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rdkit/Code/GraphMol/Substruct/testSubstructMatch.cpp
Greg Landrum 21225e63b3 Move some more tests over to catch2 (#9058) 
* move testSubstructMatch to catch2

* modernization

* modernization

* switch to catch2

* modernize

* convert to catch2

* update

* move to catch

* please be quiet

* move to catch2

* changes in response to review

---------

Co-authored-by: = <=>
2026-01-24 07:03:04 +01:00

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//
// Copyright (C) 2001-2025 Greg Landrum and other RDKit contributors
//
// @@ 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 <catch2/catch_all.hpp>
// RD bits
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include "SubstructMatch.h"
#include "SubstructUtils.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/test_fixtures.h>
#include "vf2.hpp"
using namespace RDKit;
TEST_CASE("test1", "[substruct]") {
bool updateLabel = true;
bool takeOwnership = true;
std::unique_ptr<RWMol> m = std::make_unique<RWMol>();
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
std::unique_ptr<RWMol> q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::SINGLE);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q1, matches, false);
REQUIRE(n == 2);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
CHECK(matches[0][0].first == 0);
CHECK((matches[0][0].second == 1 || matches[0][0].second == 2));
CHECK(matches[0][1].first == 1);
CHECK(matches[0][1].second != matches[0][0].second);
CHECK((matches[1][1].second == 1 || matches[0][1].second == 2));
CHECK(matches[1][0].first == 0);
CHECK((matches[1][0].second == 1 || matches[1][0].second == 2));
CHECK(matches[1][0].second != matches[0][0].second);
CHECK(matches[1][0].second == matches[0][1].second);
CHECK(matches[1][1].first == 1);
CHECK(matches[1][1].second != matches[1][0].second);
CHECK(matches[1][1].second == matches[0][0].second);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
CHECK(matches[0][0].first == 0);
CHECK((matches[0][0].second == 1 || matches[0][0].second == 2));
CHECK(matches[0][1].first == 1);
CHECK(matches[0][1].second != matches[0][0].second);
CHECK((matches[0][1].second == 1 || matches[0][1].second == 2));
MatchVectType matchV;
REQUIRE(SubstructMatch(*m, *q1, matchV));
REQUIRE(matchV.size() == 2);
// make sure we reset the match vectors.
// build a query we won't match:
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(1, 2, Bond::SINGLE);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(2, 3, Bond::SINGLE);
CHECK(!SubstructMatch(*m, *q1, matchV));
CHECK(matchV.size() == 0);
n = SubstructMatch(*m, *q1, matches, false);
CHECK(n == 0);
CHECK(matches.size() == 0);
}
TEST_CASE("test2", "[substruct]") {
std::unique_ptr<RWMol> m = std::make_unique<RWMol>();
bool updateLabel = true;
bool takeOwnership = true;
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
std::unique_ptr<RWMol> q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::SINGLE);
MatchVectType matchV;
auto n = SubstructMatch(*m, *q1, matchV);
CHECK(n);
CHECK(matchV.size() == 2);
CHECK(matchV[0].first == 0);
CHECK(matchV[0].second == 1);
CHECK(matchV[1].first == 1);
CHECK(matchV[1].second == 2);
std::vector<MatchVectType> matches;
n = SubstructMatch(*m, *q1, matches, false);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
REQUIRE(SubstructMatch(*m, *q1, matchV));
REQUIRE(matchV.size() == 2);
m.reset(new RWMol());
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::DOUBLE);
matches.clear();
n = SubstructMatch(*m, *q1, matches, false);
REQUIRE(n == 0);
REQUIRE(matches.size() == n);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 0);
REQUIRE(matches.size() == n);
REQUIRE(!SubstructMatch(*m, *q1, matchV));
}
TEST_CASE("test3", "[substruct]") {
std::unique_ptr<RWMol> m = std::make_unique<RWMol>();
bool updateLabel = true;
bool takeOwnership = true;
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
std::unique_ptr<RWMol> q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q1, matches, false);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
MatchVectType matchV;
REQUIRE(SubstructMatch(*m, *q1, matchV));
REQUIRE(matchV.size() == 2);
m = std::make_unique<RWMol>();
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::DOUBLE);
matches.clear();
n = SubstructMatch(*m, *q1, matches, false);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches.size() == n);
REQUIRE(matches[0].size() == 2);
REQUIRE(SubstructMatch(*m, *q1, matchV));
REQUIRE(matchV.size() == 2);
q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
n = SubstructMatch(*m, *q1, matches, false);
CHECK(n == 2);
CHECK(matches.size() == n);
CHECK(matches[0].size() == 2);
CHECK(matches[1].size() == 2);
CHECK(matches[0][0].second != matches[1][0].second);
CHECK(matches[0][1].second != matches[1][1].second);
n = SubstructMatch(*m, *q1, matches, true);
CHECK(n == 1);
CHECK(matches.size() == n);
}
TEST_CASE("test4", "[substruct]") {
bool updateLabel = true;
bool takeOwnership = true;
std::unique_ptr<Atom> a6 = std::make_unique<Atom>(6);
std::unique_ptr<Atom> a8 = std::make_unique<Atom>(8);
std::unique_ptr<RWMol> m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a8.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(1, 0, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(1, 3, Bond::SINGLE);
m->addBond(2, 4, Bond::SINGLE);
// this will be the recursive query
std::unique_ptr<RWMol> q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
// here's the main query
