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// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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 "DistViolationContrib.h"
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace DistGeom {
DistViolationContrib::DistViolationContrib(ForceFields::ForceField *owner,
unsigned int idx1, unsigned int idx2,
double ub, double lb,
double weight) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
dp_forceField = owner;
d_end1Idx = idx1;
d_end2Idx = idx2;
d_ub = ub;
d_lb = lb;
d_weight = weight;
}
double DistViolationContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double d =
this->dp_forceField->distance(this->d_end1Idx, this->d_end2Idx, pos);
double val = 0.0;
if (d > d_ub) {
val = ((d * d) / (d_ub * d_ub)) - 1.0;
} else if (d < d_lb) {
val = ((2 * d_lb * d_lb) / (d_lb * d_lb + d * d)) - 1.0;
}
double res;
if (val > 0.0) {
res = d_weight * val * val;
} else {
res = 0;
}
// if (res > 0.1) {
// std::cerr << "dvc:getEnergy: " << this->d_end1Idx << "-" <<
// this->d_end2Idx
// << ": " << d_lb << "-" << d_ub << " " << d << " => " << res
// << std::endl;
// }
return res;
}
void DistViolationContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
unsigned int dim = this->dp_forceField->dimension();
double d =
this->dp_forceField->distance(this->d_end1Idx, this->d_end2Idx, pos);
double preFactor = 0.0;
if (d > d_ub) {
double u2 = d_ub * d_ub;
preFactor = 4. * (((d * d) / u2) - 1.0) * (d / u2);
} else if (d < d_lb) {
double d2 = d * d;
double l2 = d_lb * d_lb;
double l2d2 = d2 + l2;
preFactor = 8. * l2 * d * (1. - 2 * l2 / l2d2) / (l2d2 * l2d2);
// preFactor = -8.*((l2-d2)/pow(l2+d2,3))*d*l2;
} else {
return;
}
double *end1Coords = &(pos[dim * this->d_end1Idx]);
double *end2Coords = &(pos[dim * this->d_end2Idx]);
for (unsigned int i = 0; i < dim; i++) {
double dGrad;
if (d > 0.0) {
dGrad = d_weight * preFactor * (end1Coords[i] - end2Coords[i]) / d;
} else {
// FIX: this likely isn't right
dGrad = d_weight * preFactor * (end1Coords[i] - end2Coords[i]);
}
grad[dim * this->d_end1Idx + i] += dGrad;
grad[dim * this->d_end2Idx + i] -= dGrad;
}
}
}
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