mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
remove no-op macros and dead code (pt 1) (#8012)
This commit is contained in:
Hussein Faara
committed by
greg landrum
greg landrum
parent
e9e13f6523
commit
17c75bf219
@@ -40,7 +40,6 @@ void MolToCairo(const ROMol &mol, cairo_t *cr, int width, int height) {
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#endif
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void DrawDemo() {
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#if 1
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{
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RWMol *mol = SmilesToMol("c1c(C#N)cccc1C~C2CC2");
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std::string svg = MolToSVG(*mol);
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@@ -87,7 +86,6 @@ void DrawDemo() {
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delete mol;
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}
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#endif
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#ifdef USE_CAIRO
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{
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RWMol *mol =
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@@ -680,10 +680,6 @@ void dfsBuildStack(ROMol &mol, int atomIdx, int inBondIdx,
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std::vector<INT_LIST> &atomTraversalBondOrder,
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const boost::dynamic_bitset<> *bondsInPlay,
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const std::vector<std::string> *bondSymbols, bool doRandom) {
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#if 0
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std::cerr<<"traverse from atom: "<<atomIdx<<" via bond "<<inBondIdx<<" num cycles available: "
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<<std::count(cyclesAvailable.begin(),cyclesAvailable.end(),1)<<std::endl;
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#endif
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Atom *atom = mol.getAtomWithIdx(atomIdx);
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INT_LIST directTravList, cycleEndList;
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@@ -892,21 +888,11 @@ void clearBondDirs(ROMol &mol, Bond *refBond, const Atom *fromAtom,
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PRECONDITION(fromAtom, "bad atom");
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PRECONDITION(&fromAtom->getOwningMol() == &mol, "bad bond");
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#if 0
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std::copy(bondDirCounts.begin(),bondDirCounts.end(),std::ostream_iterator<int>(std::cerr,", "));
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std::cerr<<"\n";
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std::copy(atomDirCounts.begin(),atomDirCounts.end(),std::ostream_iterator<int>(std::cerr,", "));
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std::cerr<<"\n";
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std::cerr<<"cBD: bond: "<<refBond->getIdx()<<" atom: "<<fromAtom->getIdx()<<": ";
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#endif
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ROMol::OEDGE_ITER beg, end;
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boost::tie(beg, end) = mol.getAtomBonds(fromAtom);
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bool nbrPossible = false, adjusted = false;
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while (beg != end) {
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Bond *oBond = mol[*beg];
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// std::cerr<<" >>"<<oBond->getIdx()<<" "<<canHaveDirection(*oBond)<<"
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// "<<bondDirCounts[oBond->getIdx()]<<"-"<<bondDirCounts[refBond->getIdx()]<<"
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// "<<atomDirCounts[oBond->getBeginAtomIdx()]<<"-"<<atomDirCounts[oBond->getEndAtomIdx()]<<std::endl;
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if (oBond != refBond && canHaveDirection(*oBond)) {
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nbrPossible = true;
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if ((bondDirCounts[oBond->getIdx()] >=
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@@ -948,12 +934,6 @@ void removeRedundantBondDirSpecs(ROMol &mol, MolStack &molStack,
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UINT_VECT &atomDirCounts,
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const UINT_VECT &bondVisitOrders) {
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PRECONDITION(bondDirCounts.size() >= mol.getNumBonds(), "bad dirCount size");
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#if 0
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std::cerr<<"rRBDS: ";
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mol.debugMol(std::cerr);
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std::copy(bondDirCounts.begin(),bondDirCounts.end(),std::ostream_iterator<int>(std::cerr,", "));
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std::cerr<<"\n";
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#endif
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// find bonds that have directions indicated that are redundant:
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for (auto &msI : molStack) {
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if (msI.type == MOL_STACK_BOND) {
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@@ -1156,24 +1136,9 @@ void canonicalizeFragment(ROMol &mol, int atomIdx,
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}
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}
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#if 0
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std::cerr<<"<11111111"<<std::endl;
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std::cerr<<"----------------------------------------->"<<std::endl;
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mol.debugMol(std::cerr);
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#endif
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// std::cerr<<"----->\ntraversal stack:"<<std::endl;
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// traverse the stack and canonicalize double bonds and atoms with (ring)
