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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
72 lines
2.1 KiB
C++
72 lines
2.1 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 "PositionConstraint.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 MMFF {
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PositionConstraintContrib::PositionConstraintContrib(ForceField *owner,
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unsigned int idx,
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double maxDispl,
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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(idx, pos.size());
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dp_forceField = owner;
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d_atIdx = idx;
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d_maxDispl = maxDispl;
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d_pos0 = *((RDGeom::Point3D *)pos[idx]);
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d_forceConstant = forceConst;
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}
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double PositionConstraintContrib::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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RDGeom::Point3D p(pos[3 * d_atIdx], pos[3 * d_atIdx + 1],
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pos[3 * d_atIdx + 2]);
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double dist = (p - d_pos0).length();
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double distTerm = (dist > d_maxDispl) ? dist - d_maxDispl : 0.0;
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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 PositionConstraintContrib::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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RDGeom::Point3D p(pos[3 * d_atIdx], pos[3 * d_atIdx + 1],
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pos[3 * d_atIdx + 2]);
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double dist = (p - d_pos0).length();
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double preFactor = 0.0;
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if (dist > d_maxDispl) {
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preFactor = dist - d_maxDispl;
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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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for (unsigned int i = 0; i < 3; ++i) {
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double dGrad = preFactor * (p[i] - d_pos0[i]) / std::max(dist, 1.0e-8);
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grad[3 * d_atIdx + i] += dGrad;
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}
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}
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}
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}
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