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710bdfa60b8cad37cbdf8da33fd62eeea488d7bd
rdkit/Code/GraphMol/catch_tests.cpp
Greg Landrum fc374a9622 Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646) 
* Fixes a molblock writing problem
with undervalent atoms from the organic subset

* Fixes #2649

Also ensures that allenes are not written as crossed bonds
(which does not make sense at the moment anyway)

* clang-format run
2019-09-20 09:13:19 -04:00

546 lines
19 KiB
C++
Raw Blame History

#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
// this in one cpp file
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
using namespace RDKit;
#if 1
TEST_CASE("SMILES Parsing works", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 3);
}
TEST_CASE("Sanitization tests", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 13);
SECTION("properties") {
mol->updatePropertyCache();
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
SECTION("aromaticity") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY);
// mol->debugMol(std::cerr);
CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
// blocked by #1730
// CHECK(mol->getAtomWithIdx(0)->getIsAromatic());
}
SECTION("kekulize") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(!mol->getAtomWithIdx(7)->getIsAromatic());
}
}
}
TEST_CASE("Github #2062", "[bug, molops]") {
SmilesParserParams ps;
ps.removeHs = false;
ps.sanitize = true;
std::unique_ptr<RWMol> mol(SmilesToMol("[C:1][C:2]([H:3])([H])[O:4][H]", ps));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 6);
mol->getAtomWithIdx(1)->setProp("intProp", 42);
MolOps::mergeQueryHs(*mol);
CHECK(mol->getNumAtoms() == 3);
SECTION("basics") { CHECK(mol->getAtomWithIdx(1)->getAtomMapNum() == 2); }
SECTION("other props") {
REQUIRE(mol->getAtomWithIdx(1)->hasProp("intProp"));
CHECK(mol->getAtomWithIdx(1)->getProp<int>("intProp") == 42);
}
}
TEST_CASE("Github #2086", "[bug, molops]") {
SECTION("reported version") {
auto mol = "C1CCCC1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
REQUIRE(mol->getNumAtoms() == 15);
mol->removeBond(4, 13);
MolOps::removeHs(*mol);
REQUIRE(mol->getNumAtoms() == 6);
}
}
TEST_CASE("github #299", "[bug, molops, SSSR]") {
SECTION("simplified") {
auto mol =
"C13%13%14.C124%18.C25%13%15.C368%17.C4679.C75%10%17.C8%11%14%16.C9%11%12%18.C%10%12%15%16"_smiles;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 9);
}
SECTION("old example from molopstest") {
auto mol = "C123C45C11C44C55C22C33C14C523"_smiles;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 9);
}
SECTION("carborane") {
std::unique_ptr<RWMol> mol(
SmilesToMol("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822["
"C]933[B]%1045[C]6123",
0, false));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 12);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
SECTION("original report from ChEbI") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> mol(
MolFileToMol(pathName + "ChEBI_50252.mol", false));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 80);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
}
TEST_CASE("github #2224", "[bug, molops, removeHs, query]") {
SECTION("the original report") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> mol(MolFileToMol(pathName + "github2224_1.mol"));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 7);
}
SECTION("basics") {
SmilesParserParams ps;
ps.removeHs = false;
ps.sanitize = true;
std::unique_ptr<ROMol> mol(SmilesToMol("C[H]", ps));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 2);
{ // The H without a query is removed
std::unique_ptr<ROMol> m2(MolOps::removeHs(*mol));
CHECK(m2->getNumAtoms() == 1);
}
{ // but if we add a query feature it's not removed
RWMol m2(*mol);
auto *qa = new QueryAtom(1);
m2.replaceAtom(1, qa);
m2.getAtomWithIdx(1)->setAtomicNum(1);
MolOps::removeHs(m2);
CHECK(m2.getNumAtoms() == 2);
delete qa;
}
}
}
TEST_CASE(
"github #2268: Recognize N in three-membered rings as potentially chiral",
"[bug,stereo]") {
SECTION("basics: N in a 3 ring") {
const auto mol = "C[N@]1CC1C"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("basics: N in a 4 ring") {
