mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
119 lines
4.3 KiB
C++
119 lines
4.3 KiB
C++
// $Id$
|
|
//
|
|
// Created by Santosh Putta, Nov 2006
|
|
//
|
|
|
|
#include "ChiralViolationContrib.h"
|
|
#include "ChiralSet.h"
|
|
#include <ForceField/ForceField.h>
|
|
|
|
namespace DistGeom {
|
|
ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner,
|
|
const ChiralSet *cset,
|
|
double weight) {
|
|
PRECONDITION(owner, "bad owner");
|
|
PRECONDITION(cset, "bad chiral set")
|
|
|
|
URANGE_CHECK(cset->d_idx1, owner->positions().size() - 1);
|
|
URANGE_CHECK(cset->d_idx2, owner->positions().size() - 1);
|
|
URANGE_CHECK(cset->d_idx3, owner->positions().size() - 1);
|
|
URANGE_CHECK(cset->d_idx4, owner->positions().size() - 1);
|
|
|
|
dp_forceField = owner;
|
|
|
|
d_idx1 = cset->d_idx1;
|
|
d_idx2 = cset->d_idx2;
|
|
d_idx3 = cset->d_idx3;
|
|
d_idx4 = cset->d_idx4;
|
|
|
|
d_volLower = cset->getLowerVolumeBound();
|
|
d_volUpper = cset->getUpperVolumeBound();
|
|
|
|
d_weight = weight;
|
|
}
|
|
|
|
double ChiralViolationContrib::getEnergy(double *pos) const {
|
|
PRECONDITION(dp_forceField, "no owner");
|
|
PRECONDITION(pos, "bad vector");
|
|
|
|
unsigned int dim = dp_forceField->dimension();
|
|
double vol = calcChiralVolume(d_idx1, d_idx2, d_idx3, d_idx4, pos, dim);
|
|
double res = 0.0;
|
|
if (vol < d_volLower) {
|
|
res = d_weight * (vol - d_volLower) * (vol - d_volLower);
|
|
} else if (vol > d_volUpper) {
|
|
res = d_weight * (vol - d_volUpper) * (vol - d_volUpper);
|
|
}
|
|
// std::cerr<<"Chiral Violation vol: "<<vol<<" E: "<<res<<std::endl;
|
|
return res;
|
|
}
|
|
|
|
void ChiralViolationContrib::getGrad(double *pos, double *grad) const {
|
|
PRECONDITION(dp_forceField, "no owner");
|
|
PRECONDITION(pos, "bad vector");
|
|
|
|
unsigned int dim = dp_forceField->dimension();
|
|
|
|
// even if we are minimizing in higher dimension the chiral volume is
|
|
// calculated using only the first 3 dimensions
|
|
RDGeom::Point3D v1(pos[d_idx1 * dim] - pos[d_idx4 * dim],
|
|
pos[d_idx1 * dim + 1] - pos[d_idx4 * dim + 1],
|
|
pos[d_idx1 * dim + 2] - pos[d_idx4 * dim + 2]);
|
|
|
|
RDGeom::Point3D v2(pos[d_idx2 * dim] - pos[d_idx4 * dim],
|
|
pos[d_idx2 * dim + 1] - pos[d_idx4 * dim + 1],
|
|
pos[d_idx2 * dim + 2] - pos[d_idx4 * dim + 2]);
|
|
|
|
RDGeom::Point3D v3(pos[d_idx3 * dim] - pos[d_idx4 * dim],
|
|
pos[d_idx3 * dim + 1] - pos[d_idx4 * dim + 1],
|
|
pos[d_idx3 * dim + 2] - pos[d_idx4 * dim + 2]);
|
|
|
|
RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
|
|
|
|
double vol = v1.dotProduct(v2xv3);
|
|
double preFactor;
|
|
|
|
if (vol < d_volLower) {
|
|
preFactor = d_weight * (vol - d_volLower);
|
|
} else if (vol > d_volUpper) {
|
|
preFactor = d_weight * (vol - d_volUpper);
|
|
} else {
|
|
return;
|
|
}
|
|
|
|
// now comes the hard part - there are a total of 12 variables involved
|
|
// 4 x 3 - four points and 3 dimensions
|
|
//
|
|
grad[dim * d_idx1] += preFactor * ((v2.y) * (v3.z) - (v3.y) * (v2.z));
|
|
grad[dim * d_idx1 + 1] += preFactor * ((v3.x) * (v2.z) - (v2.x) * (v3.z));
|
|
grad[dim * d_idx1 + 2] += preFactor * ((v2.x) * (v3.y) - (v3.x) * (v2.y));
|
|
|
|
grad[dim * d_idx2] += preFactor * ((v3.y) * (v1.z) - (v3.z) * (v1.y));
|
|
grad[dim * d_idx2 + 1] += preFactor * ((v3.z) * (v1.x) - (v3.x) * (v1.z));
|
|
grad[dim * d_idx2 + 2] += preFactor * ((v3.x) * (v1.y) - (v3.y) * (v1.x));
|
|
|
|
grad[dim * d_idx3] += preFactor * ((v2.z) * (v1.y) - (v2.y) * (v1.z));
|
|
grad[dim * d_idx3 + 1] += preFactor * ((v2.x) * (v1.z) - (v2.z) * (v1.x));
|
|
grad[dim * d_idx3 + 2] += preFactor * ((v2.y) * (v1.x) - (v2.x) * (v1.y));
|
|
|
|
grad[dim * d_idx4] +=
|
|
preFactor *
|
|
(pos[d_idx1 * dim + 2] * (pos[d_idx2 * dim + 1] - pos[d_idx3 * dim + 1]) +
|
|
pos[d_idx2 * dim + 2] * (pos[d_idx3 * dim + 1] - pos[d_idx1 * dim + 1]) +
|
|
pos[d_idx3 * dim + 2] * (pos[d_idx1 * dim + 1] - pos[d_idx2 * dim + 1]));
|
|
|
|
grad[dim * d_idx4 + 1] +=
|
|
preFactor *
|
|
(pos[d_idx1 * dim] * (pos[d_idx2 * dim + 2] - pos[d_idx3 * dim + 2]) +
|
|
pos[d_idx2 * dim] * (pos[d_idx3 * dim + 2] - pos[d_idx1 * dim + 2]) +
|
|
pos[d_idx3 * dim] * (pos[d_idx1 * dim + 2] - pos[d_idx2 * dim + 2]));
|
|
|
|
grad[dim * d_idx4 + 2] +=
|
|
preFactor *
|
|
(pos[d_idx1 * dim + 1] * (pos[d_idx2 * dim] - pos[d_idx3 * dim]) +
|
|
pos[d_idx2 * dim + 1] * (pos[d_idx3 * dim] - pos[d_idx1 * dim]) +
|
|
pos[d_idx3 * dim + 1] * (pos[d_idx1 * dim] - pos[d_idx2 * dim]));
|
|
// std::cerr<<"Chiral Violation grad: "<<preFactor<<std::endl;
|
|
}
|
|
}
|