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//
// Copyright (C) 2024 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "ChiralViolationContribs.h"
#include "ChiralSet.h"
#include <ForceField/ForceField.h>
namespace DistGeom {
double calcChiralVolume(const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, const unsigned int idx4,
const double *pos, const unsigned int dim) {
// even if we are minimizing in higher dimension the chiral volume is
// calculated using only the first 3 dimensions
RDGeom::Point3D v1(pos[idx1 * dim] - pos[idx4 * dim],
pos[idx1 * dim + 1] - pos[idx4 * dim + 1],
pos[idx1 * dim + 2] - pos[idx4 * dim + 2]);
RDGeom::Point3D v2(pos[idx2 * dim] - pos[idx4 * dim],
pos[idx2 * dim + 1] - pos[idx4 * dim + 1],
pos[idx2 * dim + 2] - pos[idx4 * dim + 2]);
RDGeom::Point3D v3(pos[idx3 * dim] - pos[idx4 * dim],
pos[idx3 * dim + 1] - pos[idx4 * dim + 1],
pos[idx3 * dim + 2] - pos[idx4 * dim + 2]);
RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
double vol = v1.dotProduct(v2xv3);
return vol;
}
double calcChiralVolume(const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, const unsigned int idx4,
const RDGeom::PointPtrVect &pts) {
// even if we are minimizing in higher dimension the chiral volume is
// calculated using only the first 3 dimensions
RDGeom::Point3D v1((*pts[idx1])[0] - (*pts[idx4])[0],
(*pts[idx1])[1] - (*pts[idx4])[1],
(*pts[idx1])[2] - (*pts[idx4])[2]);
RDGeom::Point3D v2((*pts[idx2])[0] - (*pts[idx4])[0],
(*pts[idx2])[1] - (*pts[idx4])[1],
(*pts[idx2])[2] - (*pts[idx4])[2]);
RDGeom::Point3D v3((*pts[idx3])[0] - (*pts[idx4])[0],
(*pts[idx3])[1] - (*pts[idx4])[1],
(*pts[idx3])[2] - (*pts[idx4])[2]);
RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
double vol = v1.dotProduct(v2xv3);
return vol;
}
ChiralViolationContribs::ChiralViolationContribs(
ForceFields::ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
void ChiralViolationContribs::addContrib(const ChiralSet *cset, double weight) {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(cset, "bad chiral set");
URANGE_CHECK(cset->d_idx1, dp_forceField->positions().size());
URANGE_CHECK(cset->d_idx2, dp_forceField->positions().size());
URANGE_CHECK(cset->d_idx3, dp_forceField->positions().size());
URANGE_CHECK(cset->d_idx4, dp_forceField->positions().size());
d_contribs.emplace_back(cset->d_idx1, cset->d_idx2, cset->d_idx3,
cset->d_idx4, cset->getUpperVolumeBound(),
cset->getLowerVolumeBound(), weight);
}
double ChiralViolationContribs::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
const unsigned int dim = dp_forceField->dimension();
double res = 0.0;
for (const auto &c : d_contribs) {
double vol = calcChiralVolume(c.idx1, c.idx2, c.idx3, c.idx4, pos, dim);
if (vol < c.volLower) {
res += c.weight * (vol - c.volLower) * (vol - c.volLower);
} else if (vol > c.volUpper) {
res += c.weight * (vol - c.volUpper) * (vol - c.volUpper);
}
}
return res;
}
void ChiralViolationContribs::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
const unsigned int dim = dp_forceField->dimension();
for (const auto &c : d_contribs) {
// even if we are minimizing in higher dimension the chiral volume is
// calculated using only the first 3 dimensions
RDGeom::Point3D v1(pos[c.idx1 * dim] - pos[c.idx4 * dim],
pos[c.idx1 * dim + 1] - pos[c.idx4 * dim + 1],
pos[c.idx1 * dim + 2] - pos[c.idx4 * dim + 2]);
RDGeom::Point3D v2(pos[c.idx2 * dim] - pos[c.idx4 * dim],
pos[c.idx2 * dim + 1] - pos[c.idx4 * dim + 1],
pos[c.idx2 * dim + 2] - pos[c.idx4 * dim + 2]);
RDGeom::Point3D v3(pos[c.idx3 * dim] - pos[c.idx4 * dim],
pos[c.idx3 * dim + 1] - pos[c.idx4 * dim + 1],
pos[c.idx3 * dim + 2] - pos[c.idx4 * dim + 2]);
RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
double vol = v1.dotProduct(v2xv3);
double preFactor;
if (vol < c.volLower) {
preFactor = c.weight * (vol - c.volLower);
} else if (vol > c.volUpper) {
preFactor = c.weight * (vol - c.volUpper);
} else {
continue;
}
// now comes the hard part - there are a total of 12 variables involved
// 4 x 3 - four points and 3 dimensions
//
grad[dim * c.idx1] += preFactor * ((v2.y) * (v3.z) - (v3.y) * (v2.z));
grad[dim * c.idx1 + 1] += preFactor * ((v3.x) * (v2.z) - (v2.x) * (v3.z));
grad[dim * c.idx1 + 2] += preFactor * ((v2.x) * (v3.y) - (v3.x) * (v2.y));
grad[dim * c.idx2] += preFactor * ((v3.y) * (v1.z) - (v3.z) * (v1.y));
grad[dim * c.idx2 + 1] += preFactor * ((v3.z) * (v1.x) - (v3.x) * (v1.z));
grad[dim * c.idx2 + 2] += preFactor * ((v3.x) * (v1.y) - (v3.y) * (v1.x));
grad[dim * c.idx3] += preFactor * ((v2.z) * (v1.y) - (v2.y) * (v1.z));
grad[dim * c.idx3 + 1] += preFactor * ((v2.x) * (v1.z) - (v2.z) * (v1.x));
grad[dim * c.idx3 + 2] += preFactor * ((v2.y) * (v1.x) - (v2.x) * (v1.y));
grad[dim * c.idx4] +=
preFactor * (pos[c.idx1 * dim + 2] *
(pos[c.idx2 * dim + 1] - pos[c.idx3 * dim + 1]) +
pos[c.idx2 * dim + 2] *
(pos[c.idx3 * dim + 1] - pos[c.idx1 * dim + 1]) +
pos[c.idx3 * dim + 2] *
(pos[c.idx1 * dim + 1] - pos[c.idx2 * dim + 1]));
grad[dim * c.idx4 + 1] +=
preFactor *
(pos[c.idx1 * dim] * (pos[c.idx2 * dim + 2] - pos[c.idx3 * dim + 2]) +
pos[c.idx2 * dim] * (pos[c.idx3 * dim + 2] - pos[c.idx1 * dim + 2]) +
pos[c.idx3 * dim] * (pos[c.idx1 * dim + 2] - pos[c.idx2 * dim + 2]));
grad[dim * c.idx4 + 2] +=
preFactor *
(pos[c.idx1 * dim + 1] * (pos[c.idx2 * dim] - pos[c.idx3 * dim]) +
pos[c.idx2 * dim + 1] * (pos[c.idx3 * dim] - pos[c.idx1 * dim]) +
pos[c.idx3 * dim + 1] * (pos[c.idx1 * dim] - pos[c.idx2 * dim]));
}
}
} // namespace DistGeom
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