std::unique_ptr<RWMol> q2 = std::make_unique<RWMol>();
auto *rsq = new RecursiveStructureQuery(q1.release());
auto *qA = new QueryAtom(6);
qA->expandQuery(rsq, Queries::COMPOSITE_AND);
// std::cout << "post expand: " << qA->getQuery() << std::endl;
q2->addAtom(qA, true, true);
// std::cout << "mol: " << q2->getAtomWithIdx(0)->getQuery() << std::endl;
q2->addAtom(new QueryAtom(6), true, true);
q2->addBond(0, 1, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q2, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 2);
CHECK(matchV[0].first == 0);
CHECK(matchV[0].second == 1);
CHECK(matchV[1].first == 1);
CHECK((matchV[1].second == 0 || matchV[1].second == 3));
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q2, matches, true);
CHECK(n == 2);
CHECK(matches.size() == (size_t)n);
CHECK(matches[0].size() == 2);
CHECK(matches[1].size() == 2);
CHECK(matches[0][0].second == matches[1][0].second);
CHECK(matches[0][1].second != matches[1][1].second);
}
TEST_CASE("test5", "[substruct]") {
auto a6 = std::make_unique<Atom>(6);
auto a8 = std::make_unique<Atom>(8);
// CC(OC)C
auto m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a8.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(1, 4, Bond::SINGLE);
m->addBond(2, 3, Bond::SINGLE);
// this will be the recursive query
bool updateLabel = true;
bool takeOwnership = true;
auto q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
// here's the main query
auto q2 = std::make_unique<RWMol>();
auto qA = std::make_unique<QueryAtom>();
auto *rsq = new RecursiveStructureQuery(q1.release());
qA->setQuery(rsq);
q2->addAtom(qA.release(), true, true);
q2->addAtom(new QueryAtom(6), true, true);
q2->addBond(0, 1, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q2, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 2);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q2, matches, true);
REQUIRE(n == 2);
REQUIRE(matches[0].size() == 2);
}
TEST_CASE("test5QueryRoot", "[substruct]") {
auto a6 = std::unique_ptr<Atom>(new Atom(6));
auto a8 = std::unique_ptr<Atom>(new Atom(8));
// CC(OC)C
auto m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a8.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(1, 4, Bond::SINGLE);
m->addBond(2, 3, Bond::SINGLE);
// this will be the recursive query
bool updateLabel = true;
bool takeOwnership = true;
auto q1 = std::make_unique<RWMol>();
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
q1->setProp(common_properties::_queryRootAtom, 1);
// here's the main query
auto q2 = std::make_unique<RWMol>();
auto qA = std::make_unique<QueryAtom>();
auto *rsq = new RecursiveStructureQuery(q1.release());
qA->setQuery(rsq);
q2->addAtom(qA.release(), true, true);
q2->addAtom(new QueryAtom(6), true, true);
q2->addBond(0, 1, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q2, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 2);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q2, matches, true);
REQUIRE(n == 2);
REQUIRE(matches[0].size() == 2);
}
TEST_CASE("test6", "[substruct][Issue71]") {
auto a6 = std::make_unique<Atom>(6);
auto m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
auto q1 = std::make_unique<RWMol>();
bool updateLabel = true;
bool takeOwnership = true;
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
q1->addBond(1, 2, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q1, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 3);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches[0].size() == 3);
// close the loop and try again (we should still match)
q1->addBond(0, 2, Bond::UNSPECIFIED);
found = SubstructMatch(*m, *q1, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 3);
n = SubstructMatch(*m, *q1, matches, true);
REQUIRE(n == 1);
REQUIRE(matches[0].size() == 3);
}
TEST_CASE("test7", "[substruct][leak]") {
auto a6 = std::make_unique<Atom>(6);
std::unique_ptr<RWMol> m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
std::unique_ptr<RWMol> q1 = std::make_unique<RWMol>();
bool updateLabel = true;
bool takeOwnership = true;
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
q1->addBond(1, 2, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q1, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 3);
std::vector<MatchVectType> matches;
for (int i = 0; i < 30000; i++) {
auto n = SubstructMatch(*m, *q1, matches, true, true);
REQUIRE(n == 1);
REQUIRE(matches[0].size() == 3);
}
}
TEST_CASE("test9", "[substruct][chiral]") {
auto a6 = std::make_unique<Atom>(6);
auto m = std::make_unique<RWMol>();
m->addAtom(a6.get());
bool updateLabel = true;
bool takeOwnership = true;
m->addAtom(new Atom(6), updateLabel, takeOwnership);
m->addAtom(new Atom(7), updateLabel, takeOwnership);
m->addAtom(new Atom(8), updateLabel, takeOwnership);
m->addAtom(new Atom(9), updateLabel, takeOwnership);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
m->addBond(0, 4, Bond::SINGLE);
m->getAtomWithIdx(0)->setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
auto q1 = std::make_unique<RWMol>();
q1->addAtom(a6.get());
q1->addAtom(new Atom(6));
q1->addAtom(new Atom(7));
q1->addAtom(new Atom(8));
q1->addAtom(new Atom(9));
q1->addBond(0, 1, Bond::SINGLE);
q1->addBond(0, 2, Bond::SINGLE);
q1->addBond(0, 3, Bond::SINGLE);
q1->addBond(0, 4, Bond::SINGLE);
q1->getAtomWithIdx(0)->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
MolOps::sanitizeMol(*m);
MolOps::assignStereochemistry(*m);
MolOps::sanitizeMol(*q1);
MolOps::assignStereochemistry(*q1);
// test with default options (no chirality):
MatchVectType matchV;
