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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
101 lines
2.9 KiB
C++
101 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 "BondStretch.h"
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#include "Params.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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#include <RDGeneral/utils.h>
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namespace ForceFields {
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namespace MMFF {
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namespace Utils {
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double calcBondRestLength(const MMFFBond *mmffBondParams) {
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PRECONDITION(mmffBondParams, "bond parameters not found");
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return mmffBondParams->r0;
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}
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double calcBondForceConstant(const MMFFBond *mmffBondParams) {
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PRECONDITION(mmffBondParams, "bond parameters not found");
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return mmffBondParams->kb;
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}
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double calcBondStretchEnergy(const double r0, const double kb,
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const double distance) {
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double distTerm = distance - r0;
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double distTerm2 = distTerm * distTerm;
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double const c1 = MDYNE_A_TO_KCAL_MOL;
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double const cs = -2.0;
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double const c3 = 7.0 / 12.0;
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return (0.5 * c1 * kb * distTerm2 *
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(1.0 + cs * distTerm + c3 * cs * cs * distTerm2));
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}
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} // end of namespace Utils
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BondStretchContrib::BondStretchContrib(ForceField *owner,
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const unsigned int idx1,
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const unsigned int idx2,
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const MMFFBond *mmffBondParams) {
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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_at1Idx = idx1;
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d_at2Idx = idx2;
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d_r0 = mmffBondParams->r0;
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d_kb = mmffBondParams->kb;
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}
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double BondStretchContrib::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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return Utils::calcBondStretchEnergy(
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d_r0, d_kb, dp_forceField->distance(d_at1Idx, d_at2Idx, pos));
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}
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void BondStretchContrib::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_at1Idx, d_at2Idx, pos);
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double *at1Coords = &(pos[3 * d_at1Idx]);
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double *at2Coords = &(pos[3 * d_at2Idx]);
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double *g1 = &(grad[3 * d_at1Idx]);
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double *g2 = &(grad[3 * d_at2Idx]);
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double const cs = -2.0;
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double const c1 = MDYNE_A_TO_KCAL_MOL;
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double const c3 = 7.0 / 12.0;
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double distTerm = dist - d_r0;
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double dE_dr =
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c1 * d_kb * distTerm *
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(1.0 + 1.5 * cs * distTerm + 2.0 * c3 * cs * cs * distTerm * distTerm);
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double dGrad;
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for (unsigned int i = 0; i < 3; ++i) {
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dGrad = ((dist > 0.0) ? (dE_dr * (at1Coords[i] - at2Coords[i]) / dist)
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: d_kb * 0.01);
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g1[i] += dGrad;
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g2[i] -= dGrad;
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}
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}
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}
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}
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