mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
d5d4d194ec
* atropisomer handling added * fixed non-used variables, linking directives * BOOST LIB start/stop fixes, linking fix * Fixes for RDKIT CI errors * minimalLib fix * changed vector<enum> for java builds * check for extra chars in CIP labeling * removed wrong deprecated message * fix ostrstream output error? * restored _ChiralAtomRank to lowercase first letter * changes for merged master * Fixed catch label for new Catch package * update expected psql results * get swig wrappers building * restore MolFileStereochem to FileParsers * fix java wrapper for reapplyMolBlockWedging * some suggestions * move a couple functions out of Bond * Merge branch 'master' into pr/atropisomers2 * merged master * Renamed setStereoanyFromSquiggleBond * atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol * fix for CI build * attempt to fix java build in CI * attempt to fix java build in CI #2 * New routine to remove non-explicit 3D-geneated chirality * changed to use pair for atrop atoms and related bonds * Changes as per PR reviews * PR review respnses * PR review reponse - more * Fix merge from master * fixing java ci after merge * Updated the help doc for atripisomers * update the atropisomer docs * improve the images * add the source CXSMILES --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
127 lines
4.0 KiB
C++
127 lines
4.0 KiB
C++
//
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// Copyright (C) 2018 T5 Informatics GmbH
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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 <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/StereoGroup.h>
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#include "FileParsers.h"
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/BadFileException.h>
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#include <clocale>
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#include <cstdlib>
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#include <string>
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#include <fstream>
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#include <memory>
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using namespace RDKit;
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std::unique_ptr<RWMol> readTestFile(const std::string &baseName) {
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std::string rdbase = getenv("RDBASE");
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std::string fName =
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rdbase + "/Code/GraphMol/FileParsers/test_data/" + baseName;
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auto m = MolFileToMol(fName);
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return std::unique_ptr<RWMol>(m);
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}
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void testOr() {
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BOOST_LOG(rdInfoLog) << "testing extended stereo parsing with an OR block"
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<< std::endl;
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auto m = readTestFile("two_centers_or.mol");
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TEST_ASSERT(m.get());
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TEST_ASSERT(m->getNumAtoms() == 8);
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auto stereo_groups = m->getStereoGroups();
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TEST_ASSERT(stereo_groups.size() == 2);
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TEST_ASSERT(stereo_groups[0].getGroupType() ==
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RDKit::StereoGroupType::STEREO_ABSOLUTE);
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TEST_ASSERT(stereo_groups[0].getReadId() == 0u);
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TEST_ASSERT(stereo_groups[0].getWriteId() == 0u);
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TEST_ASSERT(stereo_groups[0].getAtoms().size() == 1u);
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TEST_ASSERT(stereo_groups[1].getGroupType() ==
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RDKit::StereoGroupType::STEREO_OR);
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TEST_ASSERT(stereo_groups[1].getReadId() == 1u);
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TEST_ASSERT(stereo_groups[1].getWriteId() == 0u);
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TEST_ASSERT(stereo_groups[1].getAtoms().size() == 2u);
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forwardStereoGroupIds(*m);
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stereo_groups = m->getStereoGroups();
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TEST_ASSERT(stereo_groups[0].getWriteId() == 0u);
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TEST_ASSERT(stereo_groups[1].getWriteId() == 1u);
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void testAnd() {
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BOOST_LOG(rdInfoLog) << "testing extended stereo parsing with an AND block"
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<< std::endl;
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auto m = readTestFile("two_centers_and.mol");
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TEST_ASSERT(m.get());
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TEST_ASSERT(m->getNumAtoms() == 8);
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auto stereo_groups = m->getStereoGroups();
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TEST_ASSERT(stereo_groups.size() == 2);
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TEST_ASSERT(stereo_groups[0].getGroupType() ==
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RDKit::StereoGroupType::STEREO_ABSOLUTE);
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TEST_ASSERT(stereo_groups[0].getReadId() == 0u);
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TEST_ASSERT(stereo_groups[1].getGroupType() ==
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RDKit::StereoGroupType::STEREO_AND);
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TEST_ASSERT(stereo_groups[1].getReadId() == 1u);
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forwardStereoGroupIds(*m);
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stereo_groups = m->getStereoGroups();
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TEST_ASSERT(stereo_groups[0].getWriteId() == 0u);
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TEST_ASSERT(stereo_groups[1].getWriteId() == 1u);
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void testWrite() {
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BOOST_LOG(rdInfoLog) << "testing extended stereo file writing" << std::endl;
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auto m0 = readTestFile("two_centers_and.mol");
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TEST_ASSERT(m0.get());
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std::string block = RDKit::MolToMolBlock(*m0);
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auto m1 = RDKit::MolBlockToMol(block);
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// Check that the extended stereo information has the same extended stereo
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// types and same atoms marked for extended stereo.
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auto stereo_groups0 = m0->getStereoGroups();
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auto stereo_groups1 = m1->getStereoGroups();
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TEST_ASSERT(stereo_groups0.size() == stereo_groups1.size());
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for (unsigned i = 0u; i < 2; ++i) {
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TEST_ASSERT(stereo_groups0[i].getGroupType() ==
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stereo_groups1[i].getGroupType());
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TEST_ASSERT(stereo_groups0[i].getAtoms().size() ==
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stereo_groups1[i].getAtoms().size());
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for (auto &&atom0 = stereo_groups0[i].getAtoms().begin(),
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atom1 = stereo_groups1[i].getAtoms().begin();
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atom0 != stereo_groups0[i].getAtoms().end(); ++atom0, ++atom1) {
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TEST_ASSERT((*atom0)->getIdx() == (*atom1)->getIdx());
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}
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}
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delete (m1);
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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int main(int argc, char *argv[]) {
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(void)argc;
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(void)argv;
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testOr();
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testAnd();
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testWrite();
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return 0;
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}
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