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// stereochemistry
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for (auto &msI : molStack) {
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#if 0
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if(msI->type == MOL_STACK_ATOM) std::cerr<<" atom: "<<msI->obj.atom->getIdx()<<std::endl;
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else if(msI->type == MOL_STACK_BOND) std::cerr<<" bond: "<<msI->obj.bond->getIdx()<<" "<<msI->number<<" "<<msI->obj.bond->getBeginAtomIdx()<<"-"<<msI->obj.bond->getEndAtomIdx()<<" order: "<<msI->obj.bond->getBondType()<<std::endl;
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else if(msI->type == MOL_STACK_RING) std::cerr<<" ring: "<<msI->number<<std::endl;
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else if(msI->type == MOL_STACK_BRANCH_OPEN) std::cerr<<" branch open"<<std::endl;
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else if(msI->type == MOL_STACK_BRANCH_CLOSE) std::cerr<<" branch close"<<std::endl;
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#endif
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if (msI.type == MOL_STACK_BOND &&
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msI.obj.bond->getBondType() == Bond::DOUBLE &&
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msI.obj.bond->getStereo() > Bond::STEREOANY) {
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@@ -1265,19 +1230,8 @@ void canonicalizeFragment(ROMol &mol, int atomIdx,
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}
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}
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}
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#if 0
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std::cerr<<"<-----"<<std::endl;
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std::cerr<<"----------------------------------------->"<<std::endl;
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mol.debugMol(std::cerr);
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#endif
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Canon::removeRedundantBondDirSpecs(mol, molStack, bondDirCounts,
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atomDirCounts, bondVisitOrders);
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#if 0
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std::cerr<<"----------------------------------------->"<<std::endl;
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mol.debugMol(std::cerr);
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std::cerr<<"----------------------------------------->"<<std::endl;
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#endif
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}
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void canonicalizeEnhancedStereo(ROMol &mol,
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@@ -1350,22 +1304,6 @@ void canonicalizeEnhancedStereo(ROMol &mol,
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// referenceAtom is already CCW then we don't need to do anything more
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// with this stereogroup
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auto refState = Atom::ChiralType::CHI_TETRAHEDRAL_CCW;
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#if 0
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INT_LIST nbrs;
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auto [beg, end] = mol.getAtomBonds(*refAtom);
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while (beg != end) {
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nbrs.push_back(mol[*beg++]->getIdx());
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}
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std::cerr << "!!!! " << (*refAtom)->getDegree() << " " << nbrs.size()
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<< std::endl;
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// sort the neighbor indices by atom ranks
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nbrs.sort([&atomRanks](auto i, auto j) {
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return atomRanks->at(i) < atomRanks->at(j);
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});
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if ((*refAtom)->getPerturbationOrder(nbrs) % 1) {
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refState = Atom::ChiralType::CHI_TETRAHEDRAL_CW;
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}
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#endif
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if (foundRefState != refState) {
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// we need to flip everyone... so loop over the other atoms and bonds
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// and flip them all:
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@@ -179,43 +179,6 @@ void test190() {
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BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
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}
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void test45() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "Testing FMCS test45" << std::endl;
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std::cout << "\n test45()\n";
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std::vector<ROMOL_SPTR> mols;
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const char *smi[] = {
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// SLOW
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// test 45 # Using CHEMBL551656 CHEMBL563796 CHEMBL561978 CHEMBL559467
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// CHEMBL550503 CHEMBL562866 CHEMBL552190 CHEMBL181547 CHEMBL359567
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// CHEMBL373316
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// 45 . 1 30 32 27.01
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// n12-C-c:c(-c:2:c:c2-C(-O)(-C-C)-C(-O-C-c:2:c:1=O)=O):n:c(:c:c:c-O):c(:c):c-C-C-C
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"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCCC1 CHEMBL551656",
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"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCC1 CHEMBL563796", // Q
