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* add angles and distances * add Inversions * add torsiona angle contribs * use new contribs in test * use new inversion and torsion contribs in dg * use new distance contribs in dg * use new angle constraints in dg * use new constraints in FF tests * update docstrings * remove unused import * include new contribs * cleanup includes * make changes requested by @greglandrum * use std::move instead of release
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| // | ||
| // Copyright (C) 2024 Niels Maeder and other RDKit contributors | ||
| // | ||
| // @@ 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. | ||
| // | ||
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| #include "AngleConstraints.h" | ||
| #include "ForceField.h" | ||
| #include <cmath> | ||
| #include <RDGeneral/Invariant.h> | ||
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| #ifndef M_PI | ||
| #define M_PI 3.14159265358979323846 | ||
| #endif | ||
|
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| namespace ForceFields { | ||
| constexpr double RAD2DEG = 180.0 / M_PI; | ||
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| AngleConstraintContribs::AngleConstraintContribs(ForceField *owner) { | ||
| PRECONDITION(owner, "bad owner"); | ||
| dp_forceField = owner; | ||
| } | ||
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| void AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, | ||
| unsigned int idx3, double minAngleDeg, | ||
| double maxAngleDeg, | ||
| double forceConst) { | ||
| RANGE_CHECK(0.0, minAngleDeg, 180.0); | ||
| RANGE_CHECK(0.0, maxAngleDeg, 180.0); | ||
| URANGE_CHECK(idx1, dp_forceField->positions().size()); | ||
| URANGE_CHECK(idx2, dp_forceField->positions().size()); | ||
| URANGE_CHECK(idx3, dp_forceField->positions().size()); | ||
| PRECONDITION(maxAngleDeg >= minAngleDeg, | ||
| "minAngleDeg must be <= maxAngleDeg"); | ||
| d_contribs.emplace_back(idx1, idx2, idx3, minAngleDeg, maxAngleDeg, | ||
| forceConst); | ||
| } | ||
| void AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, | ||
| unsigned int idx3, bool relative, | ||
| double minAngleDeg, double maxAngleDeg, | ||
| double forceConst) { | ||
| const RDGeom::PointPtrVect &pos = dp_forceField->positions(); | ||
| URANGE_CHECK(idx1, pos.size()); | ||
| URANGE_CHECK(idx2, pos.size()); | ||
| URANGE_CHECK(idx3, pos.size()); | ||
| PRECONDITION(maxAngleDeg >= minAngleDeg, | ||
| "minAngleDeg must be <= maxAngleDeg"); | ||
| if (relative) { | ||
| const RDGeom::Point3D &p1 = *((RDGeom::Point3D *)pos[idx1]); | ||
| const RDGeom::Point3D &p2 = *((RDGeom::Point3D *)pos[idx2]); | ||
| const RDGeom::Point3D &p3 = *((RDGeom::Point3D *)pos[idx3]); | ||
| const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2}; | ||
| const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()), | ||
| std::max(1.0e-5, r[1].lengthSq())}; | ||
| double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]); | ||
| cosTheta = std::clamp(cosTheta, -1.0, 1.0); | ||
| const double angle = RAD2DEG * acos(cosTheta); | ||
| minAngleDeg += angle; | ||
| maxAngleDeg += angle; | ||
| } | ||
| RANGE_CHECK(0.0, minAngleDeg, 180.0); | ||
| RANGE_CHECK(0.0, maxAngleDeg, 180.0); | ||
| d_contribs.emplace_back(idx1, idx2, idx3, minAngleDeg, maxAngleDeg, | ||
| forceConst); | ||
| } | ||
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| double AngleConstraintContribs::computeAngleTerm( | ||
| const double &angle, const AngleConstraintContribsParams &contrib) const { | ||
