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98 lines
3.7 KiB
C++
98 lines
3.7 KiB
C++
//
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// Copyright (c) 2024 Glysade Inc and other RDkit contributors
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include "chemdraw.h"
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#include <catch2/catch_all.hpp>
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#include "RDGeneral/test.h"
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <RDGeneral/FileParseException.h>
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#include <boost/algorithm/string.hpp>
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#include <RDGeneral/BadFileException.h>
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#include <GraphMol/SmilesParse/CanonicalizeStereoGroups.h>
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#include <filesystem>
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using namespace RDKit;
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using namespace RDKit::v2;
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TEST_CASE("Geometry") {
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std::string path =
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std::string(getenv("RDBASE")) + "/External/ChemDraw/test_data/";
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SECTION("R/S Tetrahedral") {
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//_sleep(10 * 1000);
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{
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auto fname = path + "geometry-tetrahedral.cdxml";
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auto mols = MolsFromChemDrawFile(fname);
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REQUIRE(mols.size()); // [C@H]1(C2)[C@@H]2C1
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auto mol = "[C@H]1(C2)[C@@H]2C1"_smiles;
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auto smi = MolToSmiles(*mol);
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REQUIRE(smi == MolToSmiles(*mols[0]));
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}
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{
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auto fname = path + "geometry-tetrahedral-2.cdxml";
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auto mols = MolsFromChemDrawFile(fname);
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REQUIRE(mols.size());
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auto mol = "[C@H]1(C2)[C@@H]2C1"_smiles;
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auto smi = MolToSmiles(*mol);
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REQUIRE(smi == MolToSmiles(*mols[0]));
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}
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{
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auto fname = path + "geometry-tetrahedral-3.cdxml";
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auto mols = MolsFromChemDrawFile(fname);
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REQUIRE(mols.size());
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auto mol = "C1CC[C@H]2CCCC[C@@H]2C1"_smiles;
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auto smi = MolToSmiles(*mol);
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REQUIRE(smi == MolToSmiles(*mols[0]));
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}
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/* this one we still get wrong...
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{
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auto fname = path + "geometry-tetrahedral-4.cdxml";
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auto mols = MolsFromChemDrawFile(fname);
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REQUIRE(mols.size());
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auto mol =
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"CC(S[C@@H]1CC2=C([H])C(CC[C@]2(C)[C@@]3([H])CC([H])([H])[C@]4(C)[C@](OC5=O)(CC5([H])[H])CC[C@@]4([H])[C@]13[H])=O)=O"_smiles;
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auto smi = MolToSmiles(*mol);
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std::cerr << "** " << smi << std::endl;
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REQUIRE(smi == MolToSmiles(*mols[0]));
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}
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*/
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}
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}
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