auto found = SubstructMatch(*m, *q1, matchV);
CHECK(found);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q1, matches, true);
CHECK(n == 1);
// test with chirality
found = SubstructMatch(*m, *q1, matchV, true, true);
CHECK(!found);
n = SubstructMatch(*m, *q1, matches, true, true, true);
CHECK(n == 0);
// self matches:
found = SubstructMatch(*m, *m, matchV, true, true);
CHECK(found);
n = SubstructMatch(*m, *m, matches, true, true, true);
CHECK(n == 1);
found = SubstructMatch(*q1, *q1, matchV, true, true);
CHECK(found);
n = SubstructMatch(*q1, *q1, matches, true, true, true);
CHECK(n == 1);
}
TEST_CASE("testRecursiveSerialNumbers", "[substruct][recursive]") {
auto a6 = std::make_unique<Atom>(6);
auto a8 = std::make_unique<Atom>(8);
auto m = std::make_unique<RWMol>();
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addAtom(a8.get());
m->addAtom(a6.get());
m->addAtom(a6.get());
m->addBond(1, 0, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(1, 3, Bond::SINGLE);
m->addBond(2, 4, Bond::SINGLE);
{
// this will be the recursive query
auto q1 = std::make_unique<RWMol>();
bool updateLabel = true;
bool takeOwnership = true;
q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership);
q1->addAtom(new QueryAtom(8), updateLabel, takeOwnership);
q1->addBond(0, 1, Bond::UNSPECIFIED);
// here's the main query
auto q2 = std::make_unique<RWMol>();
auto qA = std::make_unique<QueryAtom>(6);
auto rsq = std::make_unique<RecursiveStructureQuery>(new RWMol(*q1), 1);
qA->expandQuery(rsq.release(), Queries::COMPOSITE_AND);
// std::cout << "post expand: " << qA->getQuery() << std::endl;
q2->addAtom(qA.release(), true, true);
// std::cout << "mol: " << q2->getAtomWithIdx(0)->getQuery() << std::endl;
q2->addAtom(new QueryAtom(8), true, true);
q2->addBond(0, 1, Bond::UNSPECIFIED);
qA.reset(new QueryAtom(6));
rsq.reset(new RecursiveStructureQuery(new RWMol(*q1), 1));
qA->expandQuery(rsq.release(), Queries::COMPOSITE_AND);
q2->addAtom(qA.release(), true, true);
q2->addBond(1, 2, Bond::UNSPECIFIED);
MatchVectType matchV;
bool found = SubstructMatch(*m, *q2, matchV);
REQUIRE(found);
REQUIRE(matchV.size() == 3);
std::vector<MatchVectType> matches;
auto n = SubstructMatch(*m, *q2, matches, true);
CHECK(n == 1);
CHECK(matches.size() == 1);
CHECK(matches[0].size() == 3);
}
}
#ifdef RDK_TEST_MULTITHREADED
#include <RDGeneral/BoostStartInclude.h>
#include <thread>
#include <future>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace {
void runblock(const std::vector<std::unique_ptr<ROMol>> *mols,
const ROMol *query, const boost::dynamic_bitset<> &hits,
unsigned int count, unsigned int idx) {
for (unsigned int j = 0; j < 100; j++) {
for (unsigned int i = 0; i < mols->size(); ++i) {
if (i % count != idx) {
continue;
}
const auto *mol = mols->at(i).get();
MatchVectType matchV;
bool found = SubstructMatch(*mol, *query, matchV);
CHECK(found == hits[i]);
}
}
}
} // namespace
TEST_CASE("testMultiThread", "[substruct][multithread]") {
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
SDMolSupplier suppl(fName);
std::vector<std::unique_ptr<ROMol>> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = nullptr;
try {
mol = suppl.next();
} catch (...) {
continue;
}
if (!mol) {
continue;
}
mols.emplace_back(mol);
}
std::vector<std::future<void>> tg;
auto query = v2::SmilesParse::MolFromSmarts("[#6;$([#6]([#6])[!#6])]");
boost::dynamic_bitset<> hits(mols.size());
for (unsigned int i = 0; i < mols.size(); ++i) {
MatchVectType matchV;
hits[i] = SubstructMatch(*mols[i], *query, matchV);
}
unsigned int count = 4;
for (unsigned int i = 0; i < count; ++i) {
tg.emplace_back(std::async(std::launch::async, runblock, &mols, query.get(),
hits, count, i));
}
for (auto &fut : tg) {
fut.get();
}
tg.clear();
query.reset(SmartsToMol("[#6]([#6])[!#6]"));
for (unsigned int i = 0; i < mols.size(); ++i) {
MatchVectType matchV;
hits[i] = SubstructMatch(*mols[i], *query, matchV);
}
for (unsigned int i = 0; i < count; ++i) {
tg.emplace_back(std::async(std::launch::async, runblock, &mols, query.get(),
hits, count, i));
}
for (auto &fut : tg) {
fut.get();
}
tg.clear();
query.reset(SmartsToMol("[$([O,S]-[!$(*=O)])]"));
for (unsigned int i = 0; i < mols.size(); ++i) {
MatchVectType matchV;
hits[i] = SubstructMatch(*mols[i], *query, matchV);
}
for (unsigned int i = 0; i < count; ++i) {
tg.emplace_back(std::async(std::launch::async, runblock, &mols, query.get(),
hits, count, i));
}
for (auto &fut : tg) {
fut.get();
}
}
#else
TEST_CASE("testMultiThread", "[substruct][multithread]") {}
#endif
TEST_CASE("testChiralMatch", "[substruct][chiral]") {
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@@](F)(C)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@](F)(C)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@@](Br)(C)F";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "Cl[C@](C)(F)Br";
std::string mSmi = "Cl[C@](Br)(C)F";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@](F)(Br)CC[C@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@](F)(Br)CC[C@@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@](F)(Br)CC(C[C@](O)(F)Br)C[C@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
std::vector<MatchVectType> matches;
int count = SubstructMatch(*mol, *query, matches, true, true, true);
CHECK(count == 2);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@@](F)(Br)CC(C[C@](O)(F)Br)C[C@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
std::vector<MatchVectType> matches;
int count = SubstructMatch(*mol, *query, matches, true, true, true);
