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//! Source-backed RDKit MMFF stretch-bend contribution.
use crate::chemistry::forcefield::core::{ForceField, ForceFieldContrib, ForceFieldVec3};
use super::params::{MmffAngle, MmffBond, MmffStbn};
// BEGIN RDKIT CPP CONSTANT ForceFields::MMFF::MDYNE_A_TO_KCAL_MOL (Params.h:37-40)
// RDKit✔️✔️: constexpr double DEG2RAD = M_PI / 180.0;
// RDKit✔️✔️: constexpr double RAD2DEG = 180.0 / M_PI;
// RDKit✔️✔️: constexpr double MDYNE_A_TO_KCAL_MOL = 143.9325;
const DEG2RAD: f64 = std::f64::consts::PI / 180.0;
const RAD2DEG: f64 = 180.0 / std::f64::consts::PI;
const MDYNE_A_TO_KCAL_MOL: f64 = 143.9325;
#[derive(Clone, Debug)]
pub struct StretchBendContrib {
owner: *const ForceField,
atom1_indices: Vec<usize>,
atom2_indices: Vec<usize>,
atom3_indices: Vec<usize>,
rest_lengths1: Vec<f64>,
rest_lengths2: Vec<f64>,
theta0: Vec<f64>,
force_constants1: Vec<f64>,
force_constants2: Vec<f64>,
}
impl StretchBendContrib {
#[must_use]
pub fn new(owner: &ForceField) -> Self {
// BEGIN RDKIT CPP CONSTRUCTOR ForceFields::MMFF::StretchBendContrib::StretchBendContrib (StretchBend.cpp:39-42)
// RDKit✔️✔️: StretchBendContrib::StretchBendContrib(ForceField *owner) {
// RDKit✔️✔️: PRECONDITION(owner, "bad owner");
// Rust references reproduce RDKit's non-null owner precondition.
// RDKit✔️✔️: dp_forceField = owner;
let owner = owner as *const ForceField;
// RDKit✔️✔️: }
Self {
owner,
atom1_indices: Vec::new(),
atom2_indices: Vec::new(),
atom3_indices: Vec::new(),
rest_lengths1: Vec::new(),
rest_lengths2: Vec::new(),
theta0: Vec::new(),
force_constants1: Vec::new(),
force_constants2: Vec::new(),
}
}
#[must_use]
pub fn owner(&self) -> *const ForceField {
self.owner
}
#[must_use]
pub fn len(&self) -> usize {
self.atom1_indices.len()
}
#[must_use]
pub fn is_empty(&self) -> bool {
self.atom1_indices.is_empty()
&& self.atom2_indices.is_empty()
&& self.atom3_indices.is_empty()
&& self.rest_lengths1.is_empty()
&& self.rest_lengths2.is_empty()
&& self.theta0.is_empty()
&& self.force_constants1.is_empty()
&& self.force_constants2.is_empty()
}
pub fn add_term(
&mut self,
idx1: usize,
idx2: usize,
idx3: usize,
mmff_stbn_params: &MmffStbn,
mmff_angle_params: &MmffAngle,
mmff_bond_params1: &MmffBond,
mmff_bond_params2: &MmffBond,
) {
// BEGIN RDKIT CPP METHOD ForceFields::MMFF::StretchBendContrib::addTerm (StretchBend.cpp:44-66)
// RDKit✔️✔️: void StretchBendContrib::addTerm(
// RDKit✔️✔️: const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
// RDKit✔️✔️: const ForceFields::MMFF::MMFFStbn *mmffStbnParams,
// RDKit✔️✔️: const ForceFields::MMFF::MMFFAngle *mmffAngleParams,
// RDKit✔️✔️: const ForceFields::MMFF::MMFFBond *mmffBondParams1,
// RDKit✔️✔️: const ForceFields::MMFF::MMFFBond *mmffBondParams2) {
// RDKit✔️✔️: PRECONDITION(((idx1 != idx2) && (idx2 != idx3) && (idx1 != idx3)),
// RDKit✔️✔️: "degenerate points");
assert!(idx1 != idx2 && idx2 != idx3 && idx1 != idx3);
let force_field = self.force_field();
// RDKit✔️✔️: URANGE_CHECK(idx1, dp_forceField->positions().size());
// RDKit✔️✔️: URANGE_CHECK(idx2, dp_forceField->positions().size());
// RDKit✔️✔️: URANGE_CHECK(idx3, dp_forceField->positions().size());
assert!(idx1 < force_field.positions().len());
assert!(idx2 < force_field.positions().len());
assert!(idx3 < force_field.positions().len());
// RDKit✔️✔️: d_at1Idxs.push_back(idx1);
// RDKit✔️✔️: d_at2Idxs.push_back(idx2);
// RDKit✔️✔️: d_at3Idxs.push_back(idx3);
self.atom1_indices.push(idx1);
self.atom2_indices.push(idx2);
self.atom3_indices.push(idx3);
// RDKit✔️✔️: d_restLen1s.push_back(Utils::calcBondRestLength(mmffBondParams1));
// RDKit✔️✔️: d_restLen2s.push_back(Utils::calcBondRestLength(mmffBondParams2));
self.rest_lengths1
.push(calc_bond_rest_length(mmff_bond_params1));
self.rest_lengths2
.push(calc_bond_rest_length(mmff_bond_params2));
// RDKit✔️✔️: d_theta0s.push_back(Utils::calcAngleRestValue(mmffAngleParams));
self.theta0.push(calc_angle_rest_value(mmff_angle_params));
// RDKit✔️✔️: std::pair<double, double> forceConstants =
// RDKit✔️✔️: Utils::calcStbnForceConstants(mmffStbnParams);
let force_constants = calc_stbn_force_constants(mmff_stbn_params);
// RDKit✔️✔️: d_forceConstants1.push_back(forceConstants.first);
// RDKit✔️✔️: d_forceConstants2.push_back(forceConstants.second);
self.force_constants1.push(force_constants.0);
self.force_constants2.push(force_constants.1);
// RDKit✔️✔️: }
}
#[must_use]
pub fn get_energy(&self, pos: &[f64]) -> f64 {
// BEGIN RDKIT CPP METHOD ForceFields::MMFF::StretchBendContrib::getEnergy (StretchBend.cpp:68-99)
// RDKit✔️✔️: double StretchBendContrib::getEnergy(double *pos) const {
// RDKit✔️✔️: PRECONDITION(dp_forceField, "no owner");
// RDKit✔️✔️: PRECONDITION(pos, "bad vector");
let force_field = self.force_field();
// Rust slices reproduce RDKit's non-null pos precondition.
