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//
// Copyright (C) 2002-2017 Greg Landrum and Rational Discovery LLC
//
// @@ 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/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/RDLog.h>
#include <iostream>
#include <stdlib.h>
#include <vector>
using namespace RDKit;
using namespace std;
typedef class ROMol Mol;
void test1() {
string smi = "CCOC";
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atIt;
unsigned int idx = 0;
for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
idx++;
}
atIt = m->beginAtoms();
CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
Mol::AtomIterator atIt2 = m->beginAtoms();
CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");
atIt++;
CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
atIt += 2;
CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
atIt -= 1;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");
atIt--;
--atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");
atIt++;
++atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
atIt = atIt + 2;
atIt = atIt - 2;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
atIt2 = m->beginAtoms();
atIt2 += 2;
CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");
// past the end stuff
atIt2 = m->endAtoms();
atIt = m->beginAtoms() + 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
// this is whack
atIt = m->beginAtoms();
atIt -= 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
BOOST_LOG(rdInfoLog) << "test1 done" << endl;
};
void test2() {
string smi = "C1COC1";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
bondIt = m->beginBonds();
Mol::BondIterator bondIt2 = m->beginBonds();
CHECK_INVARIANT(bondIt == bondIt2, "iterators don't compare equal");
bondIt++;
CHECK_INVARIANT((*bondIt)->getIdx() == 1, "bad idx");
bondIt++;
bondIt++;
bondIt--;
CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
CHECK_INVARIANT(bondIt != bondIt2, "iterators don't compare different");
bondIt--;
--bondIt;
CHECK_INVARIANT((*bondIt)->getIdx() == 0, "bad idx");
CHECK_INVARIANT(bondIt == bondIt2, "iterator inequality failed");
bondIt++;
++bondIt;
CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
// past the end stuff
bondIt2 = m->endBonds();
bondIt = m->beginBonds();
bondIt--;
BOOST_LOG(rdInfoLog) << "test2 done" << endl;
};
void test3() {
string smi = "C1COCCNCOCNSCC1";
unsigned char heteros[] = {2, 5, 7, 9, 10};
Mol *m = SmilesToMol(smi);
{
unsigned int nSeen = 0;
for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt != m->endHeteros(); heteroIt++) {
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
nSeen++;
}
}
{
unsigned int nSeen = 0;
for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt != m->endHeteros(); ++heteroIt) {
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
nSeen++;
}
}
{
Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt++;
heteroIt++;
heteroIt--;
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[1], "bad hetero");
CHECK_INVARIANT((*--heteroIt)->getIdx() == heteros[0], "bad hetero");
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[0], "bad hetero");
}
BOOST_LOG(rdInfoLog) << "test3 done" << endl;
};
void test4() {
string smi = "C1COCCNCOCNSCC1";
unsigned int heteros1[] = {2, 7};
Mol *m = SmilesToMol(smi);
auto *q = new QueryAtom();
q->setQuery(makeAtomNumQuery(8));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); queryIt++) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[nSeen], "bad query");
nSeen++;
}
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[1], "bad query");
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
Mol::QueryAtomIterator queryIt2 = queryIt;
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt2)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[1], "bad query");
}
smi = "CC(C)CC(C)CC(C)CC(C)C";
unsigned int heteros2[] = {1, 4, 7, 10};
m = SmilesToMol(smi);
// m->debugMol(cout);
q->setQuery(makeAtomImplicitValenceQuery(1));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros2[nSeen], "bad query");
nSeen++;
}
}
BOOST_LOG(rdInfoLog) << "test4 done" << endl;
};
void test5() {
string smi = "CCCC";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
idx = 0;
Mol::BondIterator beginP(m->beginBonds());
Mol::BondIterator endP(m->endBonds());
for (bondIt = beginP; bondIt != endP; bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
BOOST_LOG(rdInfoLog) << "test5 done" << endl;
}
#if 1
void _test6Help(const ROMol *m) {
Mol::ConstAtomIterator atIt;
unsigned int idx = 0;
for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
idx++;
}
atIt = m->beginAtoms();
CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
Mol::ConstAtomIterator atIt2 = m->beginAtoms();
CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");
atIt++;
CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
atIt += 2;
CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
atIt -= 1;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");
atIt--;
--atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");
atIt++;
++atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
atIt = atIt + 2;
atIt = atIt - 2;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
atIt2 = m->beginAtoms();
atIt2 += 2;
CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");
// past the end stuff
atIt2 = m->endAtoms();
atIt = m->beginAtoms() + 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
// this is whack
atIt = m->beginAtoms();
atIt -= 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
}
void test6() {
string smi = "CCOC";
Mol *m = SmilesToMol(smi);
_test6Help(m);
BOOST_LOG(rdInfoLog) << "test6 done" << endl;
};
#endif
void test7() {
string smi = "c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AromaticAtomIterator atomIt;
Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms());
Mol::AromaticAtomIterator endP(m->endAromaticAtoms());
unsigned int idx = 0;
for (atomIt = beginP; atomIt != endP; atomIt++) {
TEST_ASSERT((*atomIt)->getIdx() == idx);
idx++;
}
TEST_ASSERT(idx == 6);
atomIt = beginP;
atomIt++;
atomIt--;
TEST_ASSERT((*atomIt)->getIdx() == 0);
delete m;
smi = "Cc1ccccc1";
m = SmilesToMol(smi);
beginP = m->beginAromaticAtoms();
endP = m->endAromaticAtoms();
idx = 0;
for (atomIt = beginP; atomIt != endP; atomIt++) {
TEST_ASSERT((*atomIt)->getIdx() == idx + 1);
idx++;
}
TEST_ASSERT(idx == 6);
#endif
BOOST_LOG(rdInfoLog) << "test7 done" << endl;
}
void testIssue263() {
string smi = "c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atomIt;
unsigned int idx = 0;
for (atomIt = m->beginAtoms(); atomIt != m->endAtoms(); ++atomIt) {
TEST_ASSERT((*atomIt)->getIdx() == idx);
idx++;
}
TEST_ASSERT(idx == 7);
Mol::BondIterator bondIt;
idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); ++bondIt) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 7, "bad idx");
#endif
BOOST_LOG(rdInfoLog) << "testIssue263 done" << endl;
}
void test8() {
{
string smi = "CC1CC2CC1C2";
Mol *m = SmilesToMol(smi);
auto *q = new QueryAtom();
q->setQuery(makeAtomExplicitDegreeQuery(3));
q->expandQuery(makeAtomRingBondCountQuery(2));
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
TEST_ASSERT((*queryIt)->getIdx() == 1);
nSeen++;
}
TEST_ASSERT(nSeen == 1);
delete m;
delete q;
}
BOOST_LOG(rdInfoLog) << "test8 done" << endl;
};
int main() {
RDLog::InitLogs();
test1();
test2();
test3();
test4();
test5();
test6();
test7();
test8();
testIssue263();
return 0;
}
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