CHECK(count == 3);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@](F)(Br)CC(C[C@@](O)(F)Br)C[C@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
std::vector<MatchVectType> matches;
int count = SubstructMatch(*mol, *query, matches, true, true, true);
CHECK(count == 1);
}
{
std::string qSmi = "C[C@](O)(F)Br";
std::string mSmi = "O[C@](F)(Br)CC(C[C@@](O)(F)Br)C[C@@](O)(F)Br";
auto query = v2::SmilesParse::MolFromSmiles(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
std::vector<MatchVectType> matches;
// std::cerr<<"\n\n------------------------------------------\n"<<qSmi<<"
// "<<mSmi<<"\n"<<std::endl;
int count = SubstructMatch(*mol, *query, matches, true, true, true);
// std::cerr<<"res: "<<count<<std::endl;
CHECK(count == 0);
}
{
std::string qSmi = "Cl[C@](*)(F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@@](*)(F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "Cl[C@](*)(*)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@@](*)(*)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "[C@](C)(F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "[C@@](C)(F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C[C@](F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "C[C@@](F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@](F)Br";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "Cl[C@](C)F";
std::string mSmi = "Cl[C@](C)(F)Br";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
}
TEST_CASE("testCisTransMatch", "[substruct][stereochemistry]") {
{
std::string qSmi = "CC=CC";
std::string mSmi = "CC=CC";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "CC=CC";
std::string mSmi = "C/C=C/C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "CC=CC";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "C/C=C\\C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "C/C=C/C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "C/C=C(/F)C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "C/C=C(\\F)C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "C/C(F)=C(\\F)C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "CC(/F)=C(\\F)C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(matched);
}
{
std::string qSmi = "C/C=C/C";
std::string mSmi = "CC(\\F)=C(\\F)C";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true);
CHECK(!matched);
}
}
TEST_CASE("testCisTransMatch2", "[substruct][stereochemistry]") {
{
std::string qSmi = "CC=CC";
std::string mSmi = "CCC=CC";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
CHECK(query->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
query->getBondWithIdx(1)->getStereoAtoms().push_back(0);
query->getBondWithIdx(1)->getStereoAtoms().push_back(3);
query->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
CHECK(mol->getBondWithIdx(2)->getBondType() == Bond::DOUBLE);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(1);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(4);
mol->getBondWithIdx(2)->setStereo(Bond::STEREOCIS);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
mol->getBondWithIdx(2)->setStereo(Bond::STEREOTRANS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
query->getBondWithIdx(1)->setStereo(Bond::STEREONONE);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
query->getBondWithIdx(1)->setStereo(Bond::STEREOANY);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
}
{
std::string qSmi = "CC=CC";
std::string mSmi = "CC=C(C)F";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
CHECK(query->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
query->getBondWithIdx(1)->getStereoAtoms().push_back(0);
query->getBondWithIdx(1)->getStereoAtoms().push_back(3);
query->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
CHECK(mol->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
mol->getBondWithIdx(1)->getStereoAtoms().push_back(0);
mol->getBondWithIdx(1)->getStereoAtoms().push_back(3);
mol->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
mol->getBondWithIdx(1)->setStereo(Bond::STEREOTRANS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
query->getBondWithIdx(1)->setStereo(Bond::STEREONONE);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
query->getBondWithIdx(1)->setStereo(Bond::STEREOANY);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
}
{
std::string qSmi = "CC=CC";
std::string mSmi = "CCC=C(C)F";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
CHECK(query->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
query->getBondWithIdx(1)->getStereoAtoms().push_back(0);
query->getBondWithIdx(1)->getStereoAtoms().push_back(3);
query->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
CHECK(mol->getBondWithIdx(2)->getBondType() == Bond::DOUBLE);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(1);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(4);
mol->getBondWithIdx(2)->setStereo(Bond::STEREOCIS);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
mol->getBondWithIdx(2)->setStereo(Bond::STEREOTRANS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
query->getBondWithIdx(1)->setStereo(Bond::STEREONONE);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
query->getBondWithIdx(1)->setStereo(Bond::STEREOANY);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
}
{ // now make it harder: the stereoatoms don't match, but the stereochemistry
// does
std::string qSmi = "CC=CC";
std::string mSmi = "CCC=C(C)F";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
CHECK(query->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