const auto mol = "C[N@]1CCC1C"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
}
SECTION("the original molecule") {
std::string mb = R"CTAB(
Mrv1810 02131915062D
18 20 0 0 1 0 999 V2000
-0.7207 -1.3415 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
-0.0583 -0.8416 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.0083 -1.7540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3956 -0.8666 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.3250 -0.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1955 -0.6499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1499 -0.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6541 -0.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7830 -1.2291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.6081 -1.6623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4080 0.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3665 -0.8374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6416 0.3958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1996 0.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4121 1.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3498 0.8207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0790 -0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0665 0.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
1 3 1 1 0 0 0
4 1 1 0 0 0 0
5 2 1 0 0 0 0
4 6 1 0 0 0 0
7 4 1 0 0 0 0
2 8 1 6 0 0 0
9 6 2 0 0 0 0
4 10 1 1 0 0 0
11 6 1 0 0 0 0
12 8 2 0 0 0 0
13 8 1 0 0 0 0
14 11 1 0 0 0 0
15 14 1 0 0 0 0
16 13 2 0 0 0 0
17 12 1 0 0 0 0
18 16 1 0 0 0 0
2 3 1 0 0 0 0
5 7 1 0 0 0 0
17 18 2 0 0 0 0
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
}
TEST_CASE("github #2244", "[bug, molops, stereo]") {
SECTION("the original report") {
auto mol = "CC=CC=CC"_smiles;
REQUIRE(mol);
MolOps::findPotentialStereoBonds(*mol, true);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
mol->getBondWithIdx(3)->setStereo(Bond::STEREONONE);
MolOps::findPotentialStereoBonds(*mol, true);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
}
}
TEST_CASE(
"github #2258: heterocycles with exocyclic bonds not failing valence check",
"[bug, molops]") {
SECTION("the original report") {
std::vector<std::string> smiles = {"C=n1ccnc1", "C#n1ccnc1"};
for (auto smi : smiles) {
CHECK_THROWS_AS(SmilesToMol(smi), MolSanitizeException);
}
}
}
TEST_CASE("github #908: AddHs() using 3D coordinates with 2D conformations",
"[bug, molops]") {
SECTION("basics: single atom mols") {
std::vector<std::string> smiles = {"Cl", "O", "N", "C"};
for (auto smi : smiles) {
// std::cerr << smi << std::endl;
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
auto conf = new Conformer(1);
conf->set3D(false);
conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0));
mol->addConformer(conf, true);
bool explicitOnly = false;
bool addCoords = true;
MolOps::addHs(*mol, explicitOnly, addCoords);
for (size_t i = 0; i < mol->getNumAtoms(); ++i) {
// std::cerr << " " << i << " " << conf->getAtomPos(i) << std::endl;
CHECK(conf->getAtomPos(i).z == 0.0);
}
}
}
}
#endif
TEST_CASE(
"github #2437: Canon::rankMolAtoms results in crossed double bonds in "
"rings",
"[bug, molops]") {
SECTION("underlying problem") {
std::string molb = R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb, sanitize, removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
std::vector<unsigned int> ranks;
CHECK(!mol->getRingInfo()->isInitialized());
Canon::rankMolAtoms(*mol, ranks);
CHECK(!mol->getRingInfo()->isInitialized());
}
SECTION("as discovered") {
std::string molb = R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb, sanitize, removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
auto nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks);
nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
}
}
TEST_CASE(
"github #2423: Incorrect assignment of explicit Hs to Al+3 read from mol "
"block",
"[bug, molops]") {
SECTION("basics: single atom mols") {
std::string mb = R"CTAB(2300
-OEChem-01301907122D
1 0 0 0 0 0 0 0 0999 V2000
-66.7000 999.0000 0.0000 Al 0 1 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 3