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"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCCCCC1 CHEMBL561978",
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"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCC1 CHEMBL559467",
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"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCC1 CHEMBL550503",
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"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(O)cc2c1C1CCCCCC1 CHEMBL562866",
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"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCCC1 CHEMBL552190",
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"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4cc5c(cc4c(C4CCCC4)c2C3)OCO5)COC1=O "
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"CHEMBL181547",
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"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4c(c(C5CCCCC5)c2C3)cc2c(c4)OCO2)COC1=O "
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"CHEMBL359567",
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"CCCc1c(OC)ccc2nc3c(c(CC)c21)Cn1c-3cc2c(c1=O)COC(=O)C2(O)CC CHEMBL373316",
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};
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for (auto &i : smi) {
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mols.emplace_back(SmilesToMol(getSmilesOnly(i)));
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}
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t0 = nanoClock();
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MCSResult res = findMCS(mols);
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std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
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<< res.NumBonds << " bonds\n";
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printTime();
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TEST_ASSERT(res.NumAtoms == 31 && res.NumBonds == 33);
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BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
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}
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void test3() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "Testing FMCS test3" << std::endl;
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@@ -411,55 +374,6 @@ void testThreshold() {
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BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
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}
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void test330() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "Testing FMCS test330" << std::endl;
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std::cout << "\ntest330()\n";
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std::vector<ROMOL_SPTR> mols;
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const char *smi[] = {
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// TEST 330 40 sec
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"CCC(C)C(NC(=O)C(NC(C(CCC(O)=O)NC(=O)C(NC(=O)C(NC(C(CC(O)=O)NC(C(CC(C)C)"
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"NC(C(Cc1ccccc1)NC(CN)=O)=O)=O)=O)C(C)CC)C(C)CC)=O)CCCCN)C(NC(C)C(NC("
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"CCCCN)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O)=O)=O CHEMBL1240742",
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"CCC(C)C(NC(=O)C(NC(C(CCCCN)NC(=O)C(NC(=O)C(NC(C(CC(O)=O)NC(C(Cc1ccccc1)"
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"NC(C(CC(C)C)NC(CN)=O)=O)=O)=O)C(C)CC)C(C)CC)=O)CCCCN)C(NC(C)C(NC(CCC(O)="
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"O)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O)=O)=O CHEMBL1240736",
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"CCC(C)C(NC(CN)=O)C(NC(C(NC(CC(O)=O)C(NC(C(NC(C)C(NC(CCCCN)C(NC(C(NC(CC("
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"C)C)C(NC(Cc1ccccc1)C(NC(CCC(O)=O)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)="
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"O)=O)=O)=O)=O)CCCCN)=O)=O)=O)C(C)CC)=O)=O)C(C)CC)=O CHEMBL1240738",
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"CCC(C)C(NC(CN)=O)C(NC(Cc1ccccc1)C(NC(CC(O)=O)C(NC(CCCCN)C(NC(CC(C)C)C("
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"NC(C)C(NC(CCCCN)C(NC(CCC(O)=O)C(NC(C(NC(CO)C(NC(C(NC(Cc1c[nH]c2c1cccc2)"
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"C(O)=O)=O)C(C)CC)=O)=O)C(C)CC)=O)=O)=O)=O)=O)=O)=O)=O CHEMBL1240740",
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"CCC(C)C(NC(CN)=O)C(NC(Cc1c[nH]c2c1cccc2)C(NC(CO)C(NC(CC(O)=O)C(NC(CC(C)"
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"C)C(NC(C)C(NC(CCC(O)=O)C(NC(C(NC(C(NC(CCCCN)C(NC(CCCCN)C(NC(Cc1ccccc1)C("
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"O)=O)=O)=O)=O)C(C)CC)=O)C(C)CC)=O)=O)=O)=O)=O)=O)=O CHEMBL1240741",
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"CCC(C)C(NC(=O)C(NC(=O)C(CCCCN)NC(C(CC(C)C)NC(C(Cc1c[nH]c2c1cccc2)NC(CN)="
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"O)=O)=O)CCCCN)C(NC(CCC(O)=O)C(NC(CO)C(=O)NC(C(NC(C(NC(CC(O)=O)C(NC(C)C("
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"NC(Cc1ccccc1)C(O)=O)=O)=O)=O)C(C)CC)=O)C(C)CC)=O)=O CHEMBL1240743",
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"CCC(C)C(NC(C(CCC(O)=O)NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)="
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"O)=O)=O)=O)C(NC(Cc1c[nH]c2ccccc12)C(O)=O)=O CHEMBL431874",
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"CCC(C)C(NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)=O)=O)C(NC("
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"CCC(O)=O)C(NC(Cc1c[nH]c2ccccc12)C(O)=O)=O)=O CHEMBL262166",
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"CCC(C)C(NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)=O)=O)C(NC("
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"CCCCN)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O CHEMBL313122",
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"CCC(C)C(NC(C(CCCCN)NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)="
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"O)=O)=O)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O CHEMBL314239",
