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rdkit/External/INCHI-API/test.cpp

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#include <iostream>
#include <fstream>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/lexical_cast.hpp>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/StreamOps.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Descriptors/Crippen.h>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
#include "inchi.h"
using namespace RDKit;
#ifdef RDK_TEST_MULTITHREADED
namespace {
void runblock(const std::vector<ROMol *> &mols, unsigned int count,
unsigned int idx, const std::vector<std::string> &inchis,
const std::vector<std::string> &keys) {
for (unsigned int j = 0; j < 200; j++) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) {
continue;
}
ROMol *mol = mols[i];
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*mol, tmp);
TEST_ASSERT(inchi == inchis[i]);
std::string key = InchiToInchiKey(inchi);
TEST_ASSERT(key == keys[i]);
std::string key2 = MolToInchiKey(*mol);
TEST_ASSERT(key2 == keys[i]);
ROMol *mol2 = InchiToMol(inchi, tmp);
TEST_ASSERT(mol2);
ExtraInchiReturnValues tmp2;
std::string inchi2 = MolToInchi(*mol2, tmp2);
TEST_ASSERT(inchi == inchi2);
delete mol2;
std::string mol_block = MolToMolBlock(*mol);
ExtraInchiReturnValues tmp3;
std::string inchi3 = MolBlockToInchi(mol_block, tmp3);
TEST_ASSERT(inchi == inchi3);
}
}
};
} // namespace
#include <thread>
#include <future>
void testMultiThread() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test multithreading" << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
SDMolSupplier suppl(fName);
std::cerr << "reading molecules" << std::endl;
std::vector<ROMol *> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = suppl.next();
TEST_ASSERT(mol != nullptr);
mols.push_back(mol);
}
TEST_ASSERT(mols.size() == 100);
std::cerr << "generating reference data" << std::endl;
std::vector<std::string> inchis;
std::vector<std::string> keys;
for (const auto *mol : mols) {
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*mol, tmp);
std::string key = InchiToInchiKey(inchi);
inchis.push_back(inchi);
keys.push_back(key);
}
std::vector<std::future<void>> tg;
std::cerr << "processing" << std::endl;
unsigned int count = 4;
for (unsigned int i = 0; i < count; ++i) {
std::cerr << " launch :" << i << std::endl;
std::cerr.flush();
tg.emplace_back(std::async(std::launch::async, runblock, std::ref(mols),
count, i, std::ref(inchis), std::ref(keys)));
}
for (auto &fut : tg) {
fut.get();
}
for (auto &mol : mols) {
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMultiThread2() {
const char *smiles_init[] = {
"C#Cc1ccc2c(c1)C(C(=O)Nc1nncn1C1CC1)CCO2",
"C=C(C(=O)C1CCOc2ccc(Cl)cc21)c1cncn1C1CC1",
"C=CC(=O)N(C(=O)[C@@H]1CCOc2ccc(Cl)cc21)c1nncn1C1CC1",
"C=CC(=O)N[C@@]1(C(=O)Nc2nncn2C2CC2)CCOc2ccc(Cl)cc21",
"CC#CC(=O)N(C(=O)[C@@H]1CCOc2ccc(Cl)cc21)c1nncn1C1CC1",
"CC(C(=O)Nc1nncn1C1CC1)c1cccc(Cl)c1",
"CC(C)c1scnc1NC(=O)C1CCOc2ccc(Cl)cc21",
"CC(C)n1c(NC(=O)C2CCOc3ccccc32)nc2ccccc21",
};
const char *inchikeys_init[] = {
"FSPOGANMWXTKGJ-UHFFFAOYSA-N", "CIBQANUIVWKYMR-UHFFFAOYSA-N",
"GBPCXKPRLGZQQB-CYBMUJFWSA-N", "IOOIGOWFYCNXKX-SFHVURJKSA-N",
"XSYMIYIQKSFGOG-CQSZACIVSA-N", "BLJFTMZJZUGEGJ-UHFFFAOYSA-N",
"CEVCYTUHJSCLCQ-UHFFFAOYSA-N", "FHPRHOONYCYTIX-UHFFFAOYSA-N",
};
auto lambda = [](const std::string &smiles,
const std::string &expected_inchikey) {
ROMol *mol = SmilesToMol(smiles);
std::string key = MolToInchiKey(*mol);
TEST_ASSERT(key == expected_inchikey);
delete mol;
};
const std::vector<std::string> smiles(smiles_init, std::end(smiles_init));
const std::vector<std::string> inchikeys(inchikeys_init,
std::end(inchikeys_init));
std::vector<std::future<void>> futures;