// RDKit✔️✔️: double totalEnergy = 0.0;
// RDKit✔️✔️: const int numTerms = d_at1Idxs.size();
let mut total_energy = 0.0;
let num_terms = self.atom1_indices.len();
// RDKit✔️✔️: for (int i = 0; i < numTerms; i++) {
for i in 0..num_terms {
// RDKit✔️✔️: const int16_t at1Idx = d_at1Idxs[i];
// RDKit✔️✔️: const int16_t at2Idx = d_at2Idxs[i];
// RDKit✔️✔️: const int16_t at3Idx = d_at3Idxs[i];
let atom1_idx = self.atom1_indices[i];
let atom2_idx = self.atom2_indices[i];
let atom3_idx = self.atom3_indices[i];
// RDKit✔️✔️: double dist1 = dp_forceField->distance(at1Idx, at2Idx, pos);
// RDKit✔️✔️: double dist2 = dp_forceField->distance(at2Idx, at3Idx, pos);
let dist1 = force_field.distance_const(atom1_idx, atom2_idx, Some(pos));
let dist2 = force_field.distance_const(atom2_idx, atom3_idx, Some(pos));
// RDKit✔️✔️: RDGeom::Point3D p1(pos[3 * at1Idx], pos[3 * at1Idx + 1],
// RDKit✔️✔️: pos[3 * at1Idx + 2]);
// RDKit✔️✔️: RDGeom::Point3D p2(pos[3 * at2Idx], pos[3 * at2Idx + 1],
// RDKit✔️✔️: pos[3 * at2Idx + 2]);
// RDKit✔️✔️: RDGeom::Point3D p3(pos[3 * at3Idx], pos[3 * at3Idx + 1],
// RDKit✔️✔️: pos[3 * at3Idx + 2]);
let p1 = point_from_pos(pos, atom1_idx);
let p2 = point_from_pos(pos, atom2_idx);
let p3 = point_from_pos(pos, atom3_idx);
// RDKit✔️✔️: std::pair<double, double> forceConstantsPair =
// RDKit✔️✔️: std::make_pair(d_forceConstants1[i], d_forceConstants2[i]);
let force_constants_pair = (self.force_constants1[i], self.force_constants2[i]);
// RDKit✔️✔️: std::pair<double, double> stretchBendEnergies =
// RDKit✔️✔️: Utils::calcStretchBendEnergy(
// RDKit✔️✔️: dist1 - d_restLen1s[i], dist2 - d_restLen2s[i],
// RDKit✔️✔️: RAD2DEG * acos(Utils::calcCosTheta(p1, p2, p3, dist1, dist2)) -
// RDKit✔️✔️: d_theta0s[i],
// RDKit✔️✔️: forceConstantsPair);
let stretch_bend_energies = calc_stretch_bend_energy(
dist1 - self.rest_lengths1[i],
dist2 - self.rest_lengths2[i],
RAD2DEG * calc_cos_theta(p1, p2, p3, dist1, dist2).acos() - self.theta0[i],
force_constants_pair,
);
// RDKit✔️✔️: totalEnergy += (stretchBendEnergies.first + stretchBendEnergies.second);
total_energy += stretch_bend_energies.0 + stretch_bend_energies.1;
// RDKit✔️✔️: }
}
// RDKit✔️✔️: return totalEnergy;
// RDKit✔️✔️: }
total_energy
}
pub fn get_grad(&self, pos: &[f64], grad: &mut [f64]) {
// BEGIN RDKIT CPP METHOD ForceFields::MMFF::StretchBendContrib::getGrad (StretchBend.cpp:101-175)
// RDKit✔️✔️: void StretchBendContrib::getGrad(double *pos, double *grad) const {
// RDKit✔️✔️: PRECONDITION(dp_forceField, "no owner");
// RDKit✔️✔️: PRECONDITION(pos, "bad vector");
// RDKit✔️✔️: PRECONDITION(grad, "bad vector");
let force_field = self.force_field();
// Rust slices reproduce RDKit's non-null pos and grad preconditions.