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// # 330 F 42 41 30.93 sec MCS:
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//[#6]-[#6](-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6](-[#6]-[#6]-[#6])-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6])=[#8])=[#8])=[#8])=[#8])=[#8])-[#6](-[#7]-[#6](-[#6]-[#6](:[#6]):[#6]:[#6]:[#6]:[#6])-[#6](-[#8])=[#8])=[#8]
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};
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for (auto &i : smi) {
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mols.emplace_back(SmilesToMol(getSmilesOnly(i)));
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}
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MCSParameters p;
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t0 = nanoClock();
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MCSResult res = findMCS(mols, &p);
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std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
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<< res.NumBonds << " bonds\n";
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printTime();
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TEST_ASSERT(res.NumAtoms == 42 && res.NumBonds == 41);
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BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
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}
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void testTarget_no_10188_30149() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "Testing FMCS testTarget_no_10188_30149" << std::endl;
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@@ -1484,7 +1398,6 @@ void testGithub945() {
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BOOST_LOG(rdInfoLog) << "Testing Github #945: MCS returning partial rings "
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"with completeRingsOnly=True"
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<< std::endl;
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#if 1
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{
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std::vector<ROMOL_SPTR> mols;
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const char *smi[] = {"c1cc2ccccc2s1", "c1cc2ccccc2o1"};
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@@ -1533,7 +1446,6 @@ void testGithub945() {
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TEST_ASSERT(res.NumBonds == 6);
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}
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}
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#endif
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{
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std::vector<ROMOL_SPTR> mols;
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const char *smi[] = {"c1cc2ccc(C)cc2s1", "c1cc2c(cccc2s1)C"};
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@@ -3132,7 +3044,6 @@ void testAtomRingQueries() {
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int main(int argc, const char *argv[]) {
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(void)argc;
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(void)argv;
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// p.Verbose = true;
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RDLog::InitLogs();
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BOOST_LOG(rdInfoLog)
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<< "*******************************************************\n";
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@@ -3150,7 +3061,6 @@ int main(int argc, const char *argv[]) {
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T0 = nanoClock();
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t0 = nanoClock();
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#if 1
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testJSONParameters();
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test1Basics();
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@@ -3175,9 +3085,6 @@ int main(int argc, const char *argv[]) {
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test18();
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test504();
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// very SLOW optional tests:
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// test330(); // SLOW test
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// test45(); // SLOW test
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testInitialSeed();
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testInitialSeed2();
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@@ -3222,7 +3129,6 @@ int main(int argc, const char *argv[]) {
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testGitHub6773();
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testBondCompareCompleteRingsOnly();
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testAtomRingQueries();
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#endif
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unsigned long long t1 = nanoClock();
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double sec = double(t1 - T0) / 1000000.;
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@@ -503,14 +503,9 @@ void testSDMemoryCorruption() {
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auto *writer = new SDWriter(os, false);
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STR_VECT names;
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#if 1
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ROMol *m1 = sdsup.next();
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MolOps::sanitizeMol(*(RWMol *)m1);
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delete m1;
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#else
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ROMol *m1 = SmilesToMol("C1CC1");
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TEST_ASSERT(m1);
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#endif
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sdsup.reset();
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int nDone = 0;
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while (!sdsup.atEnd()) {
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@@ -536,7 +531,6 @@ void testSDMemoryCorruption() {
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delete writer;
