sci-form 0.15.1

use nalgebra::DMatrix;
use petgraph::visit::EdgeRef;
use rand::rngs::StdRng;
use rand::{Rng, SeedableRng};
use std::collections::{HashSet, VecDeque};

// Identifies rotatable bonds and optimizes torsion angles via greedy scanning.
// This approximates ETKDG's torsion knowledge terms by directly setting
// preferred torsion angles after DG embedding.

/// A rotatable bond with its torsion atom indices and the atoms to rotate.
pub struct RotatableBond {
    /// The 4 atom indices defining the dihedral: a-b-c-d
    /// b-c is the rotatable bond
    pub dihedral: [usize; 4],
    /// Atom indices on the "d side" of the bond (to be rotated)
    pub mobile_atoms: Vec<usize>,
    /// Preferred torsion angles to try (radians)
    pub preferred_angles: Vec<f32>,
}

/// Find all rotatable bonds in the molecule and prepare rotation data.
///
/// Excludes ring bonds, double bonds, and terminal groups.
/// Returns dihedral atom indices and the mobile atoms to rotate.
pub fn find_rotatable_bonds(mol: &crate::graph::Molecule) -> Vec<RotatableBond> {
    let mut bonds = Vec::new();
    let n = mol.graph.node_count();

    for edge in mol.graph.edge_references() {
        let u = edge.source();
        let v = edge.target();

        // Only single bonds
        if edge.weight().order != crate::graph::BondOrder::Single {
            continue;
        }

        // Both must have >= 2 neighbors (not terminal)
        let deg_u = mol.graph.neighbors(u).count();
        let deg_v = mol.graph.neighbors(v).count();
        if deg_u < 2 || deg_v < 2 {
            continue;
        }

        // Skip ring bonds
        if crate::graph::min_path_excluding2(mol, u, v, u, v, 7).is_some() {
            continue;
        }

        // Pick first neighbor of u (not v) as "a" and first neighbor of v (not u) as "d"
        let a = mol.graph.neighbors(u).find(|&x| x != v).unwrap();
        let d = mol.graph.neighbors(v).find(|&x| x != u).unwrap();

        // BFS from v excluding u to find atoms on v's side (mobile atoms)
        let mut mobile = Vec::new();
        let mut visited = HashSet::new();
        visited.insert(u.index());
        visited.insert(v.index());
        let mut queue = VecDeque::new();
        for nb in mol.graph.neighbors(v) {
            if nb != u {
                queue.push_back(nb.index());
                visited.insert(nb.index());
            }
        }
        while let Some(curr) = queue.pop_front() {
            mobile.push(curr);
            let ni = petgraph::graph::NodeIndex::new(curr);
            for nb in mol.graph.neighbors(ni) {
                if !visited.contains(&nb.index()) {
                    visited.insert(nb.index());
                    queue.push_back(nb.index());
                }
            }
        }

        // If mobile side has more atoms than the other side, swap to rotate the smaller side
        let other_count = n - mobile.len() - 2; // exclude u, v
        if mobile.len() > other_count {
            // Rotate the u-side instead
            let mut mobile_u = Vec::new();
            let mut visited_u = HashSet::new();
            visited_u.insert(u.index());
            visited_u.insert(v.index());
            let mut queue_u = VecDeque::new();
            for nb in mol.graph.neighbors(u) {
                if nb != v {
                    queue_u.push_back(nb.index());
                    visited_u.insert(nb.index());
                }
            }
            while let Some(curr) = queue_u.pop_front() {
                mobile_u.push(curr);
                let ni = petgraph::graph::NodeIndex::new(curr);
                for nb in mol.graph.neighbors(ni) {
                    if !visited_u.contains(&nb.index()) {
                        visited_u.insert(nb.index());
                        queue_u.push_back(nb.index());
                    }
                }
            }
            // Use swapped dihedral: d-v-u-a, mobile is u-side
            let preferred = get_preferred_angles(mol, v, u);
            bonds.push(RotatableBond {
                dihedral: [d.index(), v.index(), u.index(), a.index()],
                mobile_atoms: mobile_u,
                preferred_angles: preferred,
            });
        } else {
            let preferred = get_preferred_angles(mol, u, v);
            bonds.push(RotatableBond {
                dihedral: [a.index(), u.index(), v.index(), d.index()],
                mobile_atoms: mobile,
                preferred_angles: preferred,
            });
        }
    }
    bonds
}

