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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 "Inversion.h"
#include "Params.h"
#include <math.h>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>
namespace ForceFields {
namespace UFF {
namespace Utils {
double calculateCosY(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &jPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint) {
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
rJI /= rJI.length();
rJK /= rJK.length();
rJL /= rJL.length();
RDGeom::Point3D n = rJI.crossProduct(rJK);
n /= n.length();
return n.dotProduct(rJL);
}
boost::tuple<double, double, double, double>
calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
double res = 0.0;
double C0 = 0.0;
double C1 = 0.0;
double C2 = 0.0;
// if the central atom is sp2 carbon, nitrogen or oxygen
if ((at2AtomicNum == 6) || (at2AtomicNum == 7) || (at2AtomicNum == 8)) {
C0 = 1.0;
C1 = -1.0;
C2 = 0.0;
res = (isCBoundToO ? 50.0 : 6.0);
} else {
// group 5 elements are not clearly explained in the UFF paper
// the following code was inspired by MCCCS Towhee's ffuff.F
double w0 = M_PI / 180.0;
switch (at2AtomicNum) {
// if the central atom is phosphorous
case 15:
w0 *= 84.4339;
break;
// if the central atom is arsenic
case 33:
w0 *= 86.9735;
break;
// if the central atom is antimonium
case 51:
w0 *= 87.7047;
break;
// if the central atom is bismuth
case 83:
w0 *= 90.0;
break;
}
C2 = 1.0;
C1 = -4.0 * cos(w0);
C0 = -(C1 * cos(w0) + C2 * cos(2.0 * w0));
res = 22.0 / (C0 + C1 + C2);
}
res /= 3.0;
return boost::make_tuple(res, C0, C1, C2);
}
} // end of namespace Utils
InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
unsigned int idx4, int at2AtomicNum,
bool isCBoundToO, double oobForceScalingFactor) {
PRECONDITION(owner, "bad owner");
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;
boost::tuple<double, double, double, double> invCoeffForceCon =
Utils::calcInversionCoefficientsAndForceConstant(at2AtomicNum,
isCBoundToO);
d_forceConstant = oobForceScalingFactor * boost::tuples::get<0>(invCoeffForceCon);
d_C0 = boost::tuples::get<1>(invCoeffForceCon);
d_C1 = boost::tuples::get<2>(invCoeffForceCon);
d_C2 = boost::tuples::get<3>(invCoeffForceCon);
}
double InversionContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
RDGeom::Point3D p1(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double cosY = Utils::calculateCosY(p1, p2, p3, p4);
double sinYSq = 1.0 - cosY * cosY;
double sinY = ((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0);
// cos(2 * W) = 2 * cos(W) * cos(W) - 1 = 2 * sin(W) * sin(W) - 1
double cos2W = 2.0 * sinY * sinY - 1.0;
double res = d_forceConstant * (d_C0 + d_C1 * sinY + d_C2 * cos2W);
// std::cout << d_at1Idx + 1 << "," << d_at2Idx + 1 << "," << d_at3Idx + 1 <<
// "," << d_at4Idx + 1 << " Inversion: " << res << std::endl;
return res;
}
void InversionContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D p1(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = p1 - p2;
RDGeom::Point3D rJK = p3 - p2;
RDGeom::Point3D rJL = p4 - p2;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double cosY = n.dotProduct(rJL);
clipToOne(cosY);
double sinYSq = 1.0 - cosY * cosY;
double sinY = std::max(((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0), 1.0e-8);
double cosTheta = rJI.dotProduct(rJK);
clipToOne(cosTheta);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta =
std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
// sin(2 * W) = 2 * sin(W) * cos(W) = 2 * cos(Y) * sin(Y)
double dE_dW = -d_forceConstant * (d_C1 * cosY - 4.0 * d_C2 * cosY * sinY);
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = sinY * sinTheta;
double term2 = cosY / (sinY * sinThetaSq);
double tg1[3] = {(t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI};
double tg3[3] = {(t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK};
double tg4[3] = {(t3.x / term1 - rJL.x * cosY / sinY) / dJL,
(t3.y / term1 - rJL.y * cosY / sinY) / dJL,
(t3.z / term1 - rJL.z * cosY / sinY) / dJL};
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dW * tg1[i];
g2[i] += -dE_dW * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dW * tg3[i];
g4[i] += dE_dW * tg4[i];
}
}
}
}
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