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delete os;
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#if 1
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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@@ -549,7 +543,6 @@ void testSDMemoryCorruption() {
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delete mol;
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i++;
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}
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#endif
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}
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void testIssue3525000() {
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@@ -1594,7 +1587,7 @@ M END)CTAB"_ctab;
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}
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{
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auto m = R"CTAB(
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MJ201100
|
||||
MJ201100
|
||||
|
||||
3 2 0 0 0 0 0 0 0 0999 V2000
|
||||
-1.5623 1.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
@@ -1614,7 +1607,6 @@ M END)CTAB"_ctab;
|
||||
int main() {
|
||||
RDLog::InitLogs();
|
||||
|
||||
#if 1
|
||||
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
||||
BOOST_LOG(rdInfoLog) << "Running testSmilesWriter()\n";
|
||||
testSmilesWriter();
|
||||
@@ -1741,8 +1733,6 @@ int main() {
|
||||
testNeedsUpdatePropertyCacheSDWriter();
|
||||
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
||||
|
||||
#endif
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
||||
BOOST_LOG(rdInfoLog) << "Running testIssue3525000()\n";
|
||||
testIssue3525000();
|
||||
|
||||
@@ -74,27 +74,6 @@ const char *pqs[] = {
|
||||
//"[*]!@[R]~[R]~[R]!@[*]", Github #151: can't have !@ in an SSS pattern
|
||||
"[*]~[R](@[R])@[R](@[R])~[*]", "[*]~[R](@[R])@[R]@[R](@[R])~[*]",
|
||||
"[*]", // single atom fragment
|
||||
#if 0
|
||||
"[*]~[*](~[*])(~[*])~[*]",
|
||||
"[*]~[*]~[*]~[*]~[*]~[*]",
|
||||
"[*]~[*]~[*]~[*](~[*])~[*]",
|
||||
"[*]~[*]~[*](~[*])~[*]~[*]",
|
||||
"[*]~[*]~[*](~[*])(~[*])~[*]",
|
||||
"[*]~[*](~[*])~[*](~[*])~[*]",
|
||||
"[*]~[R]~1[R]~[R]~1(~[*])~[*]",
|
||||
"[*]~[R]~1[R](~[*])~[R]~1[*]",
|
||||
"[*]~[R]~1[R]~[R](~[*])~[R]~1",
|
||||
"[*]~[R]~1[R]~[R]~[R]~1[*]",
|
||||
"[*]~[R]~1[R]~[R]~[R]~[R]~1",
|
||||
"[*]~[R]~1(~[*])~[R]~[R]~[R]~1",
|
||||
"[*]~[*]~[*]~[*]~[*]~[*]~[*]",
|
||||
"[*]~[*]~[*]~[*]~[*](~[*])~[*]",
|
||||
"[*]~[*]~[*]~[*](~[*])~[*]~[*]",
|
||||
"[*]~[*]~[*]~[*](~[*])(~[*])~[*]",
|
||||
"[*]~[*]~[*](~[*])~[*](~[*])~[*]",
|
||||
"[*]~[*](~[*])~[*]~[*](~[*])~[*]",
|
||||
"[*]~[*](~[*])~[*](~[*])(~[*])~[*]",
|
||||
#endif
|
||||
""};
|
||||
typedef boost::flyweight<boost::flyweights::key_value<std::string, ss_matcher>,
|
||||
boost::flyweights::no_tracking>
|
||||
|
||||
@@ -31,7 +31,6 @@ void testPass() {
|
||||
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdInfoLog) << "Testing patterns which should parse." << std::endl;
|
||||
string smis[] = {
|
||||
#if 1
|
||||
"C", "CC", "C-C", "C=C", "[CH2+]C[CH+2]", "C1CC=1", "C=1CC1", "Ccc",
|
||||
"C=C-O", "C1CC1", "C1NC1", "C1=CC1", "C1CCC1", "CC(C)CC", "CC(=O)O",
|
||||
"C1C(=O)C1", "C1C(N)C1", "CC(O)C", "OC=CCC", "CC([O-])O", "C1CC2C1CC2",
|
||||
@@ -61,7 +60,6 @@ void testPass() {
|
||||
"[D{-3}]", "[D{1-}]", "[z{1-3}]", "[Z{1-3}]",
|
||||
"[2H,13C]", // github #1719
|
||||
"[+{0-3}]",
|
||||
#endif
|
||||
"[-{0-3}]", "[-{0-3},C]",
|
||||
"[-{0-3},D{1-3}]", // github #2709
|
||||
"C%(1000)CCC%(1000)", // github #2909
|
||||
@@ -433,7 +431,6 @@ void testProblems() {
|
||||
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdInfoLog) << "Testing former problems" << std::endl;
|
||||
|
||||
#if 1
|
||||
_checkMatches("[$(C(=O)O)]", "CC(=O)OC", 1, 1);
|
||||
|
||||
_checkMatches("[$(C(=O)[O,N])]", "CC(=O)OC", 1, 1);
|
||||
@@ -478,7 +475,6 @@ void testProblems() {
|
||||
_checkNoMatches("[O]-[!$(*=O)]", "CC(=O)O");
|
||||
|
||||
// BOOST_LOG(rdInfoLog) << "-*-*-*-*-*-*-*-*-" << std::endl;
|
||||
#endif
|
||||
_checkNoMatches("[$([O]-[!$(*=O)])]", "CC(=O)O");
|
||||
|
||||
// ISSUE 78
|
||||
@@ -838,53 +834,6 @@ void testIssue254() {
|
||||
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void testIssue255() {
|
||||
ROMol *matcher1;
|
||||
std::string sma;
|
||||
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdInfoLog) << "Testing Issue 255: Core leaks in smarts parsing. "
|
||||
"Watch memory consumption."
|
||||
<< std::endl;
|
||||
|
||||
for (int i = 0; i < 10000; i++) {
|
||||
#if 1
|
||||
sma = "CC";
|
||||
matcher1 = SmartsToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
|
||||
sma = "C-C";
|
||||
matcher1 = SmartsToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
|
||||
sma = "C=C";
|
||||
matcher1 = SmartsToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
|
||||
sma = "C=,#C";
|
||||
matcher1 = SmartsToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
#endif
|
||||
sma = "C-1CC-1";
|
||||
// matcher1 = SmartsToMol(sma);
|
||||
matcher1 = SmilesToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
#if 1
|
||||
|
||||
sma = "C-1CC1";
|
||||
matcher1 = SmartsToMol(sma);
|
||||
TEST_ASSERT(matcher1);
|
||||
delete matcher1;
|
||||
#endif
|
||||
}
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void testIssue330() {
|
||||
ROMol *matcher1;
|
||||
std::string sma, wsma;
|
||||
@@ -987,7 +936,6 @@ void testAtomMap() {
|
||||
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
#if 1
|
||||
void testIssue1804420() {
|
||||
ROMol *matcher1;
|
||||
std::string sma;
|
||||
@@ -1025,7 +973,6 @@ void testIssue1804420() {
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
|
||||
}
|
||||
#endif
|
||||
|
||||
void testSmartsSmiles() {
|
||||
RWMol *mol;
|
||||
@@ -2796,7 +2743,6 @@ int main(int argc, char *argv[]) {
|
||||
(void)argc;
|
||||
(void)argv;
|
||||
RDLog::InitLogs();
|
||||
#if 1
|
||||
testPass();
|
||||
testFail();
|
||||
testMatches();
|
||||
@@ -2810,8 +2756,6 @@ int main(int argc, char *argv[]) {
|
||||
testProblems();
|
||||
testIssue196();
|
||||
testIssue254();
|
||||
// testIssue255(); // this is a slow one and doesn't really actually test much
|
||||
// without someone watching memory consumption
|
||||
testIssue330();
|
||||
testIssue351();
|
||||
testAtomMap();
|
||||
@@ -2847,7 +2791,6 @@ int main(int argc, char *argv[]) {
|
||||
testGithub2565();
