        let mut grad = vec![0.0; 12];
        let e = term.evaluate_energy_and_inject_gradient(&coords, &mut grad);
        assert!(e.is_finite(), "torsion energy should be finite: {e}");
    }

    #[test]
    fn test_mmff94_atom_typing() {
        use crate::graph::Hybridization;
        let t = assign_mmff94_type(6, &Hybridization::SP3, false, false);
        assert_eq!(t, Mmff94AtomType::CR);
        let t = assign_mmff94_type(6, &Hybridization::SP2, true, false);
        assert_eq!(t, Mmff94AtomType::CB);
        let t = assign_mmff94_type(7, &Hybridization::SP3, false, true);
        assert_eq!(t, Mmff94AtomType::NAm);
    }

    #[test]
    fn test_mmff94_builder_ethane() {
        // Ethane: C-C with 6 hydrogens
        let elements = vec![6, 6, 1, 1, 1, 1, 1, 1]; // C, C, H×6
        let bonds = vec![
            (0, 1, 1), // C-C
            (0, 2, 1),
            (0, 3, 1),
            (0, 4, 1), // C-H
            (1, 5, 1),
            (1, 6, 1),
            (1, 7, 1), // C-H
        ];
        // Staggered ethane coordinates (approximate)
        let coords = vec![
            0.0, 0.0, 0.0, // C0
            1.54, 0.0, 0.0, // C1
            -0.5, 0.9, 0.0, // H
            -0.5, -0.9, 0.0, // H
            -0.5, 0.0, 0.9, // H
            2.04, 0.9, 0.0, // H
            2.04, -0.9, 0.0, // H
            2.04, 0.0, 0.9, // H
        ];
        let terms = Mmff94Builder::build(&elements, &bonds);
        assert!(!terms.is_empty(), "should produce force field terms");

        let (energy, grad) = Mmff94Builder::total_energy(&terms, &coords);
        assert!(
            energy.is_finite(),
            "total energy should be finite: {energy}"
        );
        assert!(
            grad.iter().all(|g| g.is_finite()),
            "all gradients should be finite"
        );
    }

    #[test]
    fn test_mmff94_builder_gradient_consistency() {
        // Verify total gradient is consistent with numerical for a simple system
        let elements = vec![6, 6];
        let bonds = vec![(0, 1, 1)];
        let coords = vec![0.0, 0.0, 0.0, 1.6, 0.1, 0.0];
        let terms = Mmff94Builder::build(&elements, &bonds);
        let (_, analytical_grad) = Mmff94Builder::total_energy(&terms, &coords);

        let eps = 1e-5;
        for i in 0..coords.len() {
            let mut cp = coords.clone();
            let mut cm = coords.clone();
            cp[i] += eps;
            cm[i] -= eps;
            let (ep, _) = Mmff94Builder::total_energy(&terms, &cp);
            let (em, _) = Mmff94Builder::total_energy(&terms, &cm);
            let numerical = (ep - em) / (2.0 * eps);
            let err = (analytical_grad[i] - numerical).abs();
            assert!(
                err < 0.1,
                "gradient mismatch at coord {i}: anal={:.6} num={:.6} err={:.6}",
                analytical_grad[i],
                numerical,
                err
            );
        }
    }
}