M END)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 3);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE("Specialized exceptions for sanitization errors", "[molops]") {
SECTION("AtomValenceException") {
std::vector<std::pair<std::string, unsigned int>> smiles = {
{"C=n1ccnc1", 1}, {"CCO(C)C", 2}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), AtomValenceException);
try {
auto m = SmilesToMol(pr.first);
} catch (const AtomValenceException &e) {
CHECK(e.getType() == "AtomValenceException");
CHECK(e.getAtomIdx() == pr.second);
}
}
}
SECTION("AtomKekulizeException") {
std::vector<std::pair<std::string, unsigned int>> smiles = {
{"CCcc", 2}, {"C1:c:CC1", 0}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), AtomKekulizeException);
try {
auto m = SmilesToMol(pr.first);
} catch (const AtomKekulizeException &e) {
CHECK(e.getType() == "AtomKekulizeException");
CHECK(e.getAtomIdx() == pr.second);
}
}
}
SECTION("KekulizeException") {
std::vector<std::pair<std::string, std::vector<unsigned int>>> smiles = {
{"c1cccc1", {0, 1, 2, 3, 4}}, {"Cc1cc1", {1, 2, 3}}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), KekulizeException);
try {
auto m = SmilesToMol(pr.first);
} catch (const KekulizeException &e) {
CHECK(e.getType() == "KekulizeException");
CHECK(e.getAtomIndices() == pr.second);
}
}
}
}
TEST_CASE("detectChemistryProblems", "[molops]") {
SECTION("Basics") {
SmilesParserParams ps;
ps.sanitize = false;
auto m = std::unique_ptr<ROMol>(SmilesToMol("CO(C)CFCc1cc1", ps));
REQUIRE(m);
auto res = MolOps::detectChemistryProblems(*m);
REQUIRE(res.size() == 3);
CHECK(res[0]->getType() == "AtomValenceException");
REQUIRE(dynamic_cast<AtomValenceException *>(res[0].get()));
CHECK(dynamic_cast<AtomSanitizeException *>(res[0].get())->getAtomIdx() ==
1);
CHECK(res[1]->getType() == "AtomValenceException");
REQUIRE(dynamic_cast<AtomSanitizeException *>(res[1].get()));
CHECK(dynamic_cast<AtomSanitizeException *>(res[1].get())->getAtomIdx() ==
4);
CHECK(res[2]->getType() == "KekulizeException");
REQUIRE(dynamic_cast<KekulizeException *>(res[2].get()));
CHECK(dynamic_cast<KekulizeException *>(res[2].get())->getAtomIndices() ==
std::vector<unsigned int>({6, 7, 8}));
}
SECTION("No problems") {
SmilesParserParams ps;
ps.sanitize = false;
auto m = std::unique_ptr<ROMol>(SmilesToMol("c1ccccc1", ps));
REQUIRE(m);
auto res = MolOps::detectChemistryProblems(*m);
REQUIRE(res.size() == 0);
}
}
TEST_CASE(
"github #2606: Bad valence corrections on Pb, Sn"
"[bug, molops]") {
SECTION("basics-Pb") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Sn") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Ge") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Ge 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE(
"github #2607: Pb, Sn should support valence 2"
"[bug, molops]") {
SECTION("basics-Pb") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
3 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 3 1 2 2 -1 3 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Sn") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
3 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 3 1 2 2 -1 3 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE(
"github #2649: Allenes read from mol blocks have crossed bonds assigned"
"[bug, stereochemistry]") {
SECTION("basics") {
std::string mb = R"CTAB(mol
Mrv1824 09191901002D
6 5 0 0 0 0 999 V2000
-1.6986 -7.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2522 -6.8245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1438 -8.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8095 -6.2156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3374 -7.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6162 -6.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 3 2 0 0 0 0
2 1 2 0 0 0 0
3 5 1 0 0 0 0
4 2 2 0 0 0 0
6 4 1 0 0 0 0
M END)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
auto outmolb = MolToMolBlock(*mol);
// std::cerr<<outmolb<<std::endl;
CHECK(outmolb.find("1 3 2 0") != std::string::npos);
CHECK(outmolb.find("2 1 2 0") != std::string::npos);
CHECK(outmolb.find("4 2 2 0") != std::string::npos);
}
}
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