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// $Id$
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "TorsionAngle.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace MMFF {
namespace Utils {
double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &jPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint) {
RDGeom::Point3D r1 = iPoint - jPoint;
RDGeom::Point3D r2 = kPoint - jPoint;
RDGeom::Point3D r3 = jPoint - kPoint;
RDGeom::Point3D r4 = lPoint - kPoint;
RDGeom::Point3D t1 = r1.crossProduct(r2);
RDGeom::Point3D t2 = r3.crossProduct(r4);
double cosPhi = t1.dotProduct(t2) / (t1.length() * t2.length());
clipToOne(cosPhi);
return cosPhi;
}
boost::tuple<double, double, double> calcTorsionForceConstant(
const MMFFTor *mmffTorParams) {
return boost::make_tuple(mmffTorParams->V1, mmffTorParams->V2,
mmffTorParams->V3);
}
double calcTorsionEnergy(const double V1, const double V2, const double V3,
const double cosPhi) {
double cos2Phi = 2.0 * cosPhi * cosPhi - 1.0;
double cos3Phi = cosPhi * (2.0 * cos2Phi - 1.0);
return (0.5 *
(V1 * (1.0 + cosPhi) + V2 * (1.0 - cos2Phi) + V3 * (1.0 + cos3Phi)));
}
void calcTorsionGrad(RDGeom::Point3D *r, RDGeom::Point3D *t, double *d,
double **g, double &sinTerm, double &cosPhi) {
// -------
// dTheta/dx is trickier:
double dCos_dT[6] = {1.0 / d[0] * (t[1].x - cosPhi * t[0].x),
1.0 / d[0] * (t[1].y - cosPhi * t[0].y),
1.0 / d[0] * (t[1].z - cosPhi * t[0].z),
1.0 / d[1] * (t[0].x - cosPhi * t[1].x),
1.0 / d[1] * (t[0].y - cosPhi * t[1].y),
1.0 / d[1] * (t[0].z - cosPhi * t[1].z)};
g[0][0] += sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
g[0][1] += sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
g[0][2] += sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);
g[1][0] += sinTerm *
(dCos_dT[1] * (r[1].z - r[0].z) + dCos_dT[2] * (r[0].y - r[1].y) +
dCos_dT[4] * (-r[3].z) + dCos_dT[5] * (r[3].y));
g[1][1] += sinTerm *
(dCos_dT[0] * (r[0].z - r[1].z) + dCos_dT[2] * (r[1].x - r[0].x) +
dCos_dT[3] * (r[3].z) + dCos_dT[5] * (-r[3].x));
g[1][2] += sinTerm *
(dCos_dT[0] * (r[1].y - r[0].y) + dCos_dT[1] * (r[0].x - r[1].x) +
dCos_dT[3] * (-r[3].y) + dCos_dT[4] * (r[3].x));
g[2][0] += sinTerm *
(dCos_dT[1] * (r[0].z) + dCos_dT[2] * (-r[0].y) +
dCos_dT[4] * (r[3].z - r[2].z) + dCos_dT[5] * (r[2].y - r[3].y));
g[2][1] += sinTerm *
(dCos_dT[0] * (-r[0].z) + dCos_dT[2] * (r[0].x) +
dCos_dT[3] * (r[2].z - r[3].z) + dCos_dT[5] * (r[3].x - r[2].x));
g[2][2] += sinTerm *
(dCos_dT[0] * (r[0].y) + dCos_dT[1] * (-r[0].x) +
dCos_dT[3] * (r[3].y - r[2].y) + dCos_dT[4] * (r[2].x - r[3].x));
g[3][0] += sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
g[3][1] += sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
g[3][2] += sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
}
}
TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
unsigned int idx4,
const MMFFTor *mmffTorParams) {
PRECONDITION(owner, "bad owner");
PRECONDITION((idx1 != idx2) && (idx1 != idx3) && (idx1 != idx4) &&
(idx2 != idx3) && (idx2 != idx4) && (idx3 != idx4),
"degenerate points");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
URANGE_CHECK(idx4, owner->positions().size());
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
d_V1 = mmffTorParams->V1;
d_V2 = mmffTorParams->V2;
d_V3 = mmffTorParams->V3;
}
double TorsionAngleContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
return Utils::calcTorsionEnergy(
d_V1, d_V2, d_V3,
Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
}
void TorsionAngleContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
RDGeom::Point3D r[4] = {iPoint - jPoint, kPoint - jPoint, jPoint - kPoint,
lPoint - kPoint};
RDGeom::Point3D t[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
double d[2] = {t[0].length(), t[1].length()};
if (isDoubleZero(d[0]) || isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
clipToOne(cosPhi);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
double sin2Phi = 2.0 * sinPhi * cosPhi;
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
// dE/dPhi is independent of cartesians:
double dE_dPhi =
0.5 * (-(d_V1)*sinPhi + 2.0 * d_V2 * sin2Phi - 3.0 * d_V3 * sin3Phi);
#if 0
if(dE_dPhi!=dE_dPhi){
std::cout << "\tNaN in Torsion("<<d_at1Idx<<","<<d_at2Idx<<","<<d_at3Idx<<","<<d_at4Idx<<")"<< std::endl;
std::cout << "sin: " << sinPhi << std::endl;
std::cout << "cos: " << cosPhi << std::endl;
}
#endif
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm =
-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
}
}
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