// RDKit✔️✔️: const int numTerms = d_at1Idxs.size();
let num_terms = self.atom1_indices.len();
// RDKit✔️✔️: for (int i = 0; i < numTerms; ++i) {
for i in 0..num_terms {
// RDKit✔️✔️: const int16_t at1Idx = d_at1Idxs[i];
// RDKit✔️✔️: const int16_t at2Idx = d_at2Idxs[i];
// RDKit✔️✔️: const int16_t at3Idx = d_at3Idxs[i];
let atom1_idx = self.atom1_indices[i];
let atom2_idx = self.atom2_indices[i];
let atom3_idx = self.atom3_indices[i];
// RDKit✔️✔️: const double theta0 = d_theta0s[i];
// RDKit✔️✔️: const double forceConstant1 = d_forceConstants1[i];
// RDKit✔️✔️: const double forceConstant2 = d_forceConstants2[i];
// RDKit✔️✔️: const double restLen1 = d_restLen1s[i];
// RDKit✔️✔️: const double restLen2 = d_restLen2s[i];
let theta0 = self.theta0[i];
let force_constant1 = self.force_constants1[i];
let force_constant2 = self.force_constants2[i];
let rest_len1 = self.rest_lengths1[i];
let rest_len2 = self.rest_lengths2[i];
// RDKit✔️✔️: double dist1 = dp_forceField->distance(at1Idx, at2Idx, pos);
// RDKit✔️✔️: double dist2 = dp_forceField->distance(at2Idx, at3Idx, pos);
let dist1 = force_field.distance_const(atom1_idx, atom2_idx, Some(pos));
let dist2 = force_field.distance_const(atom2_idx, atom3_idx, Some(pos));
// RDKit✔️✔️: RDGeom::Point3D p1(pos[3 * at1Idx], pos[3 * at1Idx + 1],
// RDKit✔️✔️: pos[3 * at1Idx + 2]);
// RDKit✔️✔️: RDGeom::Point3D p2(pos[3 * at2Idx], pos[3 * at2Idx + 1],
// RDKit✔️✔️: pos[3 * at2Idx + 2]);
// RDKit✔️✔️: RDGeom::Point3D p3(pos[3 * at3Idx], pos[3 * at3Idx + 1],
// RDKit✔️✔️: pos[3 * at3Idx + 2]);
let p1 = point_from_pos(pos, atom1_idx);
let p2 = point_from_pos(pos, atom2_idx);
let p3 = point_from_pos(pos, atom3_idx);
// RDKit✔️✔️: double *g1 = &(grad[3 * at1Idx]);
// RDKit✔️✔️: double *g2 = &(grad[3 * at2Idx]);
// RDKit✔️✔️: double *g3 = &(grad[3 * at3Idx]);
// Rust writes directly into the flat grad slice at RDKit's offsets.
// RDKit✔️✔️: RDGeom::Point3D p12 = (p1 - p2) / dist1;
// RDKit✔️✔️: RDGeom::Point3D p32 = (p3 - p2) / dist2;
let p12 = (p1 - p2) / dist1;
let p32 = (p3 - p2) / dist2;
// RDKit✔️✔️: double const c5 = MDYNE_A_TO_KCAL_MOL * DEG2RAD;
let c5 = MDYNE_A_TO_KCAL_MOL * DEG2RAD;
// RDKit✔️✔️: double cosTheta = p12.dotProduct(p32);
let mut cos_theta = p12.dot_product(p32);
// RDKit✔️✔️: clipToOne(cosTheta);
cos_theta = cos_theta.clamp(-1.0, 1.0);
// RDKit✔️✔️: double sinThetaSq = 1.0 - cosTheta * cosTheta;
let sin_theta_sq = 1.0 - cos_theta * cos_theta;
// RDKit✔️✔️: double sinTheta = std::max(sqrt(sinThetaSq), 1.0e-8);
let sin_theta = sin_theta_sq.sqrt().max(1.0e-8);
// RDKit✔️✔️: double angleTerm = RAD2DEG * acos(cosTheta) - theta0;
let angle_term = RAD2DEG * cos_theta.acos() - theta0;
// RDKit✔️✔️: double distTerm = RAD2DEG * (forceConstant1 * (dist1 - restLen1) +
// RDKit✔️✔️: forceConstant2 * (dist2 - restLen2));
let dist_term = RAD2DEG
* (force_constant1 * (dist1 - rest_len1) + force_constant2 * (dist2 - rest_len2));
// RDKit✔️✔️: double dCos_dS1 = 1.0 / dist1 * (p32.x - cosTheta * p12.x);
// RDKit✔️✔️: double dCos_dS2 = 1.0 / dist1 * (p32.y - cosTheta * p12.y);
// RDKit✔️✔️: double dCos_dS3 = 1.0 / dist1 * (p32.z - cosTheta * p12.z);
let d_cos_ds1 = (p32.x - cos_theta * p12.x) / dist1;
let d_cos_ds2 = (p32.y - cos_theta * p12.y) / dist1;
let d_cos_ds3 = (p32.z - cos_theta * p12.z) / dist1;
// RDKit✔️✔️: double dCos_dS4 = 1.0 / dist2 * (p12.x - cosTheta * p32.x);
// RDKit✔️✔️: double dCos_dS5 = 1.0 / dist2 * (p12.y - cosTheta * p32.y);
// RDKit✔️✔️: double dCos_dS6 = 1.0 / dist2 * (p12.z - cosTheta * p32.z);
let d_cos_ds4 = (p12.x - cos_theta * p32.x) / dist2;
let d_cos_ds5 = (p12.y - cos_theta * p32.y) / dist2;
let d_cos_ds6 = (p12.z - cos_theta * p32.z) / dist2;
