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//
// Copyright (c) 2025 Glysade Inc and other RDkit contributors
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include "chemdraw.h"
#include <catch2/catch_all.hpp>
#include "RDGeneral/test.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <RDGeneral/FileParseException.h>
#include <boost/algorithm/string.hpp>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/SmilesParse/CanonicalizeStereoGroups.h>
using namespace RDKit;
using namespace RDKit::v2;
TEST_CASE("Round TRIP") {
std::string path =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/";
std::string code_path = std::string(getenv("RDBASE"));
// Eventually this catch test is to see if round tripping mol 3d -> chemdraw returns
// reasonable coords, however chemdraw seems to forget about the original scale
// and converts to pixel drawing coords, so this test is kind of meaningless
SECTION("3D structs") {
auto fname =
code_path + "/Code/GraphMol/FileParsers/test_data/Issue3514824.mol";
auto mol = MolFileToMol(fname);
REQUIRE(mol);
auto &conf = mol->getConformer(0);
for (auto bond : mol->bonds()) {
auto p1 = conf.getAtomPos(bond->getBeginAtomIdx());
auto p2 = conf.getAtomPos(bond->getEndAtomIdx());
auto length = (p1 - p2).length();
std::cerr << bond->getIdx() << " : " << length << std::endl;
;
}
std::cerr << "----------" << std::endl;
{
auto fname2 =
code_path + "/Code/GraphMol/FileParsers/test_data/Issue3514824.cdxml";
auto mols = MolsFromChemDrawFile(fname2);
auto &conf2 = mols[0]->getConformer(0);
for (auto bond : mols[0]->bonds()) {
auto p1 = conf2.getAtomPos(bond->getBeginAtomIdx());
auto p2 = conf2.getAtomPos(bond->getEndAtomIdx());
auto length = (p1 - p2).length();
std::cerr << bond->getIdx() << " : " << length << std::endl;
}
}
std::cerr << "----------" << std::endl;
{
auto cdx = MolToChemDrawBlock(*mol);
auto mols = MolsFromChemDrawBlock(cdx);
auto &conf2 = mols[0]->getConformer(0);
for (auto bond : mols[0]->bonds()) {
auto p1 = conf2.getAtomPos(bond->getBeginAtomIdx());
auto p2 = conf2.getAtomPos(bond->getEndAtomIdx());
auto length = (p1 - p2).length();
std::cerr << bond->getIdx() << " : " << length << std::endl;
}
}
delete mol;
}
}
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