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af6347963f
* Condense MMFF electrostatics and contrib instances. Previously, a separate contrib had been added for each common term. Each of these required a separate allocation, and a separate dynamic dispatch on call. This change moves to an SOA style, making data access contiguous and drastically reducing the number of calls. * Make suggested copyright fixes and svn artifact removals
189 lines
7.0 KiB
C++
189 lines
7.0 KiB
C++
//
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// Copyright (C) 2013-2025 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 "TorsionAngle.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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namespace ForceFields {
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namespace MMFF {
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namespace Utils {
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double calcTorsionCosPhi(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 r1 = iPoint - jPoint;
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RDGeom::Point3D r2 = kPoint - jPoint;
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RDGeom::Point3D r3 = jPoint - kPoint;
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RDGeom::Point3D r4 = lPoint - kPoint;
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RDGeom::Point3D t1 = r1.crossProduct(r2);
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RDGeom::Point3D t2 = r3.crossProduct(r4);
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auto t1_len = t1.length();
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auto t2_len = t2.length();
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if (isDoubleZero(t1_len) || isDoubleZero(t2_len)) {
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return 0.0;
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}
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double cosPhi = t1.dotProduct(t2) / (t1_len * t2_len);
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clipToOne(cosPhi);
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return cosPhi;
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}
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std::tuple<double, double, double> calcTorsionForceConstant(
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const MMFFTor *mmffTorParams) {
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return std::make_tuple(mmffTorParams->V1, mmffTorParams->V2,
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mmffTorParams->V3);
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}
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double calcTorsionEnergy(const double V1, const double V2, const double V3,
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const double cosPhi) {
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double cos2Phi = 2.0 * cosPhi * cosPhi - 1.0;
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double cos3Phi = cosPhi * (2.0 * cos2Phi - 1.0);
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return (0.5 *
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(V1 * (1.0 + cosPhi) + V2 * (1.0 - cos2Phi) + V3 * (1.0 + cos3Phi)));
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}
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void calcTorsionGrad(RDGeom::Point3D *r, RDGeom::Point3D *t, double *d,
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double **g, double &sinTerm, double &cosPhi) {
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// -------
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// dTheta/dx is trickier:
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double dCos_dT[6] = {1.0 / d[0] * (t[1].x - cosPhi * t[0].x),
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1.0 / d[0] * (t[1].y - cosPhi * t[0].y),
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1.0 / d[0] * (t[1].z - cosPhi * t[0].z),
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1.0 / d[1] * (t[0].x - cosPhi * t[1].x),
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1.0 / d[1] * (t[0].y - cosPhi * t[1].y),
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1.0 / d[1] * (t[0].z - cosPhi * t[1].z)};
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g[0][0] += sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
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g[0][1] += sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
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g[0][2] += sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);
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g[1][0] += sinTerm *
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(dCos_dT[1] * (r[1].z - r[0].z) + dCos_dT[2] * (r[0].y - r[1].y) +
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dCos_dT[4] * (-r[3].z) + dCos_dT[5] * (r[3].y));
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g[1][1] += sinTerm *
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(dCos_dT[0] * (r[0].z - r[1].z) + dCos_dT[2] * (r[1].x - r[0].x) +
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dCos_dT[3] * (r[3].z) + dCos_dT[5] * (-r[3].x));
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g[1][2] += sinTerm *
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(dCos_dT[0] * (r[1].y - r[0].y) + dCos_dT[1] * (r[0].x - r[1].x) +
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dCos_dT[3] * (-r[3].y) + dCos_dT[4] * (r[3].x));
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g[2][0] += sinTerm *
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(dCos_dT[1] * (r[0].z) + dCos_dT[2] * (-r[0].y) +
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dCos_dT[4] * (r[3].z - r[2].z) + dCos_dT[5] * (r[2].y - r[3].y));
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g[2][1] += sinTerm *
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(dCos_dT[0] * (-r[0].z) + dCos_dT[2] * (r[0].x) +
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dCos_dT[3] * (r[2].z - r[3].z) + dCos_dT[5] * (r[3].x - r[2].x));
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g[2][2] += sinTerm *
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(dCos_dT[0] * (r[0].y) + dCos_dT[1] * (-r[0].x) +
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dCos_dT[3] * (r[3].y - r[2].y) + dCos_dT[4] * (r[2].x - r[3].x));
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g[3][0] += sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
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g[3][1] += sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
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g[3][2] += sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
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}
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} // namespace Utils