/// Get preferred torsion angles based on hybridization of the central bond atoms.
fn get_preferred_angles(
    mol: &crate::graph::Molecule,
    u: petgraph::graph::NodeIndex,
    v: petgraph::graph::NodeIndex,
) -> Vec<f32> {
    use crate::graph::Hybridization::*;
    use std::f32::consts::PI;

    let hyb_u = mol.graph[u].hybridization;
    let hyb_v = mol.graph[v].hybridization;

    match (hyb_u, hyb_v) {
        (SP3, SP3) => {
            // Anti and gauche: 60, 180, 300 degrees
            vec![PI / 3.0, PI, 5.0 * PI / 3.0]
        }
        (SP2, SP2) => {
            // Planar: 0 and 180
            vec![0.0, PI]
        }
        (SP2, SP3) | (SP3, SP2) => {
            // Mixed: 0, 60, 120, 180, 240, 300
            vec![
                0.0,
                PI / 3.0,
                2.0 * PI / 3.0,
                PI,
                4.0 * PI / 3.0,
                5.0 * PI / 3.0,
            ]
        }
        _ => {
            // Generic: try all 30-degree increments
            (0..12).map(|i| i as f32 * PI / 6.0).collect()
        }
    }
}

/// Compute dihedral angle (in radians, range [-PI, PI]) from 4 atom positions in a DMatrix.
pub fn compute_dihedral(coords: &DMatrix<f32>, i: usize, j: usize, k: usize, l: usize) -> f32 {
    let b1 = nalgebra::Vector3::new(
        coords[(j, 0)] - coords[(i, 0)],
        coords[(j, 1)] - coords[(i, 1)],
        coords[(j, 2)] - coords[(i, 2)],
    );
    let b2 = nalgebra::Vector3::new(
        coords[(k, 0)] - coords[(j, 0)],
        coords[(k, 1)] - coords[(j, 1)],
        coords[(k, 2)] - coords[(j, 2)],
    );
    let b3 = nalgebra::Vector3::new(
        coords[(l, 0)] - coords[(k, 0)],
        coords[(l, 1)] - coords[(k, 1)],
        coords[(l, 2)] - coords[(k, 2)],
    );

    let n1 = b1.cross(&b2).normalize();
    let n2 = b2.cross(&b3).normalize();
    let m1 = n1.cross(&b2.normalize());
    let x = n1.dot(&n2);
    let y = m1.dot(&n2);
    y.atan2(x)
}

/// Rotate a set of atoms around the axis defined by points j→k by a given angle.
pub fn rotate_atoms(coords: &mut DMatrix<f32>, mobile: &[usize], j: usize, k: usize, angle: f32) {
    if angle.abs() < 1e-8 {
        return;
    }
    // Axis of rotation: from j to k
    let axis = nalgebra::Vector3::new(
        coords[(k, 0)] - coords[(j, 0)],
        coords[(k, 1)] - coords[(j, 1)],
        coords[(k, 2)] - coords[(j, 2)],
    );
    let axis_len = axis.norm();
    if axis_len < 1e-8 {
        return;
    }
    let axis = axis / axis_len;

    // Rodrigues' rotation formula
    let cos_a = angle.cos();
    let sin_a = angle.sin();

    // Pivot point is atom j
    let px = coords[(j, 0)];
    let py = coords[(j, 1)];
    let pz = coords[(j, 2)];

    for &idx in mobile {
        let vx = coords[(idx, 0)] - px;
        let vy = coords[(idx, 1)] - py;
        let vz = coords[(idx, 2)] - pz;

        let dot = axis[0] * vx + axis[1] * vy + axis[2] * vz;
        let cx = axis[1] * vz - axis[2] * vy;
        let cy = axis[2] * vx - axis[0] * vz;
        let cz = axis[0] * vy - axis[1] * vx;

        coords[(idx, 0)] = px + vx * cos_a + cx * sin_a + axis[0] * dot * (1.0 - cos_a);
        coords[(idx, 1)] = py + vy * cos_a + cy * sin_a + axis[1] * dot * (1.0 - cos_a);
        coords[(idx, 2)] = pz + vz * cos_a + cz * sin_a + axis[2] * dot * (1.0 - cos_a);
    }
}

