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202 lines
6.9 KiB
C++
202 lines
6.9 KiB
C++
//
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// Copyright (C) 2013 Paolo Tosco and other RDKit contributors
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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 "Inversion.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 UFF {
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namespace Utils {
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double calculateCosY(const RDGeom::Point3D &iPoint,
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const RDGeom::Point3D &jPoint,
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const RDGeom::Point3D &kPoint,
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const RDGeom::Point3D &lPoint) {
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RDGeom::Point3D rJI = iPoint - jPoint;
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RDGeom::Point3D rJK = kPoint - jPoint;
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RDGeom::Point3D rJL = lPoint - jPoint;
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rJI /= rJI.length();
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rJK /= rJK.length();
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rJL /= rJL.length();
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RDGeom::Point3D n = rJI.crossProduct(rJK);
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n /= n.length();
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return n.dotProduct(rJL);
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}
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std::tuple<double, double, double, double>
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calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
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double res = 0.0;
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double C0 = 0.0;
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double C1 = 0.0;
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double C2 = 0.0;
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// if the central atom is sp2 carbon, nitrogen or oxygen
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if ((at2AtomicNum == 6) || (at2AtomicNum == 7) || (at2AtomicNum == 8)) {
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C0 = 1.0;
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C1 = -1.0;
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C2 = 0.0;
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res = (isCBoundToO ? 50.0 : 6.0);
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} else {
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// group 5 elements are not clearly explained in the UFF paper
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// the following code was inspired by MCCCS Towhee's ffuff.F
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double w0 = M_PI / 180.0;
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switch (at2AtomicNum) {
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// if the central atom is phosphorous
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case 15:
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w0 *= 84.4339;
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break;
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// if the central atom is arsenic
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case 33:
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w0 *= 86.9735;
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break;
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// if the central atom is antimonium
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case 51:
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w0 *= 87.7047;
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break;
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// if the central atom is bismuth
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case 83:
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w0 *= 90.0;
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break;
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}
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C2 = 1.0;
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C1 = -4.0 * cos(w0);
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C0 = -(C1 * cos(w0) + C2 * cos(2.0 * w0));
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res = 22.0 / (C0 + C1 + C2);
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}
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res /= 3.0;
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return std::make_tuple(res, C0, C1, C2);
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}
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} // end of namespace Utils
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InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1,
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unsigned int idx2, unsigned int idx3,
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unsigned int idx4, int at2AtomicNum,
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bool isCBoundToO,
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double oobForceScalingFactor) {
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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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URANGE_CHECK(idx3, owner->positions().size());
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URANGE_CHECK(idx4, 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_at3Idx = idx3;
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d_at4Idx = idx4;
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auto invCoeffForceCon = Utils::calcInversionCoefficientsAndForceConstant(
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at2AtomicNum, isCBoundToO);
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d_forceConstant = oobForceScalingFactor * std::get<0>(invCoeffForceCon);
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d_C0 = std::get<1>(invCoeffForceCon);
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d_C1 = std::get<2>(invCoeffForceCon);
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d_C2 = std::get<3>(invCoeffForceCon);
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}
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double InversionContrib::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 p1(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
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pos[3 * d_at1Idx + 2]);
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RDGeom::Point3D p2(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
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pos[3 * d_at2Idx + 2]);
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RDGeom::Point3D p3(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
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pos[3 * d_at3Idx + 2]);
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RDGeom::Point3D p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
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pos[3 * d_at4Idx + 2]);
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double cosY = Utils::calculateCosY(p1, p2, p3, p4);
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double sinYSq = 1.0 - cosY * cosY;
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double sinY = ((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0);
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// cos(2 * W) = 2 * cos(W) * cos(W) - 1 = 2 * sin(W) * sin(W) - 1
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double cos2W = 2.0 * sinY * sinY - 1.0;
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double res = d_forceConstant * (d_C0 + d_C1 * sinY + d_C2 * cos2W);
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// std::cout << d_at1Idx + 1 << "," << d_at2Idx + 1 << "," << d_at3Idx + 1 <<
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// "," << d_at4Idx + 1 << " Inversion: " << res << std::endl;
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return res;
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}
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void InversionContrib::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 p1(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
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pos[3 * d_at1Idx + 2]);
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RDGeom::Point3D p2(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
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pos[3 * d_at2Idx + 2]);
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RDGeom::Point3D p3(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
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pos[3 * d_at3Idx + 2]);
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RDGeom::Point3D p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
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pos[3 * d_at4Idx + 2]);
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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 *g3 = &(grad[3 * d_at3Idx]);
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double *g4 = &(grad[3 * d_at4Idx]);
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RDGeom::Point3D rJI = p1 - p2;
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RDGeom::Point3D rJK = p3 - p2;
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RDGeom::Point3D rJL = p4 - p2;
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double dJI = rJI.length();
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double dJK = rJK.length();
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double dJL = rJL.length();
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if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
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return;
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}
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rJI /= dJI;
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rJK /= dJK;
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rJL /= dJL;
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RDGeom::Point3D n = (-rJI).crossProduct(rJK);
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n /= n.length();
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double cosY = n.dotProduct(rJL);
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clipToOne(cosY);
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double sinYSq = 1.0 - cosY * cosY;
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double sinY = std::max(((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0), 1.0e-8);
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double cosTheta = rJI.dotProduct(rJK);
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clipToOne(cosTheta);
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double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
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double sinTheta =
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std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
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// sin(2 * W) = 2 * sin(W) * cos(W) = 2 * cos(Y) * sin(Y)
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double dE_dW = -d_forceConstant * (d_C1 * cosY - 4.0 * d_C2 * cosY * sinY);
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RDGeom::Point3D t1 = rJL.crossProduct(rJK);
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RDGeom::Point3D t2 = rJI.crossProduct(rJL);
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RDGeom::Point3D t3 = rJK.crossProduct(rJI);
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double term1 = sinY * sinTheta;
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double term2 = cosY / (sinY * sinThetaSq);
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double tg1[3] = {(t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
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(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
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(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI};
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double tg3[3] = {(t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
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(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
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(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK};
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double tg4[3] = {(t3.x / term1 - rJL.x * cosY / sinY) / dJL,
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(t3.y / term1 - rJL.y * cosY / sinY) / dJL,
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(t3.z / term1 - rJL.z * cosY / sinY) / dJL};
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for (unsigned int i = 0; i < 3; ++i) {
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g1[i] += dE_dW * tg1[i];
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g2[i] += -dE_dW * (tg1[i] + tg3[i] + tg4[i]);
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g3[i] += dE_dW * tg3[i];
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g4[i] += dE_dW * tg4[i];
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}
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}
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} // namespace UFF
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} // namespace ForceFields
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