query->getBondWithIdx(1)->getStereoAtoms().push_back(0);
query->getBondWithIdx(1)->getStereoAtoms().push_back(3);
query->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
CHECK(mol->getBondWithIdx(2)->getBondType() == Bond::DOUBLE);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(1);
mol->getBondWithIdx(2)->getStereoAtoms().push_back(5);
mol->getBondWithIdx(2)->setStereo(Bond::STEREOTRANS);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
mol->getBondWithIdx(2)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
query->getBondWithIdx(1)->setStereo(Bond::STEREONONE);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
query->getBondWithIdx(1)->setStereo(Bond::STEREOANY);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
}
{ // now make it harder: the stereoatoms don't match on either end, but the
// stereochemistry does
std::string qSmi = "CC=CC";
std::string mSmi = "CCC(F)=C(C)F";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
CHECK(query->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
query->getBondWithIdx(1)->getStereoAtoms().push_back(0);
query->getBondWithIdx(1)->getStereoAtoms().push_back(3);
query->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::DOUBLE);
mol->getBondWithIdx(3)->getStereoAtoms().push_back(3);
mol->getBondWithIdx(3)->getStereoAtoms().push_back(6);
mol->getBondWithIdx(3)->setStereo(Bond::STEREOCIS);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
mol->getBondWithIdx(3)->setStereo(Bond::STEREOTRANS);
CHECK(!SubstructMatch(*mol, *query, matchV, true, true));
CHECK(SubstructMatch(*mol, *query, matchV, true, false));
query->getBondWithIdx(1)->setStereo(Bond::STEREONONE);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
query->getBondWithIdx(1)->setStereo(Bond::STEREOANY);
CHECK(SubstructMatch(*mol, *query, matchV, true, true));
}
}
TEST_CASE("testGitHubIssue15", "[substruct][github][issue15]") {
{
std::string qSmi = "[R2]~[R1]~[R2]";
std::string mSmi = "CCC";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true, true);
CHECK(!matched);
}
{
std::string qSmi = "[R2]~[R1]~[R2]";
std::string mSmi = "CCC";
auto query = v2::SmilesParse::MolFromSmarts(qSmi);
auto mol = v2::SmilesParse::MolFromSmiles(mSmi);
MatchVectType matchV;
bool matched = SubstructMatch(*mol, *query, matchV, true, true, true);
CHECK(!matched);
}
}
TEST_CASE("testGitHubIssue409", "[substruct][github][issue409]") {
{
std::string smi = "FC(F)(F)CC(F)(F)F";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
std::vector<MatchVectType> matches;
unsigned int matched =
SubstructMatch(*mol, *mol, matches, false, true, false, false);
CHECK(matched == matches.size());
CHECK(matches.size() == 72);
matched =
SubstructMatch(*mol, *mol, matches, false, true, false, false, 16);
CHECK(matches.size() == 16);
}
}
TEST_CASE("testGitHubIssue688", "[substruct][github][issue688]") {
{
std::string smi = "C1CC[C@](Cl)(N)O1";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
CHECK(mol);
// mol->debugMol(std::cerr);
std::string sma = "C1CC[C@](N)O1";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
// qmol->updatePropertyCache();
// qmol->debugMol(std::cerr);
MatchVectType match;
CHECK(SubstructMatch(*mol, *qmol, match, true, false));
CHECK(match.size() == qmol->getNumAtoms());
CHECK(SubstructMatch(*mol, *qmol, match, true, true));
CHECK(match.size() == qmol->getNumAtoms());
}
{
std::string smi = "C1CC[C@](Cl)(N)O1";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
CHECK(mol);
// mol->debugMol(std::cerr);
std::string sma = "C1CC[C@@](N)O1";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
// qmol->updatePropertyCache();
// qmol->debugMol(std::cerr);
MatchVectType match;
CHECK(SubstructMatch(*mol, *qmol, match, true, false));
CHECK(match.size() == qmol->getNumAtoms());
CHECK(!SubstructMatch(*mol, *qmol, match, true, true));
}
{
std::string smi = "N[C@]1(Cl)CCCO1";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
CHECK(mol);
// mol->debugMol(std::cerr);
std::string sma = "N[C@]1CCCO1";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
// qmol->updatePropertyCache();
// qmol->debugMol(std::cerr);
// std::cerr << MolToSmiles(*qmol, true) << std::endl;
MatchVectType match;
CHECK(SubstructMatch(*mol, *qmol, match, true, false));
CHECK(match.size() == qmol->getNumAtoms());
CHECK(SubstructMatch(*mol, *qmol, match, true, true));
CHECK(match.size() == qmol->getNumAtoms());
}
{
std::string smi = "N[C@]1(Cl)CCCO1";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
CHECK(mol);
// mol->debugMol(std::cerr);
std::string sma = "N[C@@]1CCCO1";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
// qmol->updatePropertyCache();
// qmol->debugMol(std::cerr);
// std::cerr << MolToSmiles(*qmol, true) << std::endl;
MatchVectType match;
CHECK(SubstructMatch(*mol, *qmol, match, true, false));
CHECK(match.size() == qmol->getNumAtoms());
CHECK(!SubstructMatch(*mol, *qmol, match, true, true));
}
}
TEST_CASE("testDativeMatch", "[substruct][dative]") {
{
std::string smi = "[Cu]->[Fe]";
auto mol = v2::SmilesParse::MolFromSmiles(smi);
CHECK(mol);
// make sure a self-match works
MatchVectType match;
CHECK(SubstructMatch(*mol, *mol, match));
CHECK(match.size() == mol->getNumAtoms());
{ // reverse the order and make sure that works
std::string sma = "[Fe]<-[Cu]";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
MatchVectType match;
CHECK(SubstructMatch(*mol, *qmol, match));
CHECK(match.size() == qmol->getNumAtoms());
}
{ // reverse the direction and make sure that does not work.
