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8411f4535e
* remove no-op macros and dead code (pt 2) * test failures due to whitespace changes? * actually run the testFeatures tests --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
407 lines
11 KiB
C++
407 lines
11 KiB
C++
//
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// Copyright (C) 2002-2017 Greg Landrum and Rational Discovery LLC
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//
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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/test.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <RDGeneral/RDLog.h>
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#include <iostream>
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#include <cstdlib>
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#include <vector>
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using namespace RDKit;
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using namespace std;
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typedef class ROMol Mol;
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void test1() {
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string smi = "CCOC";
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Mol *m = SmilesToMol(smi);
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Mol::AtomIterator atIt;
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unsigned int idx = 0;
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for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
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CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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atIt = m->beginAtoms();
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CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");
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atIt = m->beginAtoms();
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Mol::AtomIterator atIt2 = m->beginAtoms();
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CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");
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atIt++;
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CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
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atIt += 2;
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CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
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atIt -= 1;
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CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
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CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
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CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
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CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
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CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
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CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");
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atIt--;
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--atIt;
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CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
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CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");
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atIt++;
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++atIt;
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CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
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atIt = m->beginAtoms();
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atIt = atIt + 2;
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atIt = atIt - 2;
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CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
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atIt2 = m->beginAtoms();
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atIt2 += 2;
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CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
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CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");
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// past the end stuff
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atIt2 = m->endAtoms();
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atIt = m->beginAtoms() + 10;
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CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
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// this is whack
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atIt = m->beginAtoms();
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atIt -= 10;
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CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
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delete m;
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BOOST_LOG(rdInfoLog) << "test1 done" << endl;
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};
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void test2() {
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string smi = "C1COC1";
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Mol *m = SmilesToMol(smi);
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Mol::BondIterator bondIt;
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unsigned int idx = 0;
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for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
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CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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bondIt = m->beginBonds();
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Mol::BondIterator bondIt2 = m->beginBonds();
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CHECK_INVARIANT(bondIt == bondIt2, "iterators don't compare equal");
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bondIt++;
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CHECK_INVARIANT((*bondIt)->getIdx() == 1, "bad idx");
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bondIt++;
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bondIt++;
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bondIt--;
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CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
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CHECK_INVARIANT(bondIt != bondIt2, "iterators don't compare different");
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bondIt--;
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--bondIt;
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CHECK_INVARIANT((*bondIt)->getIdx() == 0, "bad idx");
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CHECK_INVARIANT(bondIt == bondIt2, "iterator inequality failed");
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bondIt++;
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++bondIt;
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CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
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// past the end stuff
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bondIt2 = m->endBonds();
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bondIt = m->beginBonds();
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bondIt--;
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delete m;
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BOOST_LOG(rdInfoLog) << "test2 done" << endl;
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};
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void test3() {
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string smi = "C1COCCNCOCNSCC1";
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unsigned char heteros[] = {2, 5, 7, 9, 10};
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Mol *m = SmilesToMol(smi);
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{
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unsigned int nSeen = 0;
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for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
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heteroIt != m->endHeteros(); heteroIt++) {
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CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
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nSeen++;
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}
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}
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{
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unsigned int nSeen = 0;
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for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
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heteroIt != m->endHeteros(); ++heteroIt) {
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CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
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nSeen++;
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}
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}
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{
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Mol::HeteroatomIterator heteroIt = m->beginHeteros();
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heteroIt++;
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heteroIt++;
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heteroIt--;
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CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[1], "bad hetero");
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CHECK_INVARIANT((*--heteroIt)->getIdx() == heteros[0], "bad hetero");
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CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[0], "bad hetero");
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}
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delete m;
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BOOST_LOG(rdInfoLog) << "test3 done" << endl;
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};
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void test4() {
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string smi = "C1COCCNCOCNSCC1";
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unsigned int heteros1[] = {2, 7};
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Mol *m = SmilesToMol(smi);
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auto *q = new QueryAtom();
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q->setQuery(makeAtomNumQuery(8));
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{
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unsigned int nSeen = 0;
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for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
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queryIt != m->endQueryAtoms(); queryIt++) {
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CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[nSeen], "bad query");
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nSeen++;
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}
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}
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{
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Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
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queryIt++;
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queryIt--;
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CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[0], "bad query");
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CHECK_INVARIANT((*++queryIt)->getIdx() == heteros1[1], "bad query");
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CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[1], "bad query");
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}
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{
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Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
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queryIt++;
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queryIt--;
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Mol::QueryAtomIterator queryIt2 = queryIt;
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CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[0], "bad query");
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CHECK_INVARIANT((*++queryIt2)->getIdx() == heteros1[1], "bad query");
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CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[1], "bad query");
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}
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smi = "CC(C)CC(C)CC(C)CC(C)C";
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unsigned int heteros2[] = {1, 4, 7, 10};
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delete m;
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m = SmilesToMol(smi);
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// m->debugMol(cout);