// RDKit✔️✔️: g1[0] += c5 * (p12.x * forceConstant1 * angleTerm +
// RDKit✔️✔️: dCos_dS1 / (-sinTheta) * distTerm);
// RDKit✔️✔️: g1[1] += c5 * (p12.y * forceConstant1 * angleTerm +
// RDKit✔️✔️: dCos_dS2 / (-sinTheta) * distTerm);
// RDKit✔️✔️: g1[2] += c5 * (p12.z * forceConstant1 * angleTerm +
// RDKit✔️✔️: dCos_dS3 / (-sinTheta) * distTerm);
grad[3 * atom1_idx] +=
c5 * (p12.x * force_constant1 * angle_term + d_cos_ds1 / (-sin_theta) * dist_term);
grad[3 * atom1_idx + 1] +=
c5 * (p12.y * force_constant1 * angle_term + d_cos_ds2 / (-sin_theta) * dist_term);
grad[3 * atom1_idx + 2] +=
c5 * (p12.z * force_constant1 * angle_term + d_cos_ds3 / (-sin_theta) * dist_term);
// RDKit✔️✔️: g2[0] +=
// RDKit✔️✔️: c5 * ((-p12.x * forceConstant1 - p32.x * forceConstant2) * angleTerm +
// RDKit✔️✔️: (-dCos_dS1 - dCos_dS4) / (-sinTheta) * distTerm);
// RDKit✔️✔️: g2[1] +=
// RDKit✔️✔️: c5 * ((-p12.y * forceConstant1 - p32.y * forceConstant2) * angleTerm +
// RDKit✔️✔️: (-dCos_dS2 - dCos_dS5) / (-sinTheta) * distTerm);
// RDKit✔️✔️: g2[2] +=
// RDKit✔️✔️: c5 * ((-p12.z * forceConstant1 - p32.z * forceConstant2) * angleTerm +
// RDKit✔️✔️: (-dCos_dS3 - dCos_dS6) / (-sinTheta) * distTerm);
grad[3 * atom2_idx] += c5
* ((-p12.x * force_constant1 - p32.x * force_constant2) * angle_term
+ (-d_cos_ds1 - d_cos_ds4) / (-sin_theta) * dist_term);
grad[3 * atom2_idx + 1] += c5
* ((-p12.y * force_constant1 - p32.y * force_constant2) * angle_term
+ (-d_cos_ds2 - d_cos_ds5) / (-sin_theta) * dist_term);
grad[3 * atom2_idx + 2] += c5
* ((-p12.z * force_constant1 - p32.z * force_constant2) * angle_term
+ (-d_cos_ds3 - d_cos_ds6) / (-sin_theta) * dist_term);
// RDKit✔️✔️: g3[0] += c5 * (p32.x * forceConstant2 * angleTerm +
// RDKit✔️✔️: dCos_dS4 / (-sinTheta) * distTerm);
// RDKit✔️✔️: g3[1] += c5 * (p32.y * forceConstant2 * angleTerm +
// RDKit✔️✔️: dCos_dS5 / (-sinTheta) * distTerm);
// RDKit✔️✔️: g3[2] += c5 * (p32.z * forceConstant2 * angleTerm +
// RDKit✔️✔️: dCos_dS6 / (-sinTheta) * distTerm);
grad[3 * atom3_idx] +=
c5 * (p32.x * force_constant2 * angle_term + d_cos_ds4 / (-sin_theta) * dist_term);
grad[3 * atom3_idx + 1] +=
c5 * (p32.y * force_constant2 * angle_term + d_cos_ds5 / (-sin_theta) * dist_term);
grad[3 * atom3_idx + 2] +=
c5 * (p32.z * force_constant2 * angle_term + d_cos_ds6 / (-sin_theta) * dist_term);
// RDKit✔️✔️: }
}
// RDKit✔️✔️: }
}
#[must_use]
pub fn atom1_indices(&self) -> &[usize] {
&self.atom1_indices
}
#[must_use]
pub fn atom2_indices(&self) -> &[usize] {
&self.atom2_indices
}
#[must_use]
pub fn atom3_indices(&self) -> &[usize] {
&self.atom3_indices
}
#[must_use]
pub fn rest_lengths1(&self) -> &[f64] {
&self.rest_lengths1
}
#[must_use]
pub fn rest_lengths2(&self) -> &[f64] {
&self.rest_lengths2
}
#[must_use]
pub fn theta0(&self) -> &[f64] {
&self.theta0
}
#[must_use]
pub fn force_constants1(&self) -> &[f64] {
&self.force_constants1
}
#[must_use]
pub fn force_constants2(&self) -> &[f64] {
&self.force_constants2
}
fn force_field(&self) -> &ForceField {
assert!(!self.owner.is_null(), "no owner");
// SAFETY: MMFF contribs follow the same owner-pointer model as
// ForceFieldContrib objects in core.rs. Constructors store a live
// ForceField pointer before term insertion or evaluation.
unsafe { &*self.owner }
}
}
#[must_use]
fn calc_bond_rest_length(mmff_bond_params: &MmffBond) -> f64 {
// BEGIN RDKIT CPP FUNCTION ForceFields::MMFF::Utils::calcBondRestLength (BondStretch.cpp:18-23)
// RDKit✔️✔️: double calcBondRestLength(const MMFFBond *mmffBondParams) {
// RDKit✔️✔️: PRECONDITION(mmffBondParams, "bond parameters not found");
// Rust references reproduce RDKit's non-null parameter precondition.