std::string sma = "[Fe]->[Cu]";
auto qmol = v2::SmilesParse::MolFromSmarts(sma);
CHECK(qmol);
MatchVectType match;
CHECK(!SubstructMatch(*mol, *qmol, match));
}
}
}
TEST_CASE("testGithubIssue1489", "[substruct][github][issue1489]") {
{
std::string smi1 = "CCC[C@@H]1CN(CCC)CCN1";
std::string smi2 = "CCC[C@H]1CN(CCC)CCN1";
auto mol1 = v2::SmilesParse::MolFromSmiles(smi1);
CHECK(mol1);
auto mol2 = v2::SmilesParse::MolFromSmiles(smi2);
CHECK(mol2);
bool recursionPossible = true;
bool useChirality = true;
MatchVectType match;
// make sure self-matches work
CHECK(SubstructMatch(*mol1, *mol1, match, recursionPossible, useChirality));
CHECK(SubstructMatch(*mol2, *mol2, match, recursionPossible, useChirality));
// check matches using the molecules from smiles:
CHECK(
!SubstructMatch(*mol1, *mol2, match, recursionPossible, useChirality));
CHECK(SubstructMatch(*mol1, *mol2, match, recursionPossible, false));
{
auto qmol1 = v2::SmilesParse::MolFromSmarts(smi1);
qmol1->updatePropertyCache();
CHECK(qmol1);
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible, false));
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible,
useChirality));
CHECK(SubstructMatch(*mol2, *qmol1, match, recursionPossible, false));
CHECK(!SubstructMatch(*mol2, *qmol1, match, recursionPossible,
useChirality));
}
}
{
std::string smi1 = "F([C@@H](Cl)Br)";
auto mol1 = v2::SmilesParse::MolFromSmiles(smi1);
CHECK(mol1);
bool recursionPossible = true;
bool useChirality = true;
MatchVectType match;
// make sure self-matches work
CHECK(SubstructMatch(*mol1, *mol1, match, recursionPossible, useChirality));
{
auto qmol1 = v2::SmilesParse::MolFromSmarts(smi1);
qmol1->updatePropertyCache();
CHECK(qmol1);
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible, false));
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible,
useChirality));
}
{
std::string smi2 = "F([C@H](Br)Cl)";
auto qmol1 = v2::SmilesParse::MolFromSmarts(smi2);
qmol1->updatePropertyCache();
CHECK(qmol1);
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible, false));
CHECK(SubstructMatch(*mol1, *qmol1, match, recursionPossible,
useChirality));
}
}
}
TEST_CASE("testGithub2570", "[substruct][github][issue2570]") {
bool uniquify = true;
bool recursionPossible = true;
bool useChirality = true;
{
const auto mol = R"(C[C@](Cl)(Br)F)"_smiles;
{
const auto query = R"([C@](Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // Swap order of a pair of atoms
const auto query = R"([C@](Br)(Cl)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](Br)(Cl)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // Smaller fragments should always match as long as they have have a
// chiral tag,
// as these don't have enough neighbors to define CW/CCW chirality
const std::vector<std::string> smarts({"[C@](Cl)Br", "[C@@](Cl)Br",
"[C@](Br)F", "[C@@](Br)F", "[C@]F",
"[C@@]F", "[C@]", "[C@@]"});
std::vector<MatchVectType> matches;
for (const auto &sma : smarts) {
std::unique_ptr<ROMol> query(SmartsToMol(sma));
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
}
}
{ // Mol also starting with the chiral atom
const auto mol = R"([C@](C)(Cl)(Br)F)"_smiles;
{
const auto query = R"([C@](C)(Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](C)(Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@](C)(Cl)Br)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](C)(Cl)Br)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@](Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](Cl)(Br)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // Swap order of a pair of atoms
const auto query = R"([C@](Br)(Cl)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto query = R"([C@@](Br)(Cl)F)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
}
{ // Start from a physical H atom
const auto mol = R"([H][C@](O)(F)Cl)"_smiles;
const auto smarts = MolToSmarts(*mol);
std::unique_ptr<ROMol> query(SmartsToMol(smarts));
CHECK(smarts == R"([#8]-[#6@@H](-[#9])-[#17])");
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto mol = R"([H][C@](O)(F)Cl)"_smiles;
const auto query = R"([C@H](O)(F)Cl)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto mol = R"([H][C@](O)(F)Cl)"_smiles;
const auto query = R"([C@@H](O)(F)Cl)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // Start from an attached H atom
const auto mol = R"([C@H](O)(F)Cl)"_smiles;
const auto smarts = MolToSmarts(*mol);
CHECK(smarts == R"([#8]-[#6@@H](-[#9])-[#17])");
const auto query = v2::SmilesParse::MolFromSmarts(smarts);
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto mol = R"([C@H](O)(F)Cl)"_smiles;
const auto query = R"([C@H](O)(F)Cl)"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto mol = R"([C@H](O)(F)Cl)"_smiles;
const auto query = R"([C@@H](O)(F)Cl)"_smarts;
std::vector<MatchVectType> matches;
CHECK(!SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // Without H
const auto mol = R"([C@](O)(F)(Cl)C)"_smiles;
const auto smarts = MolToSmarts(*mol);
const auto query = v2::SmilesParse::MolFromSmarts(smarts);
CHECK(smarts == R"([#8]-[#6@](-[#9])(-[#17])-[#6])");
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{
const auto mol = R"([C@](O)(F)(Cl)C)"_smiles;
const auto query = R"([#6@](-[#8])(-[#9])(-[#17])-[#6])"_smarts;
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol, *query, matches, uniquify, recursionPossible,
useChirality));
}
{ // What about queries not coming from SMARTS?