/// Snap each rotatable bond's torsion to the nearest preferred angle.
/// No energy scoring — just geometric snapping.
pub fn snap_torsions_to_preferred(
    coords: &mut DMatrix<f32>,
    mol: &crate::graph::Molecule,
) -> usize {
    let rotatable = find_rotatable_bonds(mol);
    let num_rotatable = rotatable.len();

    for rb in &rotatable {
        let [a, b, c, d] = rb.dihedral;
        let current = compute_dihedral(coords, a, b, c, d);

        // Find nearest preferred angle
        let mut best_delta_abs = f32::MAX;
        let mut best_rotation = 0.0f32;
        for &target in &rb.preferred_angles {
            let mut delta = target - current;
            // Normalize to [-PI, PI]
            delta = (delta + std::f32::consts::PI).rem_euclid(2.0 * std::f32::consts::PI)
                - std::f32::consts::PI;
            if delta.abs() < best_delta_abs {
                best_delta_abs = delta.abs();
                best_rotation = delta;
            }
        }

        if best_rotation.abs() > 0.05 {
            rotate_atoms(coords, &rb.mobile_atoms, b, c, best_rotation);
        }
    }
    num_rotatable
}

/// Greedy torsion scan: for each rotatable bond, try preferred angles and pick
/// the one that minimizes the combined energy (bounds + torsion preferences).
/// Repeats for `passes` iterations.
pub fn optimize_torsions_greedy(
    coords: &mut DMatrix<f32>,
    mol: &crate::graph::Molecule,
    bounds: &DMatrix<f64>,
    passes: usize,
) -> usize {
    let rotatable = find_rotatable_bonds(mol);
    let num_rotatable = rotatable.len();
    if rotatable.is_empty() {
        return 0;
    }

    let params = super::energy::FFParams {
        kb: 300.0,
        k_theta: 200.0,
        k_omega: 10.0,
        k_oop: 20.0,
        k_bounds: 100.0,
        k_chiral: 0.0,
        k_vdw: 0.0,
    };

    for _pass in 0..passes {
        for rb in &rotatable {
            let [a, b, c, d] = rb.dihedral;
            let current_angle = compute_dihedral(coords, a, b, c, d);

            let current_energy =
                super::energy::calculate_total_energy(coords, mol, &params, bounds);
            let mut best_energy = current_energy;
            let mut best_rotation = 0.0f32;

            for &target_angle in &rb.preferred_angles {
                let delta = target_angle - current_angle;
                let delta = ((delta + std::f32::consts::PI) % (2.0 * std::f32::consts::PI))
                    - std::f32::consts::PI;

                rotate_atoms(coords, &rb.mobile_atoms, b, c, delta);

                let e = super::energy::calculate_total_energy(coords, mol, &params, bounds);
                if e < best_energy {
                    best_energy = e;
                    best_rotation = delta;
                }

                rotate_atoms(coords, &rb.mobile_atoms, b, c, -delta);
            }

            if best_rotation.abs() > 1e-6 {
                rotate_atoms(coords, &rb.mobile_atoms, b, c, best_rotation);
            }
        }
    }
    num_rotatable
}

/// Greedy torsion scan using ONLY bounds violation energy as criterion.
/// Better for matching DG-based conformations since it doesn't fight
/// the bounds constraints with torsion preferences.
pub fn optimize_torsions_bounds(
    coords: &mut DMatrix<f32>,
    mol: &crate::graph::Molecule,
    bounds: &DMatrix<f64>,
    passes: usize,
) -> usize {
    let rotatable = find_rotatable_bonds(mol);
    let num_rotatable = rotatable.len();
    if rotatable.is_empty() {
        return 0;
    }

    for _pass in 0..passes {
        for rb in &rotatable {
            let [a, b, c, d] = rb.dihedral;
            let current_angle = compute_dihedral(coords, a, b, c, d);

