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