molcrafts-molrs 0.7.0

Molecular simulation toolkit: core data structures, IO, trajectory analysis, force fields, SMILES, and 3D conformer generation (feature-gated modules)
Documentation 
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//! MMFF94 angle bending and stretch-bend coupling kernels.
//!
//! `theta0` is consumed in radians; the MMFF typifier normalizes the XML's
//! degree reference angles to radians at the reader boundary
//! (`forcefield::xml::read_mmff_params_xml_str`).

use crate::ff::forcefield::Params;
use crate::ff::potential::Potential;
use crate::ff::potential::geometry::{
    accumulate_angle_forces, compute_angle, mag3, sub3, validate_coords,
};
use molrs::store::frame::Frame;
use molrs::types::F;

use crate::ff::constants::MDYNE_A_TO_KCAL;
/// Cubic bend constant (rad^-1), = -0.007 * 180/pi.
const CB_RAD: f64 = -0.40107;

// ---------------------------------------------------------------------------
// MMFFAngleBend: E = (1/2)*143.9325*ka*dth^2*(1 + cb*dth)
// ---------------------------------------------------------------------------

pub struct MMFFAngleBend {
    atom_i: Vec<usize>,
    atom_j: Vec<usize>,
    atom_k: Vec<usize>,
    ka: Vec<F>,
    theta0: Vec<F>,
}

impl Potential for MMFFAngleBend {
    fn calc_energy_forces(&self, coords: &[F]) -> (F, Vec<F>) {
        let _n = validate_coords(coords);
        let mut energy: F = 0.0;
        let mut forces = vec![0.0 as F; coords.len()];
        let conv = MDYNE_A_TO_KCAL as F;
        let cb = CB_RAD as F;

        for idx in 0..self.atom_i.len() {
            let (i, j, k) = (self.atom_i[idx], self.atom_j[idx], self.atom_k[idx]);
            let theta = compute_angle(coords, i, j, k);
            let dth = theta - self.theta0[idx];
            energy += 0.5 * conv * self.ka[idx] * dth * dth * (1.0 + cb * dth);

            let de_dth = conv * self.ka[idx] * dth * (1.0 + 1.5 * cb * dth);
            accumulate_angle_forces(coords, i, j, k, de_dth, &mut forces);
        }
        (energy, forces)
    }
}

pub fn mmff_angle_ctor(
    _sp: &Params,
    _tp: &[(&str, &Params)],
    frame: &Frame,
) -> Result<Box<dyn Potential>, String> {
    // Per-instance parameters: the MMFF typifier baked ka and theta0 (radians)
    // onto each angle (table → equivalence → empirical). This kernel only reads
    // the columns and evaluates — no force-field-specific resolution lives here.
    let block = frame
        .get("angles")
        .ok_or("mmff_angle: missing \"angles\" block")?;
    let ic = block.get_uint("atomi").ok_or("missing atomi")?;
    let jc = block.get_uint("atomj").ok_or("missing atomj")?;
    let kc = block.get_uint("atomk").ok_or("missing atomk")?;
    let kac = block
        .get_float("ka")
        .ok_or("mmff_angle: missing \"ka\" column (typifier did not bake angle params)")?;
    let th0c = block
        .get_float("theta0")
        .ok_or("mmff_angle: missing \"theta0\" column (typifier did not bake angle params)")?;

    let n = ic.len();
    let (mut ai, mut aj, mut ak, mut ka, mut th0) = (
        Vec::with_capacity(n),
        Vec::with_capacity(n),
        Vec::with_capacity(n),
        Vec::with_capacity(n),
        Vec::with_capacity(n),
    );

    for idx in 0..n {
        ai.push(ic[idx] as usize);
        aj.push(jc[idx] as usize);
        ak.push(kc[idx] as usize);
        ka.push(kac[idx] as F);
        th0.push(th0c[idx] as F); // radians
    }
    Ok(Box::new(MMFFAngleBend {
        atom_i: ai,
        atom_j: aj,
        atom_k: ak,
        ka,
        theta0: th0,
    }))
}

// ---------------------------------------------------------------------------
// MMFFStretchBend: E = 143.9325*(kba_ijk*dr_ij + kba_kji*dr_kj)*dth
// ---------------------------------------------------------------------------

pub struct MMFFStretchBend {
    atom_i: Vec<usize>,
    atom_j: Vec<usize>,
    atom_k: Vec<usize>,
    kba_ijk: Vec<F>,
    kba_kji: Vec<F>,
    r0_ij: Vec<F>,
    r0_kj: Vec<F>,
    theta0: Vec<F>,
}

impl Potential for MMFFStretchBend {
    fn calc_energy_forces(&self, coords: &[F]) -> (F, Vec<F>) {
        let _n = validate_coords(coords);
        let mut energy: F = 0.0;
        let mut forces = vec![0.0 as F; coords.len()];
        let conv = MDYNE_A_TO_KCAL as F;

        for idx in 0..self.atom_i.len() {
            let (i, j, k) = (self.atom_i[idx], self.atom_j[idx], self.atom_k[idx]);
            let rij_vec = sub3(coords, i, coords, j);
            let rkj_vec = sub3(coords, k, coords, j);
            let rij = mag3(rij_vec);
            let rkj = mag3(rkj_vec);
            let theta = compute_angle(coords, i, j, k);
            let dr_ij = rij - self.r0_ij[idx];
            let dr_kj = rkj - self.r0_kj[idx];
            let dth = theta - self.theta0[idx];

            let term = self.kba_ijk[idx] * dr_ij + self.kba_kji[idx] * dr_kj;
            energy += conv * term * dth;