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TorsionAngleContrib::TorsionAngleContrib(ForceField *owner) {
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PRECONDITION(owner, "bad owner");
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dp_forceField = owner;
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}
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void TorsionAngleContrib::addTerm(
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unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4,
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const ForceFields::MMFF::MMFFTor *mmffTorParams) {
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PRECONDITION((idx1 != idx2) && (idx1 != idx3) && (idx1 != idx4) &&
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(idx2 != idx3) && (idx2 != idx4) && (idx3 != idx4),
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"degenerate points");
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URANGE_CHECK(idx1, dp_forceField->positions().size());
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URANGE_CHECK(idx2, dp_forceField->positions().size());
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URANGE_CHECK(idx3, dp_forceField->positions().size());
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URANGE_CHECK(idx4, dp_forceField->positions().size());
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d_at1Idx.push_back(idx1);
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d_at2Idx.push_back(idx2);
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d_at3Idx.push_back(idx3);
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d_at4Idx.push_back(idx4);
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d_V1.push_back(mmffTorParams->V1);
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d_V2.push_back(mmffTorParams->V2);
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d_V3.push_back(mmffTorParams->V3);
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}
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double TorsionAngleContrib::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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const int numTorsions = d_at1Idx.size();
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double totalEnergy = 0.0;
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for (int i = 0; i < numTorsions; ++i) {
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const int16_t at1Idx = d_at1Idx[i];
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const int16_t at2Idx = d_at2Idx[i];
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const int16_t at3Idx = d_at3Idx[i];
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const int16_t at4Idx = d_at4Idx[i];
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RDGeom::Point3D iPoint(pos[3 * at1Idx], pos[3 * at1Idx + 1],
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pos[3 * at1Idx + 2]);
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RDGeom::Point3D jPoint(pos[3 * at2Idx], pos[3 * at2Idx + 1],
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pos[3 * at2Idx + 2]);
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RDGeom::Point3D kPoint(pos[3 * at3Idx], pos[3 * at3Idx + 1],
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pos[3 * at3Idx + 2]);
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RDGeom::Point3D lPoint(pos[3 * at4Idx], pos[3 * at4Idx + 1],
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pos[3 * at4Idx + 2]);
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totalEnergy += Utils::calcTorsionEnergy(
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d_V1[i], d_V2[i], d_V3[i],
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Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
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}
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return totalEnergy;
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}
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void TorsionAngleContrib::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 d[2];
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double cosPhi;
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const int numTorsions = d_at1Idx.size();
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for (int i = 0; i < numTorsions; ++i) {
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const int16_t at1Idx = d_at1Idx[i];
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const int16_t at2Idx = d_at2Idx[i];
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const int16_t at3Idx = d_at3Idx[i];
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const int16_t at4Idx = d_at4Idx[i];
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double *g[4] = {&(grad[3 * at1Idx]), &(grad[3 * at2Idx]),
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&(grad[3 * at3Idx]), &(grad[3 * at4Idx])};
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RDGeom::Point3D r[4];
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RDGeom::Point3D t[2];
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RDKit::ForceFieldsHelper::computeDihedral(
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pos, at1Idx, at2Idx, at3Idx, at4Idx, nullptr, &cosPhi, r, t, d);
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double sinPhiSq = 1.0 - cosPhi * cosPhi;
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double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
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double sin2Phi = 2.0 * sinPhi * cosPhi;
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double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
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// dE/dPhi is independent of cartesians:
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double dE_dPhi = 0.5 * (-(d_V1[i]) * sinPhi + 2.0 * d_V2[i] * sin2Phi -
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3.0 * d_V3[i] * sin3Phi);
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// FIX: use a tolerance here
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// this is hacky, but it's per the
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// recommendation from Niketic and Rasmussen:
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double sinTerm =
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-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
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Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
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}
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}
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} // namespace MMFF
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} // namespace ForceFields
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