for (size_t i = 0; i < smiles.size(); ++i) {
futures.emplace_back(std::async(std::launch::async, lambda,
std::ref(smiles[i]),
std::ref(inchikeys[i])));
}
for (auto &fut : futures) {
fut.get();
}
}
#else
void testMultiThread() {
{}
}
void testMultiThread2() {
{}
}
#endif
void testGithubIssue3() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github issue 3: bad inchis when mol has no stereoinfo"
<< std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/External/INCHI-API/test_data/github3.mol";
auto *m = static_cast<ROMol *>(MolFileToMol(fName));
TEST_ASSERT(m);
std::string smi = MolToSmiles(*m, true);
TEST_ASSERT(smi == "CNC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO");
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi ==
"InChI=1S/C7H17NO5/c1-8-2-4(10)6(12)7(13)5(11)3-9/"
"h4-13H,2-3H2,1H3/t4-,5+,6+,7+/m0/s1");
// blow out the stereo information with a copy:
auto *m2 = new RWMol(*m);
m2->clearComputedProps();
MolOps::sanitizeMol(*m2);
inchi = MolToInchi(*m2, tmp);
TEST_ASSERT(inchi ==
"InChI=1S/C7H17NO5/c1-8-2-4(10)6(12)7(13)5(11)3-9/"
"h4-13H,2-3H2,1H3/t4-,5+,6+,7+/m0/s1");
delete m;
delete m2;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue8() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing a consequence of the fix for github issue "
"8: bad mols from some inchis"
<< std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/External/INCHI-API/test_data/github8_extra.mol";
auto *m = static_cast<ROMol *>(MolFileToMol(fName, true, false));
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi ==
"InChI=1S/C20H13IN2O3/"
"c21-15-8-14-18(9-16(15)23)26-17-7-10(22)5-6-13(17)19(14)11-3-"
"1-2-4-12(11)20(24)25/h1-9,23H,22H2,(H,24,25)/b23-16+/i21-2");
ExtraInchiReturnValues tmp2;
ROMol *m2 = InchiToMol(inchi, tmp2);
TEST_ASSERT(m2);
std::string smi = MolToSmiles(*m2, true);
TEST_ASSERT(smi ==
"[H]/N=c1\\cc2oc3cc(N)ccc3c(-c3ccccc3C(=O)O)c-2cc1[125I]");
inchi = MolToInchi(*m2, tmp2);
TEST_ASSERT(inchi ==
"InChI=1S/C20H13IN2O3/"
"c21-15-8-14-18(9-16(15)23)26-17-7-10(22)5-6-13(17)19(14)11-3-"
"1-2-4-12(11)20(24)25/h1-9,23H,22H2,(H,24,25)/b23-16+/i21-2");
delete m;
delete m2;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue40() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github issue 40: bad MWs from inchis"
<< std::endl;
{
ExtraInchiReturnValues tmp;
std::string inchi =
"InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/"
"h2-6H,1H3,(H,11,12,14)";
ROMol *m = InchiToMol(inchi, tmp);
TEST_ASSERT(m);
double mw = MolOps::getAvgMolWt(*m);
TEST_ASSERT(feq(mw, 187.202));
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue67() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github issue 67: seg fault from inchi"
<< std::endl;
{
ExtraInchiReturnValues tmp;
std::string inchi =
"InChI=1S/C18H17N3/"
"c19-18(20)21-14-17-12-10-16(11-13-17)9-5-4-8-15-6-2-1-3-7-15/"
"h1-3,6-13H,14H2,(H4,19,20,21)/b9-8+";
ROMol *m = InchiToMol(inchi, tmp);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 21);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue68() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github issue 68: hang while reading InChI"
<< std::endl;
{
ExtraInchiReturnValues tmp;
std::string inchi =
"InChI=1S/C11H20NSSi2.Li/c1-14(2)8-9-15(3,4)12(14)10-11-6-5-7-13-11;/"
"h6-7H,8-10H2,1-4H3;/q-1;+1";
BOOST_LOG(rdInfoLog) << " parse 1:" << std::endl;
ROMol *m = InchiToMol(inchi, tmp);
BOOST_LOG(rdInfoLog) << " done" << std::endl;
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 16);
delete m;
}
{
ExtraInchiReturnValues tmp;
std::string inchi =
"InChI=1S/C12H22NSSi2.Li/"
"c1-15(2)10-11-16(3,4)13(15)8-7-12-6-5-9-14-12;/"
"h6,9H,7-8,10-11H2,1-4H3;/q-1;+1";
BOOST_LOG(rdInfoLog) << " parse 2:" << std::endl;