//
// RDKit✔️✔️: return mmffBondParams->r0;
// RDKit✔️✔️: }
mmff_bond_params.r0
}
#[must_use]
fn calc_angle_rest_value(mmff_angle_params: &MmffAngle) -> f64 {
// BEGIN RDKIT CPP FUNCTION ForceFields::MMFF::Utils::calcAngleRestValue (AngleBend.cpp:18-23)
// RDKit✔️✔️: double calcAngleRestValue(const MMFFAngle *mmffAngleParams) {
// RDKit✔️✔️: PRECONDITION(mmffAngleParams, "angle parameters not found");
// Rust references reproduce RDKit's non-null parameter precondition.
//
// RDKit✔️✔️: return mmffAngleParams->theta0;
// RDKit✔️✔️: }
mmff_angle_params.theta0
}
#[must_use]
fn calc_stbn_force_constants(mmff_stbn_params: &MmffStbn) -> (f64, f64) {
// BEGIN RDKIT CPP FUNCTION ForceFields::MMFF::Utils::calcStbnForceConstants (StretchBend.cpp:18-24)
// RDKit✔️✔️: std::pair<double, double> calcStbnForceConstants(
// RDKit✔️✔️: const MMFFStbn *mmffStbnParams) {
// RDKit✔️✔️: PRECONDITION(mmffStbnParams, "stretch-bend parameters not found");
// Rust references reproduce RDKit's non-null parameter precondition.
//
// RDKit✔️✔️: return std::make_pair(mmffStbnParams->kbaIJK, mmffStbnParams->kbaKJI);
// RDKit✔️✔️: }
(mmff_stbn_params.kba_ijk, mmff_stbn_params.kba_kji)
}
#[must_use]
fn point_from_pos(pos: &[f64], atom_idx: usize) -> ForceFieldVec3 {
let offset = 3 * atom_idx;
ForceFieldVec3::new(pos[offset], pos[offset + 1], pos[offset + 2])
}
#[must_use]
fn calc_cos_theta(
p1: ForceFieldVec3,
p2: ForceFieldVec3,
p3: ForceFieldVec3,
dist1: f64,
dist2: f64,
) -> f64 {
// BEGIN RDKIT CPP FUNCTION ForceFields::MMFF::Utils::calcCosTheta (AngleBend.cpp:25-33)
// RDKit✔️✔️: double calcCosTheta(RDGeom::Point3D p1, RDGeom::Point3D p2, RDGeom::Point3D p3,
// RDKit✔️✔️: double dist1, double dist2) {
// RDKit✔️✔️: RDGeom::Point3D p12 = p1 - p2;
// RDKit✔️✔️: RDGeom::Point3D p32 = p3 - p2;
let p12 = p1 - p2;
let p32 = p3 - p2;
// RDKit✔️✔️: double cosTheta = p12.dotProduct(p32) / (dist1 * dist2);
let cos_theta = p12.dot_product(p32) / (dist1 * dist2);
// RDKit✔️✔️: clipToOne(cosTheta);
let cos_theta = cos_theta.clamp(-1.0, 1.0);
// RDKit✔️✔️: return cosTheta;
// RDKit✔️✔️: }
cos_theta
}
#[must_use]
fn calc_stretch_bend_energy(
delta_dist1: f64,
delta_dist2: f64,
delta_theta: f64,
force_constants: (f64, f64),
) -> (f64, f64) {
// BEGIN RDKIT CPP FUNCTION ForceFields::MMFF::Utils::calcStretchBendEnergy (StretchBend.cpp:26-36)
// RDKit✔️✔️: std::pair<double, double> calcStretchBendEnergy(
// RDKit✔️✔️: const double deltaDist1, const double deltaDist2, const double deltaTheta,
// RDKit✔️✔️: const std::pair<double, double> forceConstants) {
// RDKit✔️✔️: double factor = MDYNE_A_TO_KCAL_MOL * DEG2RAD * deltaTheta;
let factor = MDYNE_A_TO_KCAL_MOL * DEG2RAD * delta_theta;
// RDKit✔️✔️: return std::make_pair(factor * forceConstants.first * deltaDist1,
// RDKit✔️✔️: factor * forceConstants.second * deltaDist2);
// RDKit✔️✔️: }
(
factor * force_constants.0 * delta_dist1,
factor * force_constants.1 * delta_dist2,
)
}
impl ForceFieldContrib for StretchBendContrib {
fn copy(&self) -> Box<dyn ForceFieldContrib> {
Box::new(self.clone())
}
fn set_force_field(&mut self, owner: *const ForceField) {
self.owner = owner;
}
fn get_energy(&self, pos: &[f64]) -> f64 {
StretchBendContrib::get_energy(self, pos)
}
fn get_grad(&self, pos: &[f64], grad: &mut [f64]) {
StretchBendContrib::get_grad(self, pos, grad);
}
}
#[cfg(test)]
mod tests {
use super::{StretchBendContrib, calc_cos_theta};
use crate::chemistry::forcefield::{
core::{ForceField, ForceFieldVec3},
mmff::params::{MmffAngle, MmffBond, MmffStbn},
};
fn force_field_with_positions(count: usize) -> ForceField {
let mut force_field = ForceField::new(3);
force_field
.positions_mut()
.extend((0..count).map(|idx| ForceFieldVec3::new(idx as f64, 0.0, 0.0)));
force_field
}
fn initialized_force_field_with_positions(count: usize) -> ForceField {
let mut force_field = force_field_with_positions(count);
force_field.initialize();
force_field
}
fn source_stretch_bend_energy(
dist1: f64,
rest_len1: f64,
dist2: f64,
rest_len2: f64,
theta: f64,
theta0: f64,
force_constants: (f64, f64),
) -> f64 {
let delta_theta = theta - theta0;
let factor = 143.9325 * (std::f64::consts::PI / 180.0) * delta_theta;
