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7488840ac4
* Fixes atom documentation * Fixes #1461 This is a complicated one. Basically URANGE_CHECK when used on unsigned integers has a problem when the size of the range it’s checking is 0. The standard operations is to check URANGE(num, size-1) Which (for unsigned integers) obviously rolls over. This fixes all usage cases to be URANGE(num+1, size) And fixes the bugs found. (addBond and the mmff tests) * Fixes #1461 - Updates URANGE_CHECK to be 0<=x<hi
98 lines
2.8 KiB
C++
98 lines
2.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "DistViolationContrib.h"
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#include <ForceField/ForceField.h>
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#include <RDGeneral/Invariant.h>
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namespace DistGeom {
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DistViolationContrib::DistViolationContrib(ForceFields::ForceField *owner,
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unsigned int idx1, unsigned int idx2,
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double ub, double lb,
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double weight) {
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PRECONDITION(owner, "bad owner");
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URANGE_CHECK(idx1, owner->positions().size());
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URANGE_CHECK(idx2, owner->positions().size());
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dp_forceField = owner;
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d_end1Idx = idx1;
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d_end2Idx = idx2;
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d_ub = ub;
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d_lb = lb;
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d_weight = weight;
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}
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double DistViolationContrib::getEnergy(double *pos) const {
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PRECONDITION(dp_forceField, "no owner");
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PRECONDITION(pos, "bad vector");
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double d =
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this->dp_forceField->distance(this->d_end1Idx, this->d_end2Idx, pos);
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double val = 0.0;
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if (d > d_ub) {
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val = ((d * d) / (d_ub * d_ub)) - 1.0;
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} else if (d < d_lb) {
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val = ((2 * d_lb * d_lb) / (d_lb * d_lb + d * d)) - 1.0;
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}
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double res;
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if (val > 0.0) {
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res = d_weight * val * val;
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} else {
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res = 0;
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}
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// if (res > 0.1) {
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// std::cerr << "dvc:getEnergy: " << this->d_end1Idx << "-" <<
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// this->d_end2Idx
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// << ": " << d_lb << "-" << d_ub << " " << d << " => " << res
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// << std::endl;
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// }
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return res;
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}
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void DistViolationContrib::getGrad(double *pos, double *grad) const {
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PRECONDITION(dp_forceField, "no owner");
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PRECONDITION(pos, "bad vector");
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PRECONDITION(grad, "bad vector");
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unsigned int dim = this->dp_forceField->dimension();
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double d =
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this->dp_forceField->distance(this->d_end1Idx, this->d_end2Idx, pos);
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double preFactor = 0.0;
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if (d > d_ub) {
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double u2 = d_ub * d_ub;
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preFactor = 4. * (((d * d) / u2) - 1.0) * (d / u2);
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} else if (d < d_lb) {
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double d2 = d * d;
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double l2 = d_lb * d_lb;
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double l2d2 = d2 + l2;
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preFactor = 8. * l2 * d * (1. - 2 * l2 / l2d2) / (l2d2 * l2d2);
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// preFactor = -8.*((l2-d2)/pow(l2+d2,3))*d*l2;
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} else {
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return;
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}
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double *end1Coords = &(pos[dim * this->d_end1Idx]);
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double *end2Coords = &(pos[dim * this->d_end2Idx]);
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for (unsigned int i = 0; i < dim; i++) {
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double dGrad;
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if (d > 0.0) {
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dGrad = d_weight * preFactor * (end1Coords[i] - end2Coords[i]) / d;
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} else {
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// FIX: this likely isn't right
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dGrad = d_weight * preFactor * (end1Coords[i] - end2Coords[i]);
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}
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grad[dim * this->d_end1Idx + i] += dGrad;
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grad[dim * this->d_end2Idx + i] -= dGrad;
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}
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}
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}
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