            // dE/ddth = conv * term
            accumulate_angle_forces(coords, i, j, k, conv * term, &mut forces);
            // dE/dr_ij = conv * kba_ijk * dth
            if rij > 1e-12 as F {
                let f_r = -conv * self.kba_ijk[idx] * dth / rij;
                for dim in 0..3 {
                    forces[i * 3 + dim] += f_r * rij_vec[dim];
                    forces[j * 3 + dim] -= f_r * rij_vec[dim];
                }
            }
            // dE/dr_kj = conv * kba_kji * dth
            if rkj > 1e-12 as F {
                let f_r = -conv * self.kba_kji[idx] * dth / rkj;
                for dim in 0..3 {
                    forces[k * 3 + dim] += f_r * rkj_vec[dim];
                    forces[j * 3 + dim] -= f_r * rkj_vec[dim];
                }
            }
        }
        (energy, forces)
    }
}

pub fn mmff_stbn_ctor(
    _sp: &Params,
    _tp: &[(&str, &Params)],
    frame: &Frame,
) -> Result<Box<dyn Potential>, String> {
    // Per-instance parameters: the MMFF typifier baked the stretch-bend force
    // constants (kba_ijk/kba_kji, via the dfsb period-row default-row fallback
    // that the shared-table path lacked) plus the two reference bond lengths and
    // theta0 (radians) onto each angle. This kernel only reads the columns.
    let block = frame.get("angles").ok_or("mmff_stbn: missing \"angles\"")?;
    let ic = block.get_uint("atomi").ok_or("missing atomi")?;
    let jc = block.get_uint("atomj").ok_or("missing atomj")?;
    let kc = block.get_uint("atomk").ok_or("missing atomk")?;
    let kba_ijk_c = block.get_float("kba_ijk").ok_or(
        "mmff_stbn: missing \"kba_ijk\" column (typifier did not bake stretch-bend params)",
    )?;
    let kba_kji_c = block.get_float("kba_kji").ok_or(
        "mmff_stbn: missing \"kba_kji\" column (typifier did not bake stretch-bend params)",
    )?;
    let r0ij = block
        .get_float("r0_ij")
        .ok_or("mmff_stbn: missing \"r0_ij\" column (typifier did not bake stretch-bend params)")?;
    let r0kj = block
        .get_float("r0_kj")
        .ok_or("mmff_stbn: missing \"r0_kj\" column (typifier did not bake stretch-bend params)")?;
    let th0 = block.get_float("theta0").ok_or(
        "mmff_stbn: missing \"theta0\" column (typifier did not bake stretch-bend params)",
    )?;

    let n = ic.len();
    let mut pot = MMFFStretchBend {
        atom_i: Vec::with_capacity(n),
        atom_j: Vec::with_capacity(n),
        atom_k: Vec::with_capacity(n),
        kba_ijk: Vec::with_capacity(n),
        kba_kji: Vec::with_capacity(n),
        r0_ij: Vec::with_capacity(n),
        r0_kj: Vec::with_capacity(n),
        theta0: Vec::with_capacity(n),
    };
    for idx in 0..n {
        pot.atom_i.push(ic[idx] as usize);
        pot.atom_j.push(jc[idx] as usize);
        pot.atom_k.push(kc[idx] as usize);
        pot.kba_ijk.push(kba_ijk_c[idx] as F);
        pot.kba_kji.push(kba_kji_c[idx] as F);
        pot.r0_ij.push(r0ij[idx] as F);
        pot.r0_kj.push(r0kj[idx] as F);
        pot.theta0.push(th0[idx] as F); // radians
    }
    Ok(Box::new(pot))
}

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

    #[test]
    fn test_mmff_angle_at_equilibrium() {
        let theta0: F = (109.5 as F).to_radians();
        let pot = MMFFAngleBend {
            atom_i: vec![0],
            atom_j: vec![1],
            atom_k: vec![2],
            ka: vec![0.608],
            theta0: vec![theta0],
        };
        let r = 1.5 as F;
        let half = theta0 / 2.0;
        let coords: Vec<F> = vec![
            r * half.cos(),
            r * half.sin(),
            0.0,
            0.0,
            0.0,
            0.0,
            r * half.cos(),
            -r * half.sin(),
            0.0,
        ];
        let (e, _) = pot.calc_energy_forces(&coords);
        assert!(e.abs() < 1e-4, "angle energy at eq should be ~0, got {}", e);
    }
}