const std::vector<std::string> smiles( // These are all equivalent
{"N[C@@]([H])(C)C(=O)O", "N[C@@H](C)C(=O)O", "N[C@H](C(=O)O)C",
"[H][C@](N)(C)C(=O)O", "[C@H](N)(C)C(=O)O"});
for (const auto &smi1 : smiles) {
const auto mol1 = std::unique_ptr<ROMol>(SmilesToMol(smi1));
for (const auto &smi2 : smiles) { // Test them in both directions
const auto mol2 = std::unique_ptr<ROMol>(SmilesToMol(smi2));
std::vector<MatchVectType> matches;
CHECK(SubstructMatch(*mol1, *mol2, matches, uniquify, recursionPossible,
useChirality));
};
}
}
}
TEST_CASE("testEZVsCisTransMatch", "[substruct][stereochemistry]") {
UseLegacyStereoPerceptionFixture fx(true);
const auto mol = R"(F/C(C)=C(C)/Cl)"_smiles;
{
const Bond *stereoBnd = mol->getBondWithIdx(2);
CHECK(stereoBnd->getStereo() == Bond::STEREOE);
}
// pairs of {query, matching expectation}
const std::vector<std::pair<std::string, bool>> checks({
{R"(F/C(C)=C(C)/Cl)", true}, // identical
{R"(F\C(C)=C(C)\Cl)", true}, // symmetric
{R"(F/C(C)=C(C)\Cl)", false}, // opposite
{R"(F\C(C)=C(C)/Cl)", false} // symmetric opposite
});
// Test with same stereoatoms as mol
for (const auto &check : checks) {
auto query = v2::SmilesParse::MolFromSmiles(check.first);
{
Bond *stereoBnd = query->getBondWithIdx(2);
auto stereo = stereoBnd->getStereo();
CHECK((stereo == Bond::STEREOE || stereo == Bond::STEREOZ));
stereoBnd->setStereoAtoms(0, 5); // Same as mol
stereo = Chirality::translateEZLabelToCisTrans(stereo);
CHECK((stereo == Bond::STEREOCIS || stereo == Bond::STEREOTRANS));
stereoBnd->setStereo(stereo);
}
MatchVectType match;
bool recursionPossible = true;
bool useChirality = true;
CHECK(check.second ==
SubstructMatch(*mol, *query, match, recursionPossible, useChirality));
}
// Symmetrize stereoatoms
for (const auto &check : checks) {
auto query = v2::SmilesParse::MolFromSmiles(check.first);
{
Bond *stereoBnd = query->getBondWithIdx(2);
auto stereo = stereoBnd->getStereo();
CHECK((stereo == Bond::STEREOE || stereo == Bond::STEREOZ));
stereoBnd->setStereoAtoms(2, 4); // symmetric to mol
stereo = Chirality::translateEZLabelToCisTrans(stereo);
CHECK((stereo == Bond::STEREOCIS || stereo == Bond::STEREOTRANS));
stereoBnd->setStereo(stereo);
}
MatchVectType match;
bool recursionPossible = true;
bool useChirality = true;
CHECK(check.second ==
SubstructMatch(*mol, *query, match, recursionPossible, useChirality));
}
// Flip one stereoatom and the label
for (const auto &check : checks) {
auto query = v2::SmilesParse::MolFromSmiles(check.first);
{
Bond *stereoBnd = query->getBondWithIdx(2);
auto stereo = stereoBnd->getStereo();
CHECK((stereo == Bond::STEREOE || stereo == Bond::STEREOZ));
stereoBnd->setStereoAtoms(0, 4); // Reverse second stereoatom
if (stereo == Bond::STEREOE) {
stereo = Bond::STEREOCIS;
} else {
stereo = Bond::STEREOTRANS;
}
stereoBnd->setStereo(stereo);
}
MatchVectType match;
bool recursionPossible = true;
bool useChirality = true;
CHECK(check.second ==
SubstructMatch(*mol, *query, match, recursionPossible, useChirality));
}
}
TEST_CASE("testMostSubstitutedCoreMatch", "[substruct][core]") {
auto core = "[*:1]c1cc([*:2])ccc1[*:3]"_smarts;
auto orthoMeta = "c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1"_smiles;
auto ortho = "c1ccc(-c2ccccc2-c2ccccc2)cc1"_smiles;
auto meta = "c1ccc(-c2cccc(-c3ccccc3)c2)cc1"_smiles;
auto biphenyl = "c1ccccc1-c1ccccc1"_smiles;
auto phenyl = "c1ccccc1"_smiles;
struct numHsMatchingDummies {
static unsigned int get(const ROMol &mol, const ROMol &core,
const MatchVectType &match) {
return std::count_if(
match.begin(), match.end(),
[&mol, &core](const std::pair<int, int> &pair) {
return (core.getAtomWithIdx(pair.first)->getAtomicNum() == 0 &&
mol.getAtomWithIdx(pair.second)->getAtomicNum() == 1);
});
}
};
const auto &coreRef = *core;
for (auto &molResPair : std::vector<std::pair<RDKit::RWMol *, unsigned>>{
std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u),
std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u),
std::make_pair(phenyl.get(), 3u)}) {
auto &mol = *molResPair.first;
const auto res = molResPair.second;
MolOps::addHs(mol);
auto matches = SubstructMatch(mol, coreRef);
auto bestMatch = getMostSubstitutedCoreMatch(mol, coreRef, matches);
CHECK(numHsMatchingDummies::get(mol, coreRef, bestMatch) == res);
