diff --git a/Code/Demos/RDKit/Basement/BinaryIO/iotest.cpp b/Code/Demos/RDKit/Basement/BinaryIO/iotest.cpp index 327424b90..a2034c5f8 100644 --- a/Code/Demos/RDKit/Basement/BinaryIO/iotest.cpp +++ b/Code/Demos/RDKit/Basement/BinaryIO/iotest.cpp @@ -501,12 +501,10 @@ void test5() { int main(int argc, char *argv[]) { RDLog::InitLogs(); -#if 1 test1(); test2(); test3(); test4(); test5(); -#endif return 0; } diff --git a/Code/Demos/RDKit/Basement/TemplEnum/TemplEnumTools.cpp b/Code/Demos/RDKit/Basement/TemplEnum/TemplEnumTools.cpp index b217efbf9..aefc04376 100644 --- a/Code/Demos/RDKit/Basement/TemplEnum/TemplEnumTools.cpp +++ b/Code/Demos/RDKit/Basement/TemplEnum/TemplEnumTools.cpp @@ -350,12 +350,6 @@ RWMOL_SPTR_VECT enumerateLibrary(RWMol *templateMol, // existing result set and move the molecules we just generated // over if (tmp.size()) { -#if 0 - RWMOL_SPTR_VECT::iterator tmpMolIt; - for(tmpMolIt=res.begin();tmpMolIt!=res.end();tmpMolIt++){ - delete *tmpMolIt; - } -#endif res = tmp; tmp.clear(); } @@ -404,16 +398,6 @@ RWMOL_SPTR_VECT enumFromFiles(const char *templateName, // //-------------------------- delete templ; -#if 0 - VECT_RWMOL_SPTR_VECT::iterator vmpvI; - for(vmpvI=allSidechains.begin();vmpvI!=allSidechains.end();vmpvI++){ - RWMOL_SPTR_VECT::iterator mpvI; - for(mpvI=vmpvI->begin();mpvI!=vmpvI->end();mpvI++){ - delete *mpvI; - } - vmpvI->clear(); - } -#endif allSidechains.clear(); return library; diff --git a/Code/Features/CMakeLists.txt b/Code/Features/CMakeLists.txt index ded3726be..c7898b393 100644 --- a/Code/Features/CMakeLists.txt +++ b/Code/Features/CMakeLists.txt @@ -1,2 +1,5 @@ rdkit_headers(Feature.h DEST Features) + +rdkit_test(testBaseFeatures testFeatures.cpp +LINK_LIBRARIES RDGeneral RDGeometryLib ) diff --git a/Code/Features/testFeatures.cpp b/Code/Features/testFeatures.cpp index 356b14928..6d1c68b2c 100644 --- a/Code/Features/testFeatures.cpp +++ b/Code/Features/testFeatures.cpp @@ -1,6 +1,5 @@ -// $Id$ // -// Copyright (C) 2004-2006 Rational Discovery LLC +// Copyright (C) 2004-2040 Greg Landrum and other RDKit contributors // // @@ All Rights Reserved @@ // This file is part of the RDKit. @@ -16,10 +15,6 @@ #include -#include -#include -using namespace boost::spirit; - using namespace RDKit; using namespace RDGeom; using namespace RDFeatures; @@ -75,7 +70,7 @@ void test2() { std::cerr << "Basics for ImplicitFeatures." << std::endl; ImplicitFeature f1; - f1.setFamily(fooType); + f1.setType(fooType); TEST_ASSERT(f1.getType() == fooType); f1.setType(grnType); TEST_ASSERT(f1.getType() == grnType); @@ -86,7 +81,7 @@ void test2() { f1 = ImplicitFeature(barType, fooType); TEST_ASSERT(f1.getFamily() == barType); - TEST_ASSERT(f1.getType() == barType); + TEST_ASSERT(f1.getType() == fooType); TEST_ASSERT(feq(f1.getLoc().x, 0.0)); TEST_ASSERT(feq(f1.getLoc().y, 0.0)); TEST_ASSERT(feq(f1.getLoc().z, 0.0)); @@ -127,7 +122,7 @@ void test3() { TEST_ASSERT(f1.getDirs().size() == 0); f1 = LocalFeature("foo", "bar"); - TEST_ASSERT(f1.getFamily() == "bar"); + TEST_ASSERT(f1.getFamily() == "foo"); TEST_ASSERT(f1.getType() == "bar"); TEST_ASSERT(feq(f1.getLoc().x, 0.0)); TEST_ASSERT(feq(f1.getLoc().y, 0.0)); @@ -148,35 +143,8 @@ void test3() { std::cerr << " done" << std::endl; } -void testParser() { - std::cerr << "-------------------------------------" << std::endl; - std::cerr << "parser testing." << std::endl; - - std::string text; - int n; - bool ok; - - text = "p1"; - ok = parse(text.c_str(), (ch_p('p') >> int_p[assign_a(n)]), space_p).full; - TEST_ASSERT(ok); - TEST_ASSERT(n == 1); - - text = "p12"; - ok = parse(text.c_str(), (ch_p('p') >> int_p[assign_a(n)]), space_p).full; - TEST_ASSERT(ok); - TEST_ASSERT(n == 12); - - text = "p2 + p3"; - ok = parse(text.c_str(), (ch_p('p') >> int_p[assign_a(n)]), space_p).full; - TEST_ASSERT(!ok); - - std::cerr << " done" << std::endl; -} int main() { -#if 0 test1(); test2(); test3(); -#endif - testParser(); } diff --git a/Code/GraphMol/ChemReactions/testReaction.cpp b/Code/GraphMol/ChemReactions/testReaction.cpp index b929a175e..deb6f0af5 100644 --- a/Code/GraphMol/ChemReactions/testReaction.cpp +++ b/Code/GraphMol/ChemReactions/testReaction.cpp @@ -1716,7 +1716,6 @@ void test17Issue1920627() { TEST_ASSERT(rxn->getNumReactantTemplates() == 1); TEST_ASSERT(rxn->getNumProductTemplates() == 1); -#if 1 reacts.clear(); smi = "C[C@](Cl)(CO)CC(=O)NC"; mol = SmilesToMol(smi); @@ -1844,7 +1843,6 @@ void test17Issue1920627() { TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode)); prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip); TEST_ASSERT(cip == "R"); -#endif reacts.clear(); smi = "C(=O)N[C@@H](CC)C"; diff --git a/Code/GraphMol/ChemTransforms/testChemTransforms.cpp b/Code/GraphMol/ChemTransforms/testChemTransforms.cpp index 2b4c67c72..912c46583 100644 --- a/Code/GraphMol/ChemTransforms/testChemTransforms.cpp +++ b/Code/GraphMol/ChemTransforms/testChemTransforms.cpp @@ -1812,23 +1812,6 @@ void testFragmentOnBRICSBonds() { BOOST_LOG(rdInfoLog) << "\tdone" << std::endl; } -void benchFragmentOnBRICSBonds() { - BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl; - BOOST_LOG(rdInfoLog) << "Testing fragmentOnBRICSBonds" << std::endl; - { - std::string pathName = getenv("RDBASE"); - pathName += "/Regress/Data/mols.1000.sdf"; - SDMolSupplier suppl(pathName); - while (!suppl.atEnd()) { - ROMol *m = suppl.next(); - ROMol *nmol = MolFragmenter::fragmentOnBRICSBonds(*m); - delete m; - delete nmol; - } - } - BOOST_LOG(rdInfoLog) << "\tdone" << std::endl; -} - void testFragmentOnSomeBonds() { BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl; BOOST_LOG(rdInfoLog) << "Testing fragmentOnSomeBonds" << std::endl; @@ -2169,7 +2152,6 @@ int main() { << "********************************************************\n"; BOOST_LOG(rdInfoLog) << "Testing Chemical Transforms \n"; -#if 1 testDeleteSubstruct(); testReplaceSubstructs(); testReplaceSubstructs2(); @@ -2195,12 +2177,10 @@ int main() { testFragmentOnBonds(); testFragmentOnBRICSBonds(); testFragmentOnSomeBonds(); - // benchFragmentOnBRICSBonds(); testGithubIssue429(); testGithubIssue430(); testGithubIssue511(); testReplaceCore2(); -#endif testGithub1734(); testGithub3206(); testGithub4019(); diff --git a/Code/GraphMol/Chirality.cpp b/Code/GraphMol/Chirality.cpp index 403df4cd3..d796e60be 100644 --- a/Code/GraphMol/Chirality.cpp +++ b/Code/GraphMol/Chirality.cpp @@ -171,14 +171,6 @@ void updateDoubleBondNeighbors(ROMol &mol, Bond *dblBond, const Conformer *conf, return; } needsDir.set(dblBond->getIdx(), 0); -#if 0 - std::cerr << "**********************\n"; - std::cerr << "**********************\n"; - std::cerr << "**********************\n"; - std::cerr << "UDBN: " << dblBond->getIdx() << " " - << dblBond->getBeginAtomIdx() << "=" << dblBond->getEndAtomIdx() - << "\n"; -#endif std::vector followupBonds; @@ -380,24 +372,7 @@ void updateDoubleBondNeighbors(ROMol &mol, Bond *dblBond, const Conformer *conf, bond2->getBeginAtom() == atom2, needsDir); needsDir[obond2->getIdx()] = 0; } -#if 0 - std::cerr << " 1:" << bond1->getIdx() << " "; - if (obond1) - std::cerr << obond1->getIdx() << std::endl; - else - std::cerr << "N/A" << std::endl; - std::cerr << " 2:" << bond2->getIdx() << " "; - if (obond2) - std::cerr << obond2->getIdx() << std::endl; - else - std::cerr << "N/A" << std::endl; - std::cerr << "**********************\n"; - std::cerr << "**********************\n"; - std::cerr << "**********************\n"; -#endif for (Bond *oDblBond : followupBonds) { - // std::cerr << "FOLLOWUP: " << oDblBond->getIdx() << " " - // << needsDir[oDblBond->getIdx()] << std::endl; updateDoubleBondNeighbors(mol, oDblBond, conf, needsDir, singleBondCounts, singleBondNbrs); } @@ -820,24 +795,6 @@ std::optional atomChiralTypeFromBondDirPseudo3D( const auto crossp2 = bv1.crossProduct(bv3); const auto dotp2 = bondVects[order[1]].dotProduct(bondVects[order[3]]); auto vol2 = crossp2.dotProduct(bondVects[order[0]]); -#if 0 - std::cerr << neighborBondIndices[order[0]] << " " << - bondVects[order[0]] - << std::endl; - std::cerr << neighborBondIndices[order[1]] << " " << - bondVects[order[1]] - << std::endl; - std::cerr << neighborBondIndices[order[2]] << " " << - bondVects[order[2]] - << std::endl; - std::cerr << neighborBondIndices[order[3]] << " " << - bondVects[order[3]] - << std::endl; - std::cerr << "------------" << std::endl; - std::cerr << crossp1 << " l2=" << crossp1.lengthSq()<<" " << std::endl; - std::cerr << crossp2 << " l2=" << crossp2.lengthSq()<< " " << dotp2 << std::endl; - std::cerr << " !!! " << vol << " " << vol2 << std::endl; -#endif // detect the case where there's no chiral volume for the default // evaluation @@ -1054,27 +1011,6 @@ void buildCIPInvariants(const ROMol &mol, DOUBLE_VECT &res) { mass = mass % maxMass; } -#if 0 - // NOTE: the inclusion of hybridization in the invariant (as - // suggested in the original paper), leads to the situation - // that - // C[C@@](O)(C=C)C(C)CC - // and - // C[C@@](O)(C=C)C(C)CO - // are assigned S chirality even though the rest of the world - // seems to agree that they ought to be R (atom 3, sp2, is ranked - // higher than atom 5, sp3, no matter what their environments) - int hyb=0; - switch(atom->getHybridization()) { - case Atom::SP: hyb=6;break; - case Atom::SP2: hyb=5;break; - case Atom::SP3: hyb=1;break; - case Atom::SP3D: hyb=3;break; - case Atom::SP3D2: hyb=2;break; - default: break; - } -#endif - invariant = num; // 7 bits here invariant = (invariant << nMassBits) | mass; @@ -2332,12 +2268,6 @@ void legacyStereoPerception(ROMol &mol, bool cleanIt, MolOps::fastFindRings(mol); } -#if 0 - std::cerr << ">>>>>>>>>>>>>\n"; - std::cerr << "assign stereochem\n"; - mol.debugMol(std::cerr); -#endif - // as part of the preparation, we'll loop over the atoms and // bonds to see if anything has stereochemistry // indicated. There's no point in doing the work here if there @@ -2433,13 +2363,6 @@ void legacyStereoPerception(ROMol &mol, bool cleanIt, // update the atom ranks based on the new information we have: Chirality::rerankAtoms(mol, atomRanks); } -#if 0 - std::cout << "*************** done iteration " << keepGoing - << " ***********" << std::endl; - mol.debugMol(std::cout); - std::cout << "*************** done iteration " << keepGoing - << " ***********" << std::endl; -#endif } if (cleanIt) { @@ -2994,19 +2917,6 @@ void findPotentialStereoBonds(ROMol &mol, bool cleanIt) { // if both of the atoms have 2 neighbors (other than the one // connected // by the double bond) and .... -#if 0 - std::cerr << "Bond: " << dblBond->getIdx() << " " - << begAtom->getIdx() << "=" << endAtom->getIdx() - << std::endl; - std::cerr << " " << begAtomNeighbors[0] << "=" - << ranks[begAtomNeighbors[0]] << ":"; - std::cerr << " " << begAtomNeighbors[1] << "=" - << ranks[begAtomNeighbors[1]] << std::endl; - std::cerr << " " << endAtomNeighbors[0] << "=" - << ranks[endAtomNeighbors[0]] << ":"; - std::cerr << " " << endAtomNeighbors[1] << "=" - << ranks[endAtomNeighbors[1]] << std::endl; -#endif if ((ranks[begAtomNeighbors[0]] != ranks[begAtomNeighbors[1]]) && (ranks[endAtomNeighbors[0]] != @@ -3268,11 +3178,6 @@ static bool assignNontetrahedralChiralTypeFrom3D(ROMol &mol, } } -#if 0 - printf("count=%u pairs=%u [%u,%u,%u,%u,%u,%u]\n", count, pairs, - pair[0], pair[1], pair[2], pair[3], pair[4], pair[5]); -#endif - Atom::ChiralType tag; unsigned int perm; bool res = false; diff --git a/Code/GraphMol/Depictor/testDepictor.cpp b/Code/GraphMol/Depictor/testDepictor.cpp index 56d4ce49e..cd33193ff 100644 --- a/Code/GraphMol/Depictor/testDepictor.cpp +++ b/Code/GraphMol/Depictor/testDepictor.cpp @@ -801,10 +801,6 @@ void testGitHubIssue910() { } MolOps::addHs(*m, false, false, &chiralAts); RDDepict::compute2DCoords(*m, nullptr, true); -#if 0 - m->setProp("_Name", "github910"); - std::cerr << MolToMolBlock(*m); -#endif // now look for close contacts. const Conformer &conf = m->getConformer(); for (unsigned int i = 0; i < conf.getNumAtoms(); ++i) { @@ -971,7 +967,6 @@ void testGithub1691() { << "-----------------------\n Testing Github issue " "1691: Acetylenic hydrogens not given appropriate 2D coordinates" << std::endl; -#if 1 { SmilesParserParams ps; ps.removeHs = false; @@ -994,7 +989,6 @@ void testGithub1691() { TEST_ASSERT(v20.dotProduct(v10) <= -1.0); TEST_ASSERT(v31.dotProduct(v01) <= -1.0); } -#endif { SmilesParserParams ps; ps.removeHs = false; @@ -1799,7 +1793,6 @@ int main() { #endif RDLog::InitLogs(); -#if 1 BOOST_LOG(rdInfoLog) << "***********************************************************\n"; BOOST_LOG(rdInfoLog) << " test1 \n"; @@ -1991,7 +1984,6 @@ int main() { BOOST_LOG(rdInfoLog) << "***********************************************************\n"; testGithub1691(); -#endif testGithub2027(); testGenerate2DDepictionRefPatternMatchVect(); testGenerate2DDepictionAllowRGroupsOrig(); diff --git a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp index 7c1d1449f..6e69c0ac1 100644 --- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp @@ -76,13 +76,6 @@ void test1() { const Conformer &conf1 = m->getConformer(0); const Conformer &conf2 = m2->getConformer(0); -#if 0 - BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl; - BOOST_LOG(rdInfoLog) << MolToMolBlock(*m2) << std::endl