|
||||
testSmartsStereoBonds();
|
||||
testGithub6730();
|
||||
#endif
|
||||
testRingBondCrash();
|
||||
return 0;
|
||||
}
|
||||
|
||||
@@ -729,7 +729,6 @@ void github3881() {
|
||||
|
||||
int main() {
|
||||
RDLog::InitLogs();
|
||||
#if 1
|
||||
test1();
|
||||
test2();
|
||||
test3();
|
||||
@@ -747,6 +746,5 @@ int main() {
|
||||
testTautomerQueries();
|
||||
#endif
|
||||
github3881();
|
||||
#endif
|
||||
return 0;
|
||||
}
|
||||
|
||||
@@ -534,97 +534,6 @@ void test5() {
|
||||
delete m;
|
||||
}
|
||||
|
||||
/*
|
||||
void test6(){
|
||||
string smi;
|
||||
Mol *m;
|
||||
VECT_INT_VECT sssr;
|
||||
|
||||
int c1,c2;
|
||||
smi = "C1(Cl)C(Cl)C1Cl";
|
||||
m = SmilesToMol(smi);
|
||||
INT_SET ringAtoms,ringBonds;
|
||||
//boost::tie(c1,c2) = MolOps::findRingAtomsAndBonds(*m,ringAtoms,ringBonds);
|
||||
|
||||
CHECK_INVARIANT(c1==3,"bad nRingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(0)==1,"bad RingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(1)==0,"bad RingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(2)==1,"bad RingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(3)==0,"bad RingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(4)==1,"bad RingAtoms");
|
||||
CHECK_INVARIANT(ringAtoms.count(5)==0,"bad RingAtoms");
|
||||
|
||||
CHECK_INVARIANT(c2==3,"bad nRingBonds");
|
||||
CHECK_INVARIANT(ringBonds.count(0)==0,"");
|
||||
CHECK_INVARIANT(ringBonds.count(1)==1,"");
|
||||
CHECK_INVARIANT(ringBonds.count(2)==0,"");
|
||||
CHECK_INVARIANT(ringBonds.count(3)==1,"");
|
||||
CHECK_INVARIANT(ringBonds.count(4)==0,"");
|
||||
CHECK_INVARIANT(ringBonds.count(5)==1,"");
|
||||
|
||||
|
||||
}
|
||||
*/
|
||||
|
||||
void test7() {
|
||||
#if 0
|
||||
string smi;
|
||||
Mol *m;
|
||||
INT_VECT tree;
|
||||
#if 1
|
||||
smi = "C(CO)OCC";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==5,"bad mst");
|
||||
delete m;
|
||||
|
||||
smi = "C1CC1";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==2,"bad mst");
|
||||
delete m;
|
||||
|
||||
smi = "C1C=C1";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==2,"bad mst");
|
||||
CHECK_INVARIANT(std::find(tree.begin(),tree.end(),1)==tree.end(),"bogus idx in mst");
|
||||
delete m;
|
||||
#endif
|
||||
|
||||
smi = "C1C=CC=CC=1";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==5,"bad mst");
|
||||
delete m;
|
||||
|
||||
|
||||
smi = "C1C(=CC1)";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==3,"bad mst");
|
||||
delete m;
|
||||
|
||||
|
||||
smi = "C1C(C=C1)";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==3,"bad mst");
|
||||
delete m;
|
||||
|
||||
smi = "C1C(C2)CCC2C1";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==6,"bad mst");
|
||||
delete m;
|
||||
|
||||
smi = "C1C2CC3CCCCC3CC2CCC1";
|
||||
m = SmilesToMol(smi);
|
||||
MolOps::findSpanningTree(*m,tree);
|
||||
CHECK_INVARIANT(tree.size()==13,"bad mst");
|
||||
delete m;
|
||||
#endif
|
||||
}
|
||||
|
||||
void test8() {
|
||||
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Hydrogen Ops"
|
||||
@@ -4199,7 +4108,6 @@ void testBasicCanon() {
|
||||
BOOST_LOG(rdInfoLog) << "Testing canonicalization basics" << std::endl;
|
||||
// these are all cases that were problematic at one time or another during
|
||||
// the canonicalization rewrite.
|
||||
#if 1
|
||||
{
|
||||
std::string smi = "FC1C(=C/Cl)\\C1";
|
||||
RWMol *m = SmilesToMol(smi);
|
||||
@@ -4427,7 +4335,6 @@ void testBasicCanon() {
|
||||
delete m;
|
||||
delete m2;
|
||||
}
|
||||
#endif
|
||||
|
||||
{
|
||||
std::string pathName = getenv("RDBASE");
|
||||
@@ -5776,7 +5683,6 @@ void testAdjustQueryProperties() {
|
||||
BOOST_LOG(rdInfoLog)
|
||||
<< "-----------------------\n Testing adjustQueryProperties()"
|
||||
<< std::endl;
|
||||
#if 1
|
||||
{ // basics from SMILES
|
||||
std::string smiles = "C1CCC1C";
|
||||
ROMol *qm = SmilesToMol(smiles);
|
||||
@@ -6101,7 +6007,6 @@ void testAdjustQueryProperties() {
|
||||
delete m;
|
||||
delete t;
|
||||
}
|
||||
#endif
|
||||
{ // make atoms generic
|
||||
std::string smiles = "C1CC1CC";
|
||||
ROMol *qm = SmilesToMol(smiles);
|
||||
@@ -7664,7 +7569,6 @@ void testGithub1614() {
|
||||
"1614: AssignStereochemistry incorrectly removing "
|
||||
"CIS/TRANS bond stereo"
|
||||
<< std::endl;
|
||||
#if 1
|
||||
{
|
||||
RWMol m;
|
||||
m.addAtom(new Atom(9), true, true);
|
||||
@@ -7788,8 +7692,6 @@ void testGithub1614() {
|
||||
TEST_ASSERT(smi == "C/C(F)=C(/C)Cl");
|
||||
}
|
||||
}
|
||||
#endif
|
||||
#if 1
|
||||
{
|
||||
RWMol *m = SmilesToMol("F/C=C(\\C/C=C/C)C/C=C\\F", false, false);
|
||||
TEST_ASSERT(m);
|
||||
@@ -7808,7 +7710,6 @@ void testGithub1614() {
|
||||
}
|
||||
delete m;
|
||||
}
|
||||
#endif
|
||||
|
||||
{
|
||||
RWMol *m = SmilesToMol("FC=C(C/C=C/C)C/C=C\\F", false, false);
|
||||
@@ -7832,7 +7733,6 @@ void testGithub1614() {
|
||||
delete m;
|
||||
}
|
||||
|
||||
#if 1
|
||||
{
|
||||
RWMol *m = SmilesToMol("F/C=C(\\C/C=C/C)C/C=C\\C", false, false);
|
||||
TEST_ASSERT(m);
|
||||
@@ -7849,7 +7749,6 @@ void testGithub1614() {
|
||||
}
|
||||
delete m;
|
||||
}
|
||||
#endif
|
||||
{
|
||||
RWMol *m = SmilesToMol("FC=C(C/C=C/C)C/C=C\\C", false, false);
|
||||
TEST_ASSERT(m);
|
||||
@@ -7896,7 +7795,6 @@ void testGithub1810() {
|
||||
TEST_ASSERT(mol->getNumAtoms() == 4);
|
||||
TEST_ASSERT(mol->getBondBetweenAtoms(1, 2)->getStereo() == Bond::STEREOZ);
|
||||
}
|
||||
#if 1
|
||||
{
|
||||
std::unique_ptr<RWMol> mol(SmilesToMol("FC=C(F)[H]", false, false));
|
||||
TEST_ASSERT(mol);
|
||||
@@ -7909,7 +7807,6 @@ void testGithub1810() {
|
||||
TEST_ASSERT(mol->getBondBetweenAtoms(1, 2)->getStereoAtoms()[0] == 0);
|
||||
TEST_ASSERT(mol->getBondBetweenAtoms(1, 2)->getStereoAtoms()[1] == 3);
|
||||
}
|
||||
#endif
|
||||
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
|
||||
}
|
||||
|
||||
@@ -8643,8 +8540,6 @@ int main() {
|
||||
test3();
|
||||
test4();
|
||||
test5();
|
||||
// test6();
|
||||
test7();
|
||||
test8();
|
||||
test9();
|
||||
test10();
|
||||
|
||||
@@ -155,7 +155,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
||||
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
|
||||
TEST_ASSERT(cip == "R");
|
||||
#if 1
|
||||
smi = MolToSmiles(*m, true);
|
||||
BOOST_LOG(rdInfoLog) << "smiout: " << smi << std::endl;
|
||||
TEST_ASSERT(smi == "N[C@H](O)I");
|
||||
@@ -169,7 +168,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(cip == "R");
|
||||
smi2 = MolToSmiles(*m, true);