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q->setQuery(makeAtomImplicitValenceQuery(1));
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{
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unsigned int nSeen = 0;
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for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
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queryIt != m->endQueryAtoms(); ++queryIt) {
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CHECK_INVARIANT((*queryIt)->getIdx() == heteros2[nSeen], "bad query");
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nSeen++;
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}
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}
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delete m;
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delete q;
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BOOST_LOG(rdInfoLog) << "test4 done" << endl;
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};
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void test5() {
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string smi = "CCCC";
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Mol *m = SmilesToMol(smi);
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Mol::BondIterator bondIt;
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unsigned int idx = 0;
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for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
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CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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CHECK_INVARIANT(idx == 3, "bad idx");
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idx = 0;
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for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
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CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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CHECK_INVARIANT(idx == 3, "bad idx");
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idx = 0;
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Mol::BondIterator beginP(m->beginBonds());
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Mol::BondIterator endP(m->endBonds());
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for (bondIt = beginP; bondIt != endP; bondIt++) {
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CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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CHECK_INVARIANT(idx == 3, "bad idx");
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delete m;
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BOOST_LOG(rdInfoLog) << "test5 done" << endl;
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}
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void _test6Help(const ROMol *m) {
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Mol::ConstAtomIterator atIt;
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unsigned int idx = 0;
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for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
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CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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atIt = m->beginAtoms();
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CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");
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atIt = m->beginAtoms();
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Mol::ConstAtomIterator atIt2 = m->beginAtoms();
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CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");
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atIt++;
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CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
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atIt += 2;
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CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
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atIt -= 1;
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CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
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CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
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CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
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CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
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CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
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CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");
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atIt--;
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--atIt;
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CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
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CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");
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atIt++;
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++atIt;
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CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
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atIt = m->beginAtoms();
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atIt = atIt + 2;
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atIt = atIt - 2;
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CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
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atIt2 = m->beginAtoms();
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atIt2 += 2;
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CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
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CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");
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// past the end stuff
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atIt2 = m->endAtoms();
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atIt = m->beginAtoms() + 10;
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CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
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// this is whack
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atIt = m->beginAtoms();
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atIt -= 10;
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CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
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}
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void test6() {
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string smi = "CCOC";
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Mol *m = SmilesToMol(smi);
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_test6Help(m);
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delete m;
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BOOST_LOG(rdInfoLog) << "test6 done" << endl;
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};
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void test7() {
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string smi = "c1ccccc1C";
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Mol *m = SmilesToMol(smi);
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Mol::AromaticAtomIterator atomIt;
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Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms());
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Mol::AromaticAtomIterator endP(m->endAromaticAtoms());
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unsigned int idx = 0;
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for (atomIt = beginP; atomIt != endP; atomIt++) {
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TEST_ASSERT((*atomIt)->getIdx() == idx);
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idx++;
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}
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TEST_ASSERT(idx == 6);
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atomIt = beginP;
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atomIt++;
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atomIt--;
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TEST_ASSERT((*atomIt)->getIdx() == 0);
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delete m;
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smi = "Cc1ccccc1";
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m = SmilesToMol(smi);
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beginP = m->beginAromaticAtoms();
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endP = m->endAromaticAtoms();
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idx = 0;
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for (atomIt = beginP; atomIt != endP; atomIt++) {
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TEST_ASSERT((*atomIt)->getIdx() == idx + 1);
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idx++;
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}
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TEST_ASSERT(idx == 6);
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delete m;
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BOOST_LOG(rdInfoLog) << "test7 done" << endl;
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}
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void testIssue263() {
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string smi = "c1ccccc1C";
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Mol *m = SmilesToMol(smi);
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Mol::AtomIterator atomIt;
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unsigned int idx = 0;
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for (atomIt = m->beginAtoms(); atomIt != m->endAtoms(); ++atomIt) {
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TEST_ASSERT((*atomIt)->getIdx() == idx);
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idx++;
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}
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TEST_ASSERT(idx == 7);
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Mol::BondIterator bondIt;
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idx = 0;
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for (bondIt = m->beginBonds(); bondIt != m->endBonds(); ++bondIt) {
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CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
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idx++;
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}
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CHECK_INVARIANT(idx == 7, "bad idx");
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delete m;
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BOOST_LOG(rdInfoLog) << "testIssue263 done" << endl;
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}
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void test8() {
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{
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string smi = "CC1CC2CC1C2";
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Mol *m = SmilesToMol(smi);
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auto *q = new QueryAtom();
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q->setQuery(makeAtomExplicitDegreeQuery(3));
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q->expandQuery(makeAtomRingBondCountQuery(2));
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unsigned int nSeen = 0;
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for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
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queryIt != m->endQueryAtoms(); ++queryIt) {
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TEST_ASSERT((*queryIt)->getIdx() == 1);
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nSeen++;
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}
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TEST_ASSERT(nSeen == 1);
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delete m;
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delete q;
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}
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BOOST_LOG(rdInfoLog) << "test8 done" << endl;
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};
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int main() {
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RDLog::InitLogs();
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test1();
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test2();
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test3();
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test4();
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test5();
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test6();
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test7();
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test8();
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testIssue263();
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return 0;
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}
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