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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
104 lines
2.9 KiB
C++
104 lines
2.9 KiB
C++
// $Id$
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//
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// Copyright (C) 2013 Paolo Tosco
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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 "DistanceConstraint.h"
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#include <cmath>
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#include <ForceField/ForceField.h>
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#include <RDGeneral/Invariant.h>
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namespace ForceFields {
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namespace UFF {
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DistanceConstraintContrib::DistanceConstraintContrib(
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ForceField *owner, unsigned int idx1, unsigned int idx2, double minLen,
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double maxLen, double forceConst) {
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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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PRECONDITION(maxLen >= minLen, "bad bounds");
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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_minLen = minLen;
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d_maxLen = maxLen;
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d_forceConstant = forceConst;
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}
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DistanceConstraintContrib::DistanceConstraintContrib(
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ForceField *owner, unsigned int idx1, unsigned int idx2, bool relative,
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double minLen, double maxLen, double forceConst) {
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PRECONDITION(owner, "bad owner");
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const RDGeom::PointPtrVect &pos = owner->positions();
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URANGE_CHECK(idx1, pos.size());
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URANGE_CHECK(idx2, pos.size());
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PRECONDITION(maxLen >= minLen, "bad bounds");
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double dist = 0.0;
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if (relative) {
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RDGeom::Point3D p1 = *((RDGeom::Point3D *)pos[idx1]);
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RDGeom::Point3D p2 = *((RDGeom::Point3D *)pos[idx2]);
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dist = (p1 - p2).length();
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}
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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_minLen = std::max(dist + minLen, 0.0);
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d_maxLen = std::max(dist + maxLen, 0.0);
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d_forceConstant = forceConst;
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}
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double DistanceConstraintContrib::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 dist = dp_forceField->distance(d_end1Idx, d_end2Idx, pos);
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double distTerm = 0.0;
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if (dist < d_minLen) {
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distTerm = d_minLen - dist;
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} else if (dist > d_maxLen) {
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distTerm = dist - d_maxLen;
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}
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double res = 0.5 * d_forceConstant * distTerm * distTerm;
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return res;
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}
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void DistanceConstraintContrib::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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double dist = dp_forceField->distance(d_end1Idx, d_end2Idx, pos);
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double preFactor = 0.0;
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if (dist < d_minLen) {
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preFactor = dist - d_minLen;
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} else if (dist > d_maxLen) {
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preFactor = dist - d_maxLen;
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} else {
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return;
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}
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preFactor *= d_forceConstant;
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double *end1Coords = &(pos[3 * d_end1Idx]);
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double *end2Coords = &(pos[3 * d_end2Idx]);
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for (unsigned int i = 0; i < 3; ++i) {
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double dGrad;
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dGrad =
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preFactor * (end1Coords[i] - end2Coords[i]) / std::max(dist, 1.0e-8);
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grad[3 * d_end1Idx + i] += dGrad;
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grad[3 * d_end2Idx + i] -= dGrad;
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}
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}
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}
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}
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