mirror of
https://github.com/rdkit/rdkit.git
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a45d4d9857
* 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
114 lines
4.3 KiB
C++
114 lines
4.3 KiB
C++
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//
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// Copyright (C) 2024 Niels Maeder 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 <cmath>
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#include <RDGeneral/test.h>
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#include <catch2/catch_all.hpp>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/ForceFieldHelpers/FFConvenience.h>
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#include <ForceField/AngleConstraints.h>
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#include <ForceField/DistanceConstraints.h>
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#include <ForceField/UFF/Params.h>
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using namespace RDKit;
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namespace {
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double get_dist(const ROMol &mol, unsigned int idx1, unsigned int idx2) {
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return (mol.getConformer().getAtomPos(idx1) -
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mol.getConformer().getAtomPos(idx2))
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.length();
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}
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double get_angle(const ROMol &mol, unsigned int idx1, unsigned int idx2,
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unsigned int idx3) {
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const auto &pos1 = mol.getConformer().getAtomPos(idx1);
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const auto &pos2 = mol.getConformer().getAtomPos(idx2);
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const auto &pos3 = mol.getConformer().getAtomPos(idx3);
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const RDGeom::Point3D r[2] = {pos1 - pos2, pos3 - pos2};
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const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()),
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std::max(1.0e-5, r[1].lengthSq())};
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double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
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cosTheta = std::clamp(cosTheta, -1.0, 1.0);
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return ForceFields::UFF::RAD2DEG * acos(cosTheta);
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}
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} // namespace
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TEST_CASE("Test DistanceConstraintContribs") {
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auto mol =
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"CCCO |"
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"(-1.28533,-0.0567758,0.434662;-0.175447,0.695786,-0.299881;"
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"0.918409,-0.342619,-0.555572;1.30936,-0.801512,0.71705)|"_smiles;
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REQUIRE(mol);
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SECTION("absolute distance minimization") {
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auto forceField = ForceFieldsHelper::createEmptyForceFieldForMol(*mol);
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REQUIRE(forceField);
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forceField->initialize();
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auto contribs = std::make_unique<ForceFields::DistanceConstraintContribs>(
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forceField.get());
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contribs->addContrib(0, 1, 3.0, 3.0, 1);
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contribs->addContrib(0, 2, 4.0, 4.0, 1);
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forceField->contribs().push_back(std::move(contribs));
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CHECK(forceField->minimize() == 0);
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CHECK(feq(get_dist(*mol, 0, 1), 3.0));
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CHECK(feq(get_dist(*mol, 0, 2), 4.0));
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}
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SECTION("relative distance minimization") {
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auto forceField = ForceFieldsHelper::createEmptyForceFieldForMol(*mol);
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REQUIRE(forceField);
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forceField->initialize();
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auto contribs = std::make_unique<ForceFields::DistanceConstraintContribs>(
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forceField.get());
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contribs->addContrib(0, 1, true, 1.0, 1.0, 1);
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contribs->addContrib(0, 2, false, 4.0, 4.0, 1);
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forceField->contribs().push_back(std::move(contribs));
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auto before = get_dist(*mol, 0, 1);
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CHECK(forceField->minimize() == 0);
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CHECK(feq(get_dist(*mol, 0, 1), 1.0 + before));
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CHECK(feq(get_dist(*mol, 0, 2), 4.0));
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}
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}
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TEST_CASE("Test AngleConstraintContribs") {
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auto mol =
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"CCCO |"
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"(-1.28533,-0.0567758,0.434662;-0.175447,0.695786,-0.299881;"
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"0.918409,-0.342619,-0.555572;1.30936,-0.801512,0.71705)|"_smiles;
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REQUIRE(mol);
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SECTION("absolute angle minimization") {
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auto forceField = ForceFieldsHelper::createEmptyForceFieldForMol(*mol);
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REQUIRE(forceField);
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forceField->initialize();
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auto contribs = std::make_unique<ForceFields::AngleConstraintContribs>(
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forceField.get());
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contribs->addContrib(0, 1, 2, 120.0, 120.0, 1);
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contribs->addContrib(1, 2, 3, 160.0, 160.0, 1);
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forceField->contribs().push_back(std::move(contribs));
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CHECK(forceField->minimize() == 0);
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CHECK(feq(get_angle(*mol, 0, 1, 2), 120.0));
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CHECK(feq(get_angle(*mol, 1, 2, 3), 160.0));
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}
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SECTION("relative angle minimization") {
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auto forceField = ForceFieldsHelper::createEmptyForceFieldForMol(*mol);
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REQUIRE(forceField);
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forceField->initialize();
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auto contribs = std::make_unique<ForceFields::AngleConstraintContribs>(
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forceField.get());
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contribs->addContrib(0, 1, 2, true, 5.0, 5.0, 1);
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contribs->addContrib(1, 2, 3, false, 160.0, 160.0, 1);
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forceField->contribs().push_back(std::move(contribs));
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auto before = get_angle(*mol, 0, 1, 2);
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CHECK(forceField->minimize() == 0);
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CHECK(feq(get_angle(*mol, 0, 1, 2), before + 5.0));
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CHECK(feq(get_angle(*mol, 1, 2, 3), 160.0));
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}
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}
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