std::vector<unsigned int> ctrlCounts(matches.size());
std::transform(matches.begin(), matches.end(), ctrlCounts.begin(),
[&mol, &coreRef](const MatchVectType &match) {
return numHsMatchingDummies::get(mol, coreRef, match);
});
std::sort(ctrlCounts.begin(), ctrlCounts.end());
std::vector<unsigned int> sortedCounts(matches.size());
auto sortedMatches =
sortMatchesByDegreeOfCoreSubstitution(mol, coreRef, matches);
std::transform(sortedMatches.begin(), sortedMatches.end(),
sortedCounts.begin(),
[&mol, &coreRef](const MatchVectType &match) {
return numHsMatchingDummies::get(mol, coreRef, match);
});
CHECK(ctrlCounts == sortedCounts);
}
std::vector<MatchVectType> emptyMatches;
bool raised = false;
try {
getMostSubstitutedCoreMatch(*orthoMeta, coreRef, emptyMatches);
} catch (const Invar::Invariant &) {
raised = true;
}
CHECK(raised);
raised = false;
try {
sortMatchesByDegreeOfCoreSubstitution(*orthoMeta, coreRef, emptyMatches);
} catch (const Invar::Invariant &) {
raised = true;
}
CHECK(raised);
}
TEST_CASE("testLongRing", "[substruct][ring]") {
std::string mol_smiles = "c12ccc(CCCCCCCc5ccc(C2)cc5)cc1";
std::string query_smiles = "c1cc2ccc1CCCCCCCc1ccc(cc1)C2";
auto mol = v2::SmilesParse::MolFromSmiles(mol_smiles);
auto query = v2::SmilesParse::MolFromSmiles(query_smiles);
CHECK(MolToSmiles(*query) == MolToSmiles(*mol));
MatchVectType match1;
MatchVectType match2;
SubstructMatchParameters params;
CHECK(SubstructMatch(*mol, *query, match1));
CHECK(SubstructMatch(*query, *mol, match2));
}
TEST_CASE("testIsAtomTerminalRGroupOrQueryHydrogen", "[substruct][rgroup]") {
{
auto mol = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-0.3795 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0939 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0939 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3795 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3349 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3349 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0494 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 1 4 0 0 0 0
6 7 1 0 0 0 0
M RGP 1 7 1
M END
)CTAB"_ctab;
const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
CHECK(isAtomTerminalRGroupOrQueryHydrogen(rAtom));
}
{
auto mol = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-0.7589 1.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4733 1.0152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4733 0.1901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7589 -0.2223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0444 0.1901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0444 1.0152 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
M RGP 1 6 1
M END
)CTAB"_ctab;
const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
CHECK(!isAtomTerminalRGroupOrQueryHydrogen(rAtom));
}
{
auto mol = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-0.9152 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6296 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6296 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9152 -1.3607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2007 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2007 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5137 0.2893 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 1 4 0 0 0 0
6 7 1 0 0 0 0
M ALS 7 10 F H C N O F P S Cl Br I
M END
)CTAB"_ctab;
const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
CHECK(isAtomTerminalRGroupOrQueryHydrogen(rAtom));
}
{
auto mol = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-0.9152 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6296 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6296 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9152 -1.3607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2007 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2007 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5137 0.2893 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 1 4 0 0 0 0
6 7 1 0 0 0 0
M ALS 7 9 F C N O F P S Cl Br I
M END
)CTAB"_ctab;
const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
CHECK(!isAtomTerminalRGroupOrQueryHydrogen(rAtom));
}
}
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