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//
// Copyright (C) 2018 T5 Informatics GmbH
// @@ 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 <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/StereoGroup.h>
#include "FileParsers.h"
#include "MolFileStereochem.h"
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <clocale>
#include <cstdlib>
#include <string>
#include <fstream>
#include <memory>
using namespace RDKit;
std::unique_ptr<RWMol> readTestFile(const std::string &baseName) {
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/" + baseName;
auto m = MolFileToMol(fName);
return std::unique_ptr<RWMol>(m);
}
void testOr() {
BOOST_LOG(rdInfoLog) << "testing extended stereo parsing with an OR block"
<< std::endl;
auto m = readTestFile("two_centers_or.mol");
TEST_ASSERT(m.get());
TEST_ASSERT(m->getNumAtoms() == 8);
auto stereo_groups = m->getStereoGroups();
TEST_ASSERT(stereo_groups.size() == 2);
TEST_ASSERT(stereo_groups[0].getGroupType() ==
RDKit::StereoGroupType::STEREO_ABSOLUTE);
TEST_ASSERT(stereo_groups[0].getAtoms().size() == 1u);
TEST_ASSERT(stereo_groups[1].getGroupType() == RDKit::StereoGroupType::STEREO_OR);
TEST_ASSERT(stereo_groups[1].getAtoms().size() == 2u);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAnd() {
BOOST_LOG(rdInfoLog) << "testing extended stereo parsing with an AND block"
<< std::endl;
auto m = readTestFile("two_centers_and.mol");
TEST_ASSERT(m.get());
TEST_ASSERT(m->getNumAtoms() == 8);
auto stereo_groups = m->getStereoGroups();
TEST_ASSERT(stereo_groups.size() == 2);
TEST_ASSERT(stereo_groups[0].getGroupType() ==
RDKit::StereoGroupType::STEREO_ABSOLUTE);
TEST_ASSERT(stereo_groups[1].getGroupType() == RDKit::StereoGroupType::STEREO_AND);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testWrite() {
BOOST_LOG(rdInfoLog) << "testing extended stereo file writing" << std::endl;
auto m0 = readTestFile("two_centers_and.mol");
TEST_ASSERT(m0.get());
std::string block = RDKit::MolToMolBlock(*m0);
auto m1 = RDKit::MolBlockToMol(block);
// Check that the extended stereo information has the same extended stereo
// types and same atoms marked for extended stereo.
auto stereo_groups0 = m0->getStereoGroups();
auto stereo_groups1 = m1->getStereoGroups();
TEST_ASSERT(stereo_groups0.size() == stereo_groups1.size());
for (unsigned i = 0u; i < 2; ++i) {
TEST_ASSERT(stereo_groups0[i].getGroupType() == stereo_groups1[i].getGroupType());
TEST_ASSERT(stereo_groups0[i].getAtoms().size() ==
stereo_groups1[i].getAtoms().size());
for (auto &&atom0 = stereo_groups0[i].getAtoms().begin(),
atom1 = stereo_groups1[i].getAtoms().begin();
atom0 != stereo_groups0[i].getAtoms().end(); ++atom0, ++atom1) {
TEST_ASSERT((*atom0)->getIdx() == (*atom1)->getIdx());
}
}
delete (m1);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
testOr();
testAnd();
testWrite();
return 0;
}
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