ROMol *m = InchiToMol(inchi, tmp);
BOOST_LOG(rdInfoLog) << " done" << std::endl;
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 17);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue296() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github issue 296: problems with chiral S and inchi"
<< std::endl;
{
std::string smiles = "C[S@@](=O)C(C)(C)C";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m1/s1");
delete m;
}
{
std::string fName = getenv("RDBASE");
fName += "/External/INCHI-API/test_data/github296.mol";
auto *m = static_cast<ROMol *>(MolFileToMol(fName));
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m1/s1");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue437() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github issue 437: problems with InChI and "
"ring stereochemistry"
<< std::endl;
// start with some general chirality checks
{
std::string smiles = "C[C@@H](F)Cl";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi == "InChI=1S/C2H4ClF/c1-2(3)4/h2H,1H3/t2-/m1/s1");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
// std::cerr<<" smi1: "<<smi1<<std::endl;
// std::cerr<<" smi2: "<<smi2<<std::endl;
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "O=[S@](Cl)F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi == "InChI=1S/ClFOS/c1-4(2)3/t4-/m1/s1");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
// std::cerr<<" smi1: "<<smi1<<std::endl;
// std::cerr<<" smi2: "<<smi2<<std::endl;
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@@H](F)[C@H](C)[C@H](C)F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C6H12F2/c1-4(5(2)7)6(3)8/h4-6H,1-3H3/t4-,5+,6-");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@@H](F)[C@H](C)[C@@H](C)F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C6H12F2/c1-4(5(2)7)6(3)8/h4-6H,1-3H3/t5-,6-/m1/s1");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
// std::cerr<<" smi1: "<<smi1<<std::endl;
// std::cerr<<" smi2: "<<smi2<<std::endl;
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@H](F)[C@H](C)[C@H](C)F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C6H12F2/c1-4(5(2)7)6(3)8/h4-6H,1-3H3/t5-,6-/m0/s1");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@H](F)[C@H](C)[C@@H](C)F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C6H12F2/c1-4(5(2)7)6(3)8/h4-6H,1-3H3/t4-,5-,6+");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
// now the rings
{
std::string smiles = "C[C@@H]1CC[C@@H](O)C[C@@H]1F";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C7H13FO/c1-5-2-3-6(9)4-7(5)8/h5-7,9H,2-4H2,1H3/"
"t5-,6-,7+/m1/s1");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@@]1(F)CC[C@@](O)(F)CC1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(
inchi ==
"InChI=1S/C7H12F2O/c1-6(8)2-4-7(9,10)5-3-6/h10H,2-5H2,1H3/t6-,7+");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@H]1CC[C@H](O)CC1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C7H14O/c1-6-2-4-7(8)5-3-6/h6-8H,2-5H2,1H3/t6-,7-");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
std::string smiles = "C[C@H]1CC[C@](O)(F)CC1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
// std::cerr<<" result: "<<inchi<<std::endl;
TEST_ASSERT(inchi ==
"InChI=1S/C7H13FO/c1-6-2-4-7(8,9)5-3-6/h6,9H,2-5H2,1H3/t6-,7+");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
{
// this was the original molecule in the bug report
std::string smiles =
"OC(=NCCc1ccccc1)[C@H]1CC[C@H](Cn2c(O)nc3ccccc3c2=O)CC1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi ==
"InChI=1S/C24H27N3O3/"
"c28-22(25-15-14-17-6-2-1-3-7-17)19-12-10-18(11-13-19)16-27-23("
"29)20-8-4-5-9-21(20)26-24(27)30/"
"h1-9,18-19H,10-16H2,(H,25,28)(H,26,30)/t18-,19-");
delete m;
m = InchiToMol(inchi, tmp);
std::string smi2 = MolToSmiles(*m, true);