            let current_energy = super::bounds_ff::bounds_violation_energy(coords, bounds);
            let mut best_energy = current_energy;
            let mut best_rotation = 0.0f32;

            for &target_angle in &rb.preferred_angles {
                let delta = target_angle - current_angle;
                let delta = ((delta + std::f32::consts::PI) % (2.0 * std::f32::consts::PI))
                    - std::f32::consts::PI;

                rotate_atoms(coords, &rb.mobile_atoms, b, c, delta);

                let e = super::bounds_ff::bounds_violation_energy(coords, bounds);
                if e < best_energy {
                    best_energy = e;
                    best_rotation = delta;
                }

                rotate_atoms(coords, &rb.mobile_atoms, b, c, -delta);
            }

            if best_rotation.abs() > 1e-6 {
                rotate_atoms(coords, &rb.mobile_atoms, b, c, best_rotation);
            }
        }
    }
    num_rotatable
}

/// Monte Carlo torsion sampling using bounds-violation energy as acceptance criterion.
///
/// A random rotatable bond is selected each step and perturbed to a random angle.
/// Moves are accepted by Metropolis criterion with a lightweight temperature parameter.
pub fn optimize_torsions_monte_carlo_bounds(
    coords: &mut DMatrix<f32>,
    mol: &crate::graph::Molecule,
    bounds: &DMatrix<f64>,
    seed: u64,
    n_steps: usize,
    temperature: f32,
) -> usize {
    let rotatable = find_rotatable_bonds(mol);
    let num_rotatable = rotatable.len();
    if rotatable.is_empty() || n_steps == 0 {
        return num_rotatable;
    }

    let mut rng = StdRng::seed_from_u64(seed);
    let temp = temperature.max(1e-6);
    let two_pi = 2.0 * std::f32::consts::PI;
    let mut current_energy = super::bounds_ff::bounds_violation_energy(coords, bounds);

    for _ in 0..n_steps {
        let rb = &rotatable[rng.gen_range(0..rotatable.len())];
        let [a, b, c, d] = rb.dihedral;
        let current_angle = compute_dihedral(coords, a, b, c, d);
        let target = rng.gen_range(-std::f32::consts::PI..std::f32::consts::PI);
        let mut delta = target - current_angle;
        delta = (delta + std::f32::consts::PI).rem_euclid(two_pi) - std::f32::consts::PI;

        rotate_atoms(coords, &rb.mobile_atoms, b, c, delta);
        let trial_energy = super::bounds_ff::bounds_violation_energy(coords, bounds);
        let d_e = trial_energy - current_energy;

        let accept = if d_e <= 0.0 {
            true
        } else {
            let p_accept = (-d_e / temp).exp();
            rng.gen::<f32>() < p_accept
        };

        if accept {
            current_energy = trial_energy;
        } else {
            rotate_atoms(coords, &rb.mobile_atoms, b, c, -delta);
        }
    }

    num_rotatable
}

/// Systematic rotor search: enumerate all combinations of torsion angles
/// for ≤4 rotatable bonds (12 angles per rotor = 30° increments).
///
/// For each combination, evaluate the UFF energy and return the coordinates
/// of all evaluated conformers as flat `Vec<f64>`.
///
/// Use with Butina clustering to get a diverse set.
pub fn systematic_rotor_search(
    smiles: &str,
    coords: &[f64],
    max_rotors: usize,
) -> Result<Vec<(Vec<f64>, f64)>, String> {
    use std::f32::consts::PI;

    let mol = crate::graph::Molecule::from_smiles(smiles)?;
    let n_atoms = mol.graph.node_count();
    if coords.len() != n_atoms * 3 {
        return Err("coords length mismatch".to_string());
    }

    let rotatable = find_rotatable_bonds(&mol);
    let n_rot = rotatable.len().min(max_rotors);

    if n_rot == 0 {
        let e = crate::compute_uff_energy(smiles, coords).unwrap_or(0.0);
        return Ok(vec![(coords.to_vec(), e)]);
    }

    let ff = super::builder::build_uff_force_field(&mol);
    let angles: Vec<f32> = (0..12).map(|i| i as f32 * PI / 6.0).collect();