factor * force_constants.0 * (dist1 - rest_len1)
+ factor * force_constants.1 * (dist2 - rest_len2)
}
fn assert_close(actual: f64, expected: f64) {
assert!(
(actual - expected).abs() < 1.0e-12,
"actual={actual}, expected={expected}"
);
}
fn assert_slice_close(actual: &[f64], expected: &[f64]) {
assert_eq!(actual.len(), expected.len());
for (index, (actual, expected)) in actual.iter().zip(expected.iter()).enumerate() {
assert!(
(actual - expected).abs() < 1.0e-12,
"index={index}, actual={actual}, expected={expected}"
);
}
}
fn source_stretch_bend_grad(
pos: &[f64],
atom_indices: [usize; 3],
rest_lengths: (f64, f64),
theta0: f64,
force_constants: (f64, f64),
) -> Vec<f64> {
let atom1_idx = atom_indices[0];
let atom2_idx = atom_indices[1];
let atom3_idx = atom_indices[2];
let p1 = ForceFieldVec3::new(
pos[3 * atom1_idx],
pos[3 * atom1_idx + 1],
pos[3 * atom1_idx + 2],
);
let p2 = ForceFieldVec3::new(
pos[3 * atom2_idx],
pos[3 * atom2_idx + 1],
pos[3 * atom2_idx + 2],
);
let p3 = ForceFieldVec3::new(
pos[3 * atom3_idx],
pos[3 * atom3_idx + 1],
pos[3 * atom3_idx + 2],
);
let dist1 = (p1 - p2).length();
let dist2 = (p3 - p2).length();
let p12 = (p1 - p2) / dist1;
let p32 = (p3 - p2) / dist2;
let c5 = 143.9325 * (std::f64::consts::PI / 180.0);
let cos_theta = p12.dot_product(p32).clamp(-1.0, 1.0);
let sin_theta_sq = 1.0 - cos_theta * cos_theta;
let sin_theta = sin_theta_sq.sqrt().max(1.0e-8);
let angle_term = (180.0 / std::f64::consts::PI) * cos_theta.acos() - theta0;
let dist_term = (180.0 / std::f64::consts::PI)
* (force_constants.0 * (dist1 - rest_lengths.0)
+ force_constants.1 * (dist2 - rest_lengths.1));
let d_cos_ds1 = (p32.x - cos_theta * p12.x) / dist1;
let d_cos_ds2 = (p32.y - cos_theta * p12.y) / dist1;
let d_cos_ds3 = (p32.z - cos_theta * p12.z) / dist1;
let d_cos_ds4 = (p12.x - cos_theta * p32.x) / dist2;
let d_cos_ds5 = (p12.y - cos_theta * p32.y) / dist2;
let d_cos_ds6 = (p12.z - cos_theta * p32.z) / dist2;
let mut grad = vec![0.0; pos.len()];
grad[3 * atom1_idx] +=
c5 * (p12.x * force_constants.0 * angle_term + d_cos_ds1 / (-sin_theta) * dist_term);
grad[3 * atom1_idx + 1] +=
c5 * (p12.y * force_constants.0 * angle_term + d_cos_ds2 / (-sin_theta) * dist_term);
grad[3 * atom1_idx + 2] +=
c5 * (p12.z * force_constants.0 * angle_term + d_cos_ds3 / (-sin_theta) * dist_term);
grad[3 * atom2_idx] += c5
* ((-p12.x * force_constants.0 - p32.x * force_constants.1) * angle_term
+ (-d_cos_ds1 - d_cos_ds4) / (-sin_theta) * dist_term);
grad[3 * atom2_idx + 1] += c5
* ((-p12.y * force_constants.0 - p32.y * force_constants.1) * angle_term
+ (-d_cos_ds2 - d_cos_ds5) / (-sin_theta) * dist_term);
grad[3 * atom2_idx + 2] += c5
* ((-p12.z * force_constants.0 - p32.z * force_constants.1) * angle_term
+ (-d_cos_ds3 - d_cos_ds6) / (-sin_theta) * dist_term);
grad[3 * atom3_idx] +=
c5 * (p32.x * force_constants.1 * angle_term + d_cos_ds4 / (-sin_theta) * dist_term);
grad[3 * atom3_idx + 1] +=
c5 * (p32.y * force_constants.1 * angle_term + d_cos_ds5 / (-sin_theta) * dist_term);
grad[3 * atom3_idx + 2] +=
c5 * (p32.z * force_constants.1 * angle_term + d_cos_ds6 / (-sin_theta) * dist_term);
grad
}
#[test]
fn mmff_stretchbendcontrib_constructor_stores_owner_pointer() {
let force_field = ForceField::new(3);
let contrib = StretchBendContrib::new(&force_field);
assert_eq!(contrib.owner(), &force_field as *const ForceField);
}
#[test]
fn mmff_stretchbendcontrib_constructor_initializes_no_terms() {
let force_field = ForceField::new(3);
let contrib = StretchBendContrib::new(&force_field);
assert_eq!(contrib.len(), 0);
assert!(contrib.is_empty());
}
#[test]
fn mmff_stretchbendcontrib_constructor_accepts_empty_force_field_like_rdkit() {
let force_field = ForceField::new(3);
let contrib = StretchBendContrib::new(&force_field);
assert_eq!(force_field.positions().len(), 0);
assert!(contrib.is_empty());
}
#[test]
fn mmff_stretchbendcontrib_add_term_pushes_source_fields() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
contrib.add_term(0, 1, 2, &stbn, &angle, &bond1, &bond2);
assert_eq!(contrib.atom1_indices(), &[0]);
assert_eq!(contrib.atom2_indices(), &[1]);