|
||||
TEST_ASSERT(smi == smi2);
|
||||
#endif
|
||||
|
||||
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> mol file <<<<<<<<<<<<<< "
|
||||
<< std::endl;
|
||||
@@ -183,7 +181,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
||||
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
||||
TEST_ASSERT(cip == "R");
|
||||
#if 1
|
||||
smi = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi);
|
||||
@@ -195,7 +192,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(cip == "R");
|
||||
smi2 = MolToSmiles(*m, true);
|
||||
TEST_ASSERT(smi == smi2);
|
||||
#endif
|
||||
|
||||
delete m;
|
||||
fName =
|
||||
@@ -207,7 +203,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
||||
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
||||
TEST_ASSERT(cip == "R");
|
||||
#if 1
|
||||
smi = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi);
|
||||
@@ -219,7 +214,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(cip == "R");
|
||||
smi2 = MolToSmiles(*m, true);
|
||||
TEST_ASSERT(smi == smi2);
|
||||
#endif
|
||||
|
||||
delete m;
|
||||
fName =
|
||||
@@ -231,7 +225,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
||||
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
||||
TEST_ASSERT(cip == "R");
|
||||
#if 1
|
||||
smi = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi);
|
||||
@@ -243,7 +236,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(cip == "R");
|
||||
smi2 = MolToSmiles(*m, true);
|
||||
TEST_ASSERT(smi == smi2);
|
||||
#endif
|
||||
|
||||
delete m;
|
||||
fName =
|
||||
@@ -255,7 +247,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
||||
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
||||
TEST_ASSERT(cip == "R");
|
||||
#if 1
|
||||
smi = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi);
|
||||
@@ -267,7 +258,6 @@ void testRoundTrip() {
|
||||
TEST_ASSERT(cip == "R");
|
||||
smi2 = MolToSmiles(*m, true);
|
||||
TEST_ASSERT(smi == smi2);
|
||||
#endif
|
||||
|
||||
delete m;
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
@@ -893,14 +883,6 @@ void testRingStereochemistry() {
|
||||
TEST_ASSERT(smi1 == "B[C@H]1CC[C@H](C)CC1");
|
||||
|
||||
delete m;
|
||||
#if 0
|
||||
smi="B[C@@H]1CC[C@@H](C)CC1";
|
||||
m = SmilesToMol(smi);
|
||||
std::string smi2=MolToSmiles(*m,true);
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
|
||||
TEST_ASSERT(smi2==smi);
|
||||
delete m;
|
||||
#endif
|
||||
}
|
||||
|
||||
{
|
||||
@@ -911,14 +893,6 @@ void testRingStereochemistry() {
|
||||
BOOST_LOG(rdInfoLog) << " : " << smi << " " << smi1 << std::endl;
|
||||
TEST_ASSERT(smi1 == smi);
|
||||
delete m;
|
||||
#if 0
|
||||
smi="C1[C@H](B)CC[C@@H](C)C1";
|
||||
m = SmilesToMol(smi);
|
||||
std::string smi2=MolToSmiles(*m,true);
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
|
||||
TEST_ASSERT(smi2==smi1);
|
||||
delete m;
|
||||
#endif
|
||||
}
|
||||
|
||||
{
|
||||
@@ -928,14 +902,6 @@ void testRingStereochemistry() {
|
||||
BOOST_LOG(rdInfoLog) << " : " << smi << " " << smi1 << std::endl;
|
||||
TEST_ASSERT(smi1 == "C[C@H]1CC[C@H](F)CC1");
|
||||
delete m;
|
||||
#if 0
|
||||
smi="C[C@@H]1CC[C@@H](F)CC1";
|
||||
m = SmilesToMol(smi);
|
||||
std::string smi2=MolToSmiles(*m,true);
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
|
||||
TEST_ASSERT(smi2==smi1);
|
||||
delete m;
|
||||
#endif
|
||||
}
|
||||
|
||||
{
|
||||
@@ -943,14 +909,6 @@ void testRingStereochemistry() {
|
||||
RWMol *m = SmilesToMol(smi);
|
||||
std::string smi1 = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
#if 0
|
||||
smi="F[C@@H]1CC[C@@H](C)CC1";
|
||||
m = SmilesToMol(smi);
|
||||
std::string smi2=MolToSmiles(*m,true);
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
|
||||
TEST_ASSERT(smi2==smi1);
|
||||
delete m;
|
||||
#endif
|
||||
}
|
||||
|
||||
{
|
||||
@@ -1006,30 +964,6 @@ void testRingStereochemistry() {
|
||||
delete m;
|
||||
}
|
||||
|
||||
#if 0
|
||||
// FIX : these tests do not pass
|
||||
{
|
||||
std::string smi = "C[C@H]1CC[C@H](C)CC1";
|
||||
RWMol *m = SmilesToMol(smi);
|
||||
std::string smi1=MolToSmiles(*m,true);
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
|
||||
TEST_ASSERT(smi1==smi);
|
||||
delete m;
|
||||
}
|
||||
|
||||
{
|
||||
std::string smi = "C1[C@@H](C)CC[C@H](C)C1";
|
||||
RWMol *m = SmilesToMol(smi);
|
||||
m->debugMol(std::cerr);
|
||||
std::string smi1=MolToSmiles(*m,true);
|
||||
smi = "C[C@H]1CC[C@H](C)CC1";
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
|
||||
m->debugMol(std::cerr);
|
||||
TEST_ASSERT(smi1==smi);
|
||||
delete m;
|
||||
}
|
||||
#endif
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
}
|
||||
|
||||
@@ -1124,7 +1058,6 @@ void testIterativeChirality() {
|
||||
|
||||
// unless otherwise noted, the R/S and Z/E assignments here
|
||||
// match Marvin and ChemDraw.
|
||||
#if 1
|
||||
{ // atom-chirality -> atom-chirality
|
||||
std::string cip;
|
||||
|
||||
@@ -1205,7 +1138,6 @@ void testIterativeChirality() {
|
||||
|
||||
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
||||
|
||||
#if 1 // this fails due to sf.net bug 1896935
|
||||
std::string smi1 = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi1);
|
||||
@@ -1213,7 +1145,6 @@ void testIterativeChirality() {
|
||||
std::string smi2 = MolToSmiles(*m, true);
|
||||
BOOST_LOG(rdInfoLog) << " : " << smi1 << " " << smi2 << std::endl;
|
||||
TEST_ASSERT(smi1 == smi2);
|
||||
#endif
|
||||
|
||||
delete m;
|
||||
}
|
||||
@@ -1236,7 +1167,6 @@ void testIterativeChirality() {
|
||||
|
||||
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
||||
|
||||
#if 1 // this fails due to sf.net bug 1896935
|
||||
std::string smi1 = MolToSmiles(*m, true);
|
||||
delete m;
|
||||
m = SmilesToMol(smi1);
|
||||
@@ -1244,7 +1174,6 @@ void testIterativeChirality() {
|
||||
std::string smi2 = MolToSmiles(*m, true);
|
||||
BOOST_LOG(rdInfoLog) << " : " << smi1 << " " << smi2 << std::endl;
|
||||
TEST_ASSERT(smi1 == smi2);
|
||||
#endif
|
||||
delete m;
|
||||
}
|
||||
|
||||
@@ -1260,27 +1189,6 @@ void testIterativeChirality() {
|
||||
TEST_ASSERT(!m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
|
||||
TEST_ASSERT(!m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
|
||||
|
||||
#if 0 // this fails due to sf.net bug 1896935
|
||||
std::cerr<<"m pre -----"<<std::endl;
|
||||
m->debugMol(std::cerr);
|
||||
std::cerr<<"-----"<<std::endl;
|
||||
std::string smi1=MolToSmiles(*m,true);
|
||||
std::cerr<<"m post -----"<<std::endl;