| double angleTerm = 0.0; | ||
| if (angle < contrib.minAngle) { | ||
| angleTerm = angle - contrib.minAngle; | ||
| } else if (angle > contrib.maxAngle) { | ||
| angleTerm = angle - contrib.maxAngle; | ||
| } | ||
| return angleTerm; | ||
| } | ||
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| double AngleConstraintContribs::getEnergy(double *pos) const { | ||
| PRECONDITION(dp_forceField, "no owner"); | ||
| PRECONDITION(pos, "bad vector"); | ||
| double accum = 0.0; | ||
| for (const auto &contrib : d_contribs) { | ||
| const RDGeom::Point3D p1(pos[3 * contrib.idx1], pos[3 * contrib.idx1 + 1], | ||
| pos[3 * contrib.idx1 + 2]); | ||
| const RDGeom::Point3D p2(pos[3 * contrib.idx2], pos[3 * contrib.idx2 + 1], | ||
| pos[3 * contrib.idx2 + 2]); | ||
| const RDGeom::Point3D p3(pos[3 * contrib.idx3], pos[3 * contrib.idx3 + 1], | ||
| pos[3 * contrib.idx3 + 2]); | ||
| const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2}; | ||
| const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()), | ||
| std::max(1.0e-5, r[1].lengthSq())}; | ||
| double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]); | ||
| cosTheta = std::clamp(cosTheta, -1.0, 1.0); | ||
| const double angle = RAD2DEG * acos(cosTheta); | ||
| const double angleTerm = computeAngleTerm(angle, contrib); | ||
| accum += contrib.forceConstant * angleTerm * angleTerm; | ||
| } | ||
| return accum; | ||
| } | ||
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| void AngleConstraintContribs::getGrad(double *pos, double *grad) const { | ||
| PRECONDITION(dp_forceField, "no owner"); | ||
| PRECONDITION(pos, "bad vector"); | ||
| PRECONDITION(grad, "bad vector"); | ||
| for (const auto &contrib : d_contribs) { | ||
| const RDGeom::Point3D p1(pos[3 * contrib.idx1], pos[3 * contrib.idx1 + 1], | ||
| pos[3 * contrib.idx1 + 2]); | ||
| const RDGeom::Point3D p2(pos[3 * contrib.idx2], pos[3 * contrib.idx2 + 1], | ||
| pos[3 * contrib.idx2 + 2]); | ||
| const RDGeom::Point3D p3(pos[3 * contrib.idx3], pos[3 * contrib.idx3 + 1], | ||
| pos[3 * contrib.idx3 + 2]); | ||
| const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2}; | ||
| const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()), | ||
| std::max(1.0e-5, r[1].lengthSq())}; | ||
| double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]); | ||
| cosTheta = std::clamp(cosTheta, -1.0, 1.0); | ||
| const double angle = RAD2DEG * acos(cosTheta); | ||
| const double angleTerm = computeAngleTerm(angle, contrib); | ||
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| const double dE_dTheta = 2.0 * RAD2DEG * contrib.forceConstant * angleTerm; | ||
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| const RDGeom::Point3D rp = r[1].crossProduct(r[0]); | ||
| const double prefactor = dE_dTheta / std::max(1.0e-5, rp.length()); | ||
| const double t[2] = {-prefactor / rLengthSq[0], prefactor / rLengthSq[1]}; | ||
| RDGeom::Point3D dedp[3]; | ||
| dedp[0] = r[0].crossProduct(rp) * t[0]; | ||
| dedp[2] = r[1].crossProduct(rp) * t[1]; | ||
| dedp[1] = -dedp[0] - dedp[2]; | ||
| double *g[3] = {&(grad[3 * contrib.idx1]), &(grad[3 * contrib.idx2]), | ||
| &(grad[3 * contrib.idx3])}; | ||
| for (unsigned int i = 0; i < 3; ++i) { | ||
| g[i][0] += dedp[i].x; | ||
| g[i][1] += dedp[i].y; | ||
| g[i][2] += dedp[i].z; | ||
| } | ||
| } | ||
| } | ||
|
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| } // namespace ForceFields |
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