    // Total combos = 12^n_rot
    let total: usize = 12usize.pow(n_rot as u32);

    let base_matrix = flat_to_matrix_internal(coords, n_atoms);

    let eval_combo = |combo_idx: usize| -> Option<(Vec<f64>, f64)> {
        let mut matrix = base_matrix.clone();

        let mut idx = combo_idx;
        for r in 0..n_rot {
            let angle_idx = idx % 12;
            idx /= 12;

            let rb = &rotatable[r];
            let [a, b, c, d] = rb.dihedral;
            let current = compute_dihedral(&matrix, a, b, c, d);
            let target = angles[angle_idx];
            let mut delta = target - current;
            delta = (delta + PI).rem_euclid(2.0 * PI) - PI;
            rotate_atoms(&mut matrix, &rb.mobile_atoms, b, c, delta);
        }

        let flat = matrix_to_flat(&matrix, n_atoms);
        let mut grad = vec![0.0f64; n_atoms * 3];
        let energy = ff.compute_system_energy_and_gradients(&flat, &mut grad);

        if energy.is_finite() {
            Some((flat, energy))
        } else {
            None
        }
    };

    #[cfg(feature = "parallel")]
    let mut results: Vec<(Vec<f64>, f64)> = {
        use rayon::prelude::*;
        (0..total).into_par_iter().filter_map(eval_combo).collect()
    };

    #[cfg(not(feature = "parallel"))]
    let mut results: Vec<(Vec<f64>, f64)> = (0..total).filter_map(eval_combo).collect();

    // Sort by energy
    results.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal));
    Ok(results)
}

/// Simulated annealing torsion search with exponential cooling schedule.
///
/// Suitable for molecules with >4 rotatable bonds where systematic search is infeasible.
/// Uses Metropolis acceptance with temperature decreasing from `t_start` to `t_end`.
pub fn simulated_annealing_torsion_search(
    smiles: &str,
    coords: &[f64],
    n_steps: usize,
    t_start: f64,
    t_end: f64,
    seed: u64,
) -> Result<Vec<(Vec<f64>, f64)>, String> {
    let mol = crate::graph::Molecule::from_smiles(smiles)?;
    let n_atoms = mol.graph.node_count();
    if coords.len() != n_atoms * 3 {
        return Err("coords length mismatch".to_string());
    }

    let rotatable = find_rotatable_bonds(&mol);
    if rotatable.is_empty() {
        let e = crate::compute_uff_energy(smiles, coords).unwrap_or(0.0);
        return Ok(vec![(coords.to_vec(), e)]);
    }

    let ff = super::builder::build_uff_force_field(&mol);
    let mut rng = StdRng::seed_from_u64(seed);
    let mut matrix = flat_to_matrix_internal(coords, n_atoms);

    let flat = matrix_to_flat(&matrix, n_atoms);
    let mut grad = vec![0.0f64; n_atoms * 3];
    let mut current_energy = ff.compute_system_energy_and_gradients(&flat, &mut grad);

    let mut best_coords = flat;
    let mut best_energy = current_energy;

    let cooling_rate = if n_steps > 1 {
        (t_end / t_start).powf(1.0 / (n_steps - 1) as f64)
    } else {
        1.0
    };

    let mut collected = Vec::new();
    let collect_interval = (n_steps / 50).max(1); // collect ~50 snapshots

    let mut temp = t_start;
    for step in 0..n_steps {
        let rb_idx = rng.gen_range(0..rotatable.len());
        let rb = &rotatable[rb_idx];
        let [a, b, c, d] = rb.dihedral;
        let current_angle = compute_dihedral(&matrix, a, b, c, d);
        let perturbation: f32 = rng.gen_range(-std::f32::consts::PI..std::f32::consts::PI);
        let mut delta = perturbation - current_angle;
        delta = (delta + std::f32::consts::PI).rem_euclid(2.0 * std::f32::consts::PI)
            - std::f32::consts::PI;

        rotate_atoms(&mut matrix, &rb.mobile_atoms, b, c, delta);

        let trial_flat = matrix_to_flat(&matrix, n_atoms);
        let trial_energy = ff.compute_system_energy_and_gradients(&trial_flat, &mut grad);

