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https://github.com/rdkit/rdkit.git
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497c32a147
* does not work * basically works (at least it seems to) needs more tesing and verification * optimization and improved tests passes local tests * response to review
122 lines
4.4 KiB
C++
122 lines
4.4 KiB
C++
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//
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// Copyright (C) 2024 Niels Maeder and other RDKit contributors
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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/FileParsers/FileParsers.h>
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#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
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#include <ForceField/MMFF/Params.h>
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#include <ForceField/MMFF/BondStretch.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include "FFConvenience.h"
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using namespace RDKit;
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TEST_CASE("Test empty force field") {
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auto mol =
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"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;
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REQUIRE(mol);
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SECTION("basics") {
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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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CHECK(forceField->minimize() == 0);
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CHECK(forceField->calcEnergy() == 0.0);
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REQUIRE(forceField->numPoints() == mol->getNumAtoms());
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REQUIRE(forceField->positions().size() == mol->getNumAtoms());
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auto dist = forceField->distance(0, 1);
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auto pos1 = mol->getConformer().getAtomPos(0);
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auto pos2 = mol->getConformer().getAtomPos(1);
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CHECK(dist == (pos2 - pos1).length());
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}
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SECTION("add contrib and minimize") {
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auto forceField = ForceFieldsHelper::createEmptyForceFieldForMol(*mol);
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forceField->initialize();
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auto params = ForceFields::MMFF::MMFFBond{6.0, 100.0};
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auto *contrib = new ForceFields::MMFF::BondStretchContrib(forceField.get(),
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0, 1, ¶ms);
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forceField->contribs().push_back(ForceFields::ContribPtr(contrib));
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CHECK(forceField->minimize() == 0);
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CHECK(std::round(forceField->distance(0, 1)) == 100);
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auto pos1 = mol->getConformer().getAtomPos(0);
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auto pos2 = mol->getConformer().getAtomPos(1);
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auto dist = (pos2 - pos1).length();
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CHECK(std::round(dist) == 100);
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}
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}
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TEST_CASE("github #7901") {
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#if 1
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auto mb = R"CTAB(Acetone, enolate form
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RDKit 3D
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9 8 0 0 0 0 0 0 0 0999 V2000
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-1.2143 -0.3494 0.0962 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1072 0.3398 0.0041 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1682 1.7287 0.0554 O 0 0 0 0 0 1 0 0 0 0 0 0
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1.2210 -0.3737 -0.1263 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.2311 -1.0203 0.9811 H 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3951 -0.9468 -0.8225 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.0281 0.3987 0.2006 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.1862 0.1115 -0.1943 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.8861 0.1115 -0.1943 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0
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2 3 1 0
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2 4 2 0
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1 5 1 0
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1 6 1 0
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1 7 1 0
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4 8 1 0
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4 9 1 0
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M CHG 1 3 -1
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M END)CTAB";
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#else
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auto mb = R"CTAB(Acetone, enolate form
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RDKit 3D
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9 8 0 0 0 0 0 0 0 0999 V2000
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-1.2143 -0.3494 0.0962 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1072 0.3398 0.0041 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1682 1.7287 0.0554 O 0 0 0 0 0 1 0 0 0 0 0 0
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1.2210 -0.3737 -0.1263 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.2311 -1.0203 0.9811 H 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3951 -0.9468 -0.8225 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.0281 0.3987 0.2006 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.1862 0.1115 -0.1943 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.8861 -1.3115 -0.1943 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0
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2 3 1 0
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2 4 2 0
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1 5 1 0
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1 6 1 0
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1 7 1 0
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4 8 1 0
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4 9 1 0
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M CHG 1 3 -1
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M END)CTAB";
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#endif
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v2::FileParsers::MolFileParserParams params;
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params.removeHs = false;
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auto mol = v2::FileParsers::MolFromMolBlock(mb, params);
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REQUIRE(mol);
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auto &conf = mol->getConformer();
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std::unique_ptr<ForceFields::ForceField> ff{UFF::constructForceField(*mol)};
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ff->initialize();
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auto needsMore = ff->minimize(200);
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CHECK(!needsMore);
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CHECK((conf.getAtomPos(7) - conf.getAtomPos(8)).length() > 1.80);
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CHECK(MolTransforms::getAngleDeg(conf, 1, 3, 8) > 110);
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CHECK(MolTransforms::getAngleDeg(conf, 1, 3, 7) > 110);
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CHECK(MolTransforms::getAngleDeg(conf, 7, 3, 8) > 110);
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} |