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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 <boost/foreach.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, 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;
}
}
};
}
#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 = 0;
try {
mol = suppl.next();
} catch (...) {
continue;
}
if (!mol) continue;
mols.push_back(mol);
}
std::cerr << "generating reference data" << std::endl;
std::vector<std::string> inchis;
std::vector<std::string> keys;
BOOST_FOREACH (const ROMol *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 (unsigned int i = 0; i < mols.size(); ++i) delete mols[i];
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#else
void testMultiThread() {
{}
}
#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";
ROMol *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:
RWMol *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";
ROMol *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 = Descriptors::calcAMW(*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";
ROMol *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;
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;
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);
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;
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);
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);
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);
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);
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);
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);
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);
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);
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;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
#if 1
testGithubIssue3();
testGithubIssue8();
testGithubIssue40();
testGithubIssue67();
testGithubIssue68();
testGithubIssue296();
testMultiThread();
testGithubIssue437();
testGithubIssue562();
testGithubIssue614();
#endif
testGithubIssue1572();
}
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