delete m;
TEST_ASSERT(smi1 == smi2);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue562() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github issue 562: InChI radicals not properly converted"
<< std::endl;
{
std::string inchi = "InChI=1S/HO/h1H";
ExtraInchiReturnValues tmp;
ROMol *m = InchiToMol(inchi, tmp);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumExplicitHs() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getNoImplicit() == true);
std::string oinchi = MolToInchi(*m, tmp);
TEST_ASSERT(oinchi == inchi);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue614() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github issue 614: segfault from MolToInchi "
"when bad bond stereochem info is present"
<< std::endl;
{
std::string smiles = "C/C=C/C";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
m->removeAtom(3);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
std::cerr << " inchi: " << inchi << std::endl;
TEST_ASSERT(inchi == "InChI=1S/C3H6/c1-3-2/h3H,1H2,2H3");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithubIssue1572() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github issue 1572: Incorrect conversion from InChI"
<< std::endl;
{
std::string inchi =
"InChI=1S/C16H10N6O2/"
"c23-21(15-9-17-11-5-1-3-7-13(11)19-15)22(24)16-10-18-12-6-2-4-8-14(12)"
"20-16/h1-10H";
ExtraInchiReturnValues tmp;
RWMol *m = InchiToMol(inchi, tmp, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 24);
m->updatePropertyCache(false);
TEST_ASSERT(m->getAtomWithIdx(20)->getAtomicNum() == 7);
TEST_ASSERT(m->getAtomWithIdx(21)->getAtomicNum() == 7);
TEST_ASSERT(m->getAtomWithIdx(22)->getAtomicNum() == 8);
TEST_ASSERT(m->getAtomWithIdx(23)->getAtomicNum() == 8);
TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(21)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(22)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(23)->getFormalCharge() == 0);
// and the molecule should be sanitizable:
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(21)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(22)->getFormalCharge() == -1);
TEST_ASSERT(m->getAtomWithIdx(23)->getFormalCharge() == -1);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolBlockToInchi() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing mol block to InChI" << std::endl;
{
std::string molb = R"MOL(
Mrv1824 02111920092D
6 6 0 0 0 0 999 V2000
-5.5134 3.5259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.2279 3.1134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.2279 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5134 1.8759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7989 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7989 3.1134 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
1 6 1 0 0 0 0
2 3 2 0 0 0 0
M END
)MOL";
ExtraInchiReturnValues tmp;
std::string inchi = MolBlockToInchi(molb, tmp);
TEST_ASSERT(inchi == "InChI=1S/C5H8O/c1-2-4-6-5-3-1/h1-2H,3-5H2");
}
{
std::string molb = R"MOL(BDBM163075
RDKit 2D
27 30 0 0 0 0 0 0 0 0999 V2000
1.6146 -5.5162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9260 -4.0489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0484 1.6535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.2594 1.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4379 3.0237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1670 0.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.6489 0.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.3781 3.