mirror of
https://github.com/rdkit/rdkit.git
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ba4a48ce05
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp which caused misassignment of atom types in CYGUAN01 upon shuffling the order of atoms in the validation SDF files - added checks for acos and asin function parameters to be within a (-1, 1) range
105 lines
3.0 KiB
C++
105 lines
3.0 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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{
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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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{
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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, const double distance)
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{
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double distTerm = distance - r0;
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double distTerm2 = distTerm * distTerm;
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double const c1 = 143.9325;
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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, const unsigned int idx2,
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const MMFFBond *mmffBondParams)
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{
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PRECONDITION(owner,"bad owner");
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RANGE_CHECK(0, idx1, owner->positions().size() - 1);
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RANGE_CHECK(0, idx2, owner->positions().size() - 1);
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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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{
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PRECONDITION(dp_forceField,"no owner");
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PRECONDITION(pos,"bad vector");
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return Utils::calcBondStretchEnergy(d_r0, d_kb,
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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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{
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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
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(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 = 143.9325;
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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 = 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)
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? (dE_dr * (at1Coords[i] - at2Coords[i]) / dist) : 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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