assert_eq!(contrib.atom3_indices(), &[2]);
assert_eq!(contrib.rest_lengths1(), &[1.508]);
assert_eq!(contrib.rest_lengths2(), &[1.093]);
assert_eq!(contrib.theta0(), &[110.549]);
assert_eq!(contrib.force_constants1(), &[0.227]);
assert_eq!(contrib.force_constants2(), &[0.070]);
}
#[test]
fn mmff_stretchbendcontrib_add_term_appends_multiple_terms() {
let force_field = force_field_with_positions(4);
let mut contrib = StretchBendContrib::new(&force_field);
let first_stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let second_stbn = MmffStbn {
kba_ijk: 0.300,
kba_kji: 0.400,
};
let first_angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let second_angle = MmffAngle {
ka: 1.006,
theta0: 110.265,
};
let first_bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let first_bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let second_bond1 = MmffBond {
kb: 3.529,
r0: 1.330,
};
let second_bond2 = MmffBond {
kb: 3.366,
r0: 1.520,
};
contrib.add_term(
0,
1,
2,
&first_stbn,
&first_angle,
&first_bond1,
&first_bond2,
);
contrib.add_term(
1,
2,
3,
&second_stbn,
&second_angle,
&second_bond1,
&second_bond2,
);
assert_eq!(contrib.atom1_indices(), &[0, 1]);
assert_eq!(contrib.atom2_indices(), &[1, 2]);
assert_eq!(contrib.atom3_indices(), &[2, 3]);
assert_eq!(contrib.rest_lengths1(), &[1.508, 1.330]);
assert_eq!(contrib.rest_lengths2(), &[1.093, 1.520]);
assert_eq!(contrib.theta0(), &[110.549, 110.265]);
assert_eq!(contrib.force_constants1(), &[0.227, 0.300]);
assert_eq!(contrib.force_constants2(), &[0.070, 0.400]);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_first_second_degenerate() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(0, 0, 2, &stbn, &angle, &bond, &bond);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_second_third_degenerate() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(0, 1, 1, &stbn, &angle, &bond, &bond);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_first_third_degenerate() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(0, 1, 0, &stbn, &angle, &bond, &bond);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_first_index_out_of_range() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(3, 1, 2, &stbn, &angle, &bond, &bond);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_second_index_out_of_range() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(0, 3, 2, &stbn, &angle, &bond, &bond);
}
#[test]
#[should_panic]
fn mmff_stretchbendcontrib_add_term_rejects_third_index_out_of_range() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond = MmffBond {
kb: 4.258,
r0: 1.508,
};
contrib.add_term(0, 1, 3, &stbn, &angle, &bond, &bond);
}
#[test]
fn mmff_stretchbendcontrib_get_energy_returns_zero_without_terms() {
let force_field = force_field_with_positions(3);
let contrib = StretchBendContrib::new(&force_field);
let pos = [0.0, 0.0, 0.0, 1.4, 0.0, 0.0, 1.4, 1.2, 0.0];
assert_close(contrib.get_energy(&pos), 0.0);
}
#[test]
fn mmff_stretchbendcontrib_get_energy_uses_source_formula() {
let force_field = initialized_force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let pos = [0.0, 0.0, 0.0, 1.6, 0.0, 0.0, 1.6, 1.4, 0.0];
contrib.add_term(0, 1, 2, &stbn, &angle, &bond1, &bond2);
let expected =
source_stretch_bend_energy(1.6, 1.508, 1.4, 1.093, 90.0, 110.549, (0.227, 0.070));
assert_close(contrib.get_energy(&pos), expected);
}
#[test]
fn mmff_stretchbendcontrib_get_energy_sums_multiple_source_terms() {
let force_field = initialized_force_field_with_positions(4);
let mut contrib = StretchBendContrib::new(&force_field);
let first_stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let second_stbn = MmffStbn {
kba_ijk: 0.300,
kba_kji: 0.400,
};
let first_angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let second_angle = MmffAngle {
ka: 1.006,
theta0: 110.265,
};
let first_bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let first_bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let second_bond1 = MmffBond {
kb: 3.529,
r0: 1.330,
};
let second_bond2 = MmffBond {
kb: 3.366,
r0: 1.520,
};
let pos = [
0.0, 0.0, 0.0, //
1.6, 0.0, 0.0, //
1.6, 1.4, 0.0, //
2.9, 1.4, 0.0,
];
contrib.add_term(
0,