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9796 -3.6396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9460 3.1800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6752 0.5961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1571 0.3205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8863 2.9045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0946 -2.6362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4878 -3.7959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5729 2.1226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7839 1.3780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0647 1.9663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2758 1.5343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0711 -1.5187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6916 0.9089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6816 -0.1486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4207 -1.6751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1734 0.0078 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.1997 1.0652 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.3020 -0.4613 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.8110 -3.0456 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 27 1 0
3 5 2 0
3 6 1 0
4 7 2 0
4 8 1 0
5 10 1 0
6 11 2 0
7 12 1 0
8 13 2 0
9 14 2 0
9 15 1 0
10 18 2 0
11 18 1 0
12 19 2 0
13 19 1 0
14 20 1 0
15 27 1 0
16 18 1 0
16 21 1 0
17 19 1 0
17 24 1 0
20 22 2 0
20 23 1 0
21 25 2 0
21 26 1 0
22 24 1 0
22 25 1 0
23 26 2 0
23 27 1 0
M CHG 2 15 -1 27 1
M END
)MOL";
ExtraInchiReturnValues tmp;
std::string inchi = MolBlockToInchi(molb, tmp);
TEST_ASSERT(inchi ==
"InChI=1S/C23H23N3O/"
"c1-2-27-15-9-14-20-22(24-17-19-12-7-4-8-13-19)25-21(26-23(20)"
"27)16-18-10-5-3-6-11-18/h3-15H,2,16-17H2,1H3,(H,24,25,26)");
TEST_ASSERT(tmp.messagePtr ==
"Charges were rearranged; Accepted unusual valence(s): O(4)");
}
{
std::string molb = R"MOL(
Mrv1824 02121905282D
10 11 0 0 0 0 999 V2000
-4.6875 -1.1393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4020 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4020 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6875 -2.7893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9730 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9730 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2586 -2.7893 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.5441 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5441 -2.3768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.9608 -0.9684 0.0000 C 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
1 6 1 0 0 0 0
7 9 1 0 0 0 0
6 8 1 0 0 0 0
7 5 1 0 0 0 0
8 10 1 0 0 0 0
8 9 2 0 0 0 0
M END
)MOL";
{
ExtraInchiReturnValues tmp;
std::string inchi = MolBlockToInchi(molb, tmp);
TEST_ASSERT(
inchi ==
"InChI=1S/C8H8N2/c1-6-7-4-2-3-5-8(7)10-9-6/h2-5H,1H3,(H,9,10)");
}
{
ExtraInchiReturnValues tmp;
std::string inchi = MolBlockToInchi(molb, tmp, "/FixedH");
TEST_ASSERT(
inchi ==
"InChI=1/C8H8N2/c1-6-7-4-2-3-5-8(7)10-9-6/h2-5H,1H3,(H,9,10)/f/h10H");
}
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub3365() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github #3365: problems with high radical counts" << std::endl;
{
auto m = "[C]"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 4);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/C");
}
{
auto m = "[CH]"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 3);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/CH/h1H");
}
{
auto m = "[CH2]"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 2);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/CH2/h1H2");
}
{
auto m = "[CH3]"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/CH3/h1H3");
}
{
auto m = "C[SH](C)=O"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 1);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/C2H7OS/c1-4(2)3/h4H,1-2H3");
}
{
auto m = "C[SH](C)(O)O"_smiles;