        let d_e = trial_energy - current_energy;
        let accept = if d_e <= 0.0 {
            true
        } else {
            let p = (-d_e / temp).exp();
            rng.gen::<f64>() < p
        };

        if accept && trial_energy.is_finite() {
            current_energy = trial_energy;
            if current_energy < best_energy {
                best_energy = current_energy;
                best_coords = trial_flat;
            }
        } else {
            rotate_atoms(&mut matrix, &rb.mobile_atoms, b, c, -delta);
        }

        if step % collect_interval == 0 {
            let snap = matrix_to_flat(&matrix, n_atoms);
            collected.push((snap, current_energy));
        }

        temp *= cooling_rate;
    }

    // Always include the best
    collected.push((best_coords, best_energy));
    collected.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal));
    Ok(collected)
}

/// Generate a diverse conformer ensemble by torsional sampling + Butina clustering.
///
/// For ≤4 rotatable bonds, uses systematic search; for >4, uses simulated annealing.
/// Results are filtered through Butina RMSD clustering for diversity.
pub fn torsional_sampling_diverse(
    smiles: &str,
    coords: &[f64],
    rmsd_cutoff: f64,
    seed: u64,
) -> Result<Vec<(Vec<f64>, f64)>, String> {
    let mol = crate::graph::Molecule::from_smiles(smiles)?;
    let rotatable = find_rotatable_bonds(&mol);
    let n_rot = rotatable.len();

    let conformers = if n_rot <= 4 {
        systematic_rotor_search(smiles, coords, 4)?
    } else {
        simulated_annealing_torsion_search(smiles, coords, 500, 5.0, 0.1, seed)?
    };

    if conformers.len() <= 1 {
        return Ok(conformers);
    }

    let coords_vecs: Vec<Vec<f64>> = conformers.iter().map(|(c, _)| c.clone()).collect();
    let cluster_result = crate::clustering::butina_cluster(&coords_vecs, rmsd_cutoff);

    let diverse: Vec<(Vec<f64>, f64)> = cluster_result
        .centroid_indices
        .iter()
        .map(|&ci| conformers[ci].clone())
        .collect();

    Ok(diverse)
}

fn flat_to_matrix_internal(coords: &[f64], n_atoms: usize) -> DMatrix<f32> {
    let mut m = DMatrix::<f32>::zeros(n_atoms, 3);
    for i in 0..n_atoms {
        m[(i, 0)] = coords[3 * i] as f32;
        m[(i, 1)] = coords[3 * i + 1] as f32;
        m[(i, 2)] = coords[3 * i + 2] as f32;
    }
    m
}

fn matrix_to_flat(matrix: &DMatrix<f32>, n_atoms: usize) -> Vec<f64> {
    let mut flat = vec![0.0f64; n_atoms * 3];
    for i in 0..n_atoms {
        flat[3 * i] = matrix[(i, 0)] as f64;
        flat[3 * i + 1] = matrix[(i, 1)] as f64;
        flat[3 * i + 2] = matrix[(i, 2)] as f64;
    }
    flat
}

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

    fn flat_to_matrix(coords: &[f64], n_atoms: usize) -> DMatrix<f32> {
        let mut m = DMatrix::<f32>::zeros(n_atoms, 3);
        for i in 0..n_atoms {
            m[(i, 0)] = coords[3 * i] as f32;
            m[(i, 1)] = coords[3 * i + 1] as f32;
            m[(i, 2)] = coords[3 * i + 2] as f32;
        }
        m
    }

    #[test]
    fn test_monte_carlo_torsion_optimizer_runs_for_butane() {
        let smiles = "CCCC";
        let mol = crate::graph::Molecule::from_smiles(smiles).unwrap();
        let conf = crate::embed(smiles, 42);
        assert!(conf.error.is_none());

        let bounds =
            crate::distgeom::smooth_bounds_matrix(crate::distgeom::calculate_bounds_matrix(&mol));
        let mut coords = flat_to_matrix(&conf.coords, mol.graph.node_count());
        let rot = optimize_torsions_monte_carlo_bounds(&mut coords, &mol, &bounds, 123, 64, 0.3);

        assert!(rot >= 1);
        assert!(coords.iter().all(|v| v.is_finite()));
    }
}