|
||||
m->debugMol(std::cerr);
|
||||
std::cerr<<"-----"<<std::endl;
|
||||
delete m;
|
||||
m = SmilesToMol(smi1);
|
||||
TEST_ASSERT(m);
|
||||
std::cerr<<"m2 pre -----"<<std::endl;
|
||||
m->debugMol(std::cerr);
|
||||
std::cerr<<"-----"<<std::endl;
|
||||
std::string smi2=MolToSmiles(*m,true);
|
||||
std::cerr<<"m post -----"<<std::endl;
|
||||
m->debugMol(std::cerr);
|
||||
std::cerr<<"-----"<<std::endl;
|
||||
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
|
||||
TEST_ASSERT(smi1==smi2);
|
||||
#endif
|
||||
delete m;
|
||||
}
|
||||
|
||||
@@ -1512,7 +1420,6 @@ void testIterativeChirality() {
|
||||
|
||||
delete m;
|
||||
}
|
||||
#endif
|
||||
|
||||
{ // bond stereochemistry -> bond stereochemistry
|
||||
std::string cip;
|
||||
@@ -1794,14 +1701,6 @@ void testIssue2705543() {
|
||||
MolOps::assignChiralTypesFrom3D(*m);
|
||||
MolOps::assignStereochemistry(*m, true);
|
||||
|
||||
#if 0
|
||||
for(unsigned int i=0;i<m->getNumAtoms();++i){
|
||||
if(m->getAtomWithIdx(i)->hasProp(common_properties::_CIPCode)){
|
||||
m->getAtomWithIdx(i)->getProp(common_properties::_CIPCode,cip);
|
||||
std::cerr<<" >> "<<i<<" "<<cip<<std::endl;
|
||||
}
|
||||
}
|
||||
#endif
|
||||
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
||||
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag() ==
|
||||
Atom::CHI_TETRAHEDRAL_CCW);
|
||||
@@ -3208,9 +3107,7 @@ void testGithub7115() {
|
||||
|
||||
int main() {
|
||||
RDLog::InitLogs();
|
||||
// boost::logging::enable_logs("rdApp.debug");
|
||||
|
||||
#if 1
|
||||
testSmiles1();
|
||||
testMol1();
|
||||
testMol2();
|
||||
@@ -3236,7 +3133,6 @@ int main() {
|
||||
testDoubleBondStereoInRings();
|
||||
testIssue1735();
|
||||
testStereoGroupUpdating();
|
||||
#endif
|
||||
testClearDirsOnDoubleBondsWithoutStereo();
|
||||
testAssignChiralTypesFromMolParity();
|
||||
testIncorrectBondDirsOnWedging();
|
||||
|
||||
@@ -76,67 +76,6 @@ void test1(bool doLong = 0) {
|
||||
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void _createPickleFile() {
|
||||
std::string smiName = getenv("RDBASE");
|
||||
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
|
||||
std::string pklName = getenv("RDBASE");
|
||||
#ifdef OLD_PICKLE
|
||||
pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
|
||||
#else
|
||||
pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
|
||||
#endif
|
||||
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdErrorLog) << "creating pickle file." << std::endl;
|
||||
|
||||
SmilesMolSupplier suppl(smiName, "\t", 0, 1, false);
|
||||
std::ofstream outStream(pklName.c_str(), std::ios_base::binary);
|
||||
while (!suppl.atEnd()) {
|
||||
ROMol *m = suppl.next();
|
||||
TEST_ASSERT(m);
|
||||
|
||||
std::string pickle;
|
||||
MolPickler::pickleMol(*m, outStream);
|
||||
delete m;
|
||||
}
|
||||
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void test2(bool doLong = 0) {
|
||||
std::string smiName = getenv("RDBASE");
|
||||
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
|
||||
std::string pklName = getenv("RDBASE");
|
||||
pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
|
||||
|
||||
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdErrorLog) << "Testing reading existing pickle file (v1)."
|
||||
<< std::endl;
|
||||
|
||||
SmilesMolSupplier suppl(smiName, "\t", 0, 1, false);
|
||||
std::ifstream inStream(pklName.c_str(), std::ios_base::binary);
|
||||
int count = 0;
|
||||
while (!suppl.atEnd()) {
|
||||
ROMol *m1 = suppl.next();
|
||||
TEST_ASSERT(m1);
|
||||
ROMol m2;
|
||||
MolPickler::molFromPickle(inStream, m2);
|
||||
|
||||
std::string smi1 = MolToSmiles(*m1);
|
||||
std::string smi2 = MolToSmiles(m2);
|
||||
|
||||
if (smi1 != smi2) {
|
||||
BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1
|
||||
<< "\n != \n " << smi2 << std::endl;
|
||||
}
|
||||
TEST_ASSERT(smi1 == smi2);
|
||||
delete m1;
|
||||
count++;
|
||||
if (!doLong && count >= 100) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void test3(bool doLong = 0) {
|
||||
std::string smiName = getenv("RDBASE");
|
||||
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
|
||||
@@ -173,52 +112,6 @@ void test3(bool doLong = 0) {
|
||||
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void timeTest(bool doLong = 0) {
|
||||
time_t t1, t2;
|
||||
std::string smiName = getenv("RDBASE");
|
||||
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
|
||||
|
||||
std::string pklName = getenv("RDBASE");
|
||||
pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
|
||||
|
||||
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdErrorLog) << "Timing reads." << std::endl;
|
||||
|
||||
t1 = std::time(nullptr);
|
||||
SmilesMolSupplier suppl(smiName, "\t", 0, 1, false);
|
||||
int count = 0;
|
||||
while (!suppl.atEnd()) {
|
||||
ROMol *m1 = suppl.next();
|
||||
TEST_ASSERT(m1);
|
||||
count++;
|
||||
if (!doLong && count >= 100) {
|
||||
break;
|
||||
}
|
||||
delete m1;
|
||||
}
|
||||
t2 = std::time(nullptr);
|
||||
BOOST_LOG(rdInfoLog) << " Smiles time: " << std::difftime(t2, t1)
|
||||
<< std::endl;
|
||||
;
|
||||
|
||||
std::ifstream inStream(pklName.c_str(), std::ios_base::binary);
|
||||
t1 = std::time(nullptr);
|
||||
while (count > 0) {
|
||||
ROMol m2;
|
||||
MolPickler::molFromPickle(inStream, m2);
|
||||
count--;
|
||||
if (!doLong && count >= 100) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
t2 = std::time(nullptr);
|
||||
BOOST_LOG(rdInfoLog) << " Pickle time: " << std::difftime(t2, t1)
|
||||
<< std::endl;
|
||||
;
|
||||
|
||||
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
||||
}
|
||||
|
||||
void test4() {
|
||||
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdErrorLog) << "Testing combining molecules using pickles."
|
||||
@@ -1851,16 +1744,12 @@ int main(int argc, char *argv[]) {
|
||||
}
|
||||
}
|
||||
|
||||
//_createPickleFile();
|
||||
#if 1
|
||||
test1(doLong);
|
||||
// test2(doLong);
|
||||
test3(doLong);
|
||||
test4();
|
||||
testIssue164();
|
||||
testIssue219();
|
||||
testIssue220();
|
||||
// timeTest(doLong);
|
||||
testQueries();
|
||||
testRadicals();
|
||||
testPickleProps();
|
||||
@@ -1880,7 +1769,6 @@ int main(int argc, char *argv[]) {
|
||||
testCustomPickler();
|
||||
testGithub2441();
|
||||
testGithubIssue2510();
|
||||
#endif
|
||||
testNegativeMaps();
|
||||
testHistoricalConfs();
|
||||
testConformerOptions();
|
||||
|
||||
Reference in New Issue
Block a user