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 1);
ExtraInchiReturnValues tmp;
std::string inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/C2H9O2S/c1-5(2,3)4/h3-5H,1-2H3");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub3645() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github #3645: Seg fault when parsing InChI"
<< std::endl;
{
std::string inchi =
"InChI=1S/C9H22O3SSi/c1-5-9-13(14,10-6-2,11-7-3)12-8-4/h5-9H2,1-4H3";
ExtraInchiReturnValues tmp;
bool ok = false;
try {
std::unique_ptr<ROMol> m{InchiToMol(inchi, tmp)};
} catch (const MolSanitizeException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
std::string inchi =
"InChI=1S/C8H20O3SSi/c1-5-9-12(13,8-4,10-6-2)11-7-3/h5-8H2,1-4H3";
ExtraInchiReturnValues tmp;
bool ok = false;
try {
std::unique_ptr<ROMol> m{InchiToMol(inchi, tmp)};
} catch (const MolSanitizeException &) {
ok = true;
}
TEST_ASSERT(ok);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test_clean_up_on_kekulization_error() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "To INCHI conversion leaks on kekulization failure"
<< std::endl;
{
// This will fail kekulization because of the ambiguous valence
// on the N atom
SmilesParserParams params;
params.sanitize = false;
std::unique_ptr<ROMol> mol{SmilesToMol("c1ccnc1", params)};
TEST_ASSERT(mol);
ExtraInchiReturnValues tmp;
bool ok = true;
try {
auto inchi = MolToInchi(*mol, tmp);
} catch (const std::exception &) {
ok = true;
}
TEST_ASSERT(ok);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub6172() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "testing github #6172: bogus bond type when parsing InChI"
<< std::endl;
{
std::string inchi =
"InChI=1S/2C18H36N3OP.2CH3.2ClH.Sn/c2*22-23(19-16-10-4-1-5-11-16,20-17-12-6-2-7-13-17)21-18-14-8-3-9-15-18;;;;;/h2*16-18H,1-15H2,(H3,19,20,21,22);2*1H3;2*1H;/q;;2*-1;;;+4/p-2";
ExtraInchiReturnValues tmp;
std::unique_ptr<ROMol> m{InchiToMol(inchi, tmp)};
TEST_ASSERT(!m);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub5311() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github #5311" << std::endl;
{
auto m = "O[PH2]=O"_smiles;
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "InChI=1S/H3O2P/c1-3-2/h3H2,(H,1,2)");
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
}
void testGithub8123() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing github #8123" << std::endl;
{
// fails due to the presence of a dative bond
auto m =
"Cc1cc(C)c(N2CCN(c3c(C)cc(C)cc3C)C2[Ru@OH28]2(Cl)(Cl)=Cc3cc([S@SP3](=O)(=O)N(C)C)ccc3O->2C(C)C)c(C)c1"_smiles;
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi.empty());
}
{
auto m =
"CC[C@H]1OC(=O)C[C@@H](O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)[C@@H](O)C(N(C)C)C2O)[C@@H](CC=O)C[C@@H](C)C(=O)/C=C/C(C)=C/[C@@H]1CO.CC[C@H]1OC(=O)C[C@@H](O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)[C@@H](O[C@H]3CC(C)(O)[C@@H](O)C(C)O3)C(N(C)C)C2O)[C@@H](CC=O)C[C@@H](C)C(=O)/C=C/C(C)=C/[C@@H]1CO[C@@H]1OC(C)[C@@H](O)[C@H](OC)C1OC.[3H][Y]([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])([3H])[3H]"_smiles;
TEST_ASSERT(m);
ExtraInchiReturnValues tmp;
auto inchi = MolToInchi(*m, tmp);
TEST_ASSERT(inchi == "");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
boost::logging::enable_logs("rdApp.info");
testGithubIssue3();
testGithubIssue8();
testGithubIssue40();
testGithubIssue67();
testGithubIssue68();
testGithubIssue296();
testMultiThread();
testMultiThread2();
testGithubIssue437();
testGithubIssue614();
testGithubIssue1572();
testMolBlockToInchi();
testGithubIssue562();
testGithub3365();
testGithub3645();
test_clean_up_on_kekulization_error();
testGithub6172();
testGithub5311();
testGithub8123();
}
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