1,
2,
&first_stbn,
&first_angle,
&first_bond1,
&first_bond2,
);
contrib.add_term(
1,
2,
3,
&second_stbn,
&second_angle,
&second_bond1,
&second_bond2,
);
let first =
source_stretch_bend_energy(1.6, 1.508, 1.4, 1.093, 90.0, 110.549, (0.227, 0.070));
let second =
source_stretch_bend_energy(1.4, 1.330, 1.3, 1.520, 90.0, 110.265, (0.300, 0.400));
assert_close(contrib.get_energy(&pos), first + second);
}
#[test]
fn mmff_stretchbendcontrib_get_energy_cos_theta_clips_upper_source_bound() {
let p1 = ForceFieldVec3::new(1.0 + f64::EPSILON, 0.0, 0.0);
let p2 = ForceFieldVec3::new(0.0, 0.0, 0.0);
let p3 = ForceFieldVec3::new(1.0, 0.0, 0.0);
assert_close(calc_cos_theta(p1, p2, p3, 1.0, 1.0), 1.0);
}
#[test]
fn mmff_stretchbendcontrib_get_energy_cos_theta_clips_lower_source_bound() {
let p1 = ForceFieldVec3::new(-(1.0 + f64::EPSILON), 0.0, 0.0);
let p2 = ForceFieldVec3::new(0.0, 0.0, 0.0);
let p3 = ForceFieldVec3::new(1.0, 0.0, 0.0);
assert_close(calc_cos_theta(p1, p2, p3, 1.0, 1.0), -1.0);
}
#[test]
fn mmff_stretchbendcontrib_get_grad_leaves_gradient_without_terms() {
let force_field = ForceField::new(3);
let contrib = StretchBendContrib::new(&force_field);
let mut grad = vec![1.0, 2.0, 3.0];
contrib.get_grad(&[], &mut grad);
assert_eq!(grad, vec![1.0, 2.0, 3.0]);
}
#[test]
fn mmff_stretchbendcontrib_get_grad_uses_source_formula() {
let force_field = initialized_force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let pos = [0.0, 0.0, 0.0, 1.6, 0.0, 0.0, 1.6, 1.4, 0.0];
let mut grad = vec![0.0; pos.len()];
contrib.add_term(0, 1, 2, &stbn, &angle, &bond1, &bond2);
contrib.get_grad(&pos, &mut grad);
let expected =
source_stretch_bend_grad(&pos, [0, 1, 2], (1.508, 1.093), 110.549, (0.227, 0.070));
assert_slice_close(&grad, &expected);
}
#[test]
fn mmff_stretchbendcontrib_get_grad_accumulates_multiple_terms() {
let force_field = initialized_force_field_with_positions(4);
let mut contrib = StretchBendContrib::new(&force_field);
let first_stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let second_stbn = MmffStbn {
kba_ijk: 0.300,
kba_kji: 0.400,
};
let first_angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let second_angle = MmffAngle {
ka: 1.006,
theta0: 110.265,
};
let first_bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let first_bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let second_bond1 = MmffBond {
kb: 3.529,
r0: 1.330,
};
let second_bond2 = MmffBond {
kb: 3.366,
r0: 1.520,
};
let pos = [
0.0, 0.0, 0.0, //
1.6, 0.0, 0.0, //
1.6, 1.4, 0.0, //
2.9, 1.4, 0.0,
];
let mut grad = vec![0.0; pos.len()];
contrib.add_term(
0,
1,
2,
&first_stbn,
&first_angle,
&first_bond1,
&first_bond2,
);
contrib.add_term(
1,
2,
3,
&second_stbn,
&second_angle,
&second_bond1,
&second_bond2,
);
contrib.get_grad(&pos, &mut grad);
let mut expected =
source_stretch_bend_grad(&pos, [0, 1, 2], (1.508, 1.093), 110.549, (0.227, 0.070));
let second =
source_stretch_bend_grad(&pos, [1, 2, 3], (1.330, 1.520), 110.265, (0.300, 0.400));
for (expected, second) in expected.iter_mut().zip(second.iter()) {
*expected += second;
}
assert_slice_close(&grad, &expected);
}
#[test]
#[should_panic(expected = "not initialized")]
fn mmff_stretchbendcontrib_get_grad_requires_initialized_force_field_for_terms() {
let force_field = force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let mut grad = vec![0.0; 9];
contrib.add_term(0, 1, 2, &stbn, &angle, &bond1, &bond2);
contrib.get_grad(&[0.0, 0.0, 0.0, 1.6, 0.0, 0.0, 1.6, 1.4, 0.0], &mut grad);
}
#[test]
fn mmff_stretchbendcontrib_get_grad_uses_singularity_sine_clamp() {
let force_field = initialized_force_field_with_positions(3);
let mut contrib = StretchBendContrib::new(&force_field);
let stbn = MmffStbn {
kba_ijk: 0.227,
kba_kji: 0.070,
};
let angle = MmffAngle {
ka: 0.636,
theta0: 110.549,
};
let bond1 = MmffBond {
kb: 4.258,
r0: 1.508,
};
let bond2 = MmffBond {
kb: 4.766,
r0: 1.093,
};
let pos = [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0];
let mut grad = vec![0.0; pos.len()];
contrib.add_term(0, 1, 2, &stbn, &angle, &bond1, &bond2);
contrib.get_grad(&pos, &mut grad);
assert!(grad.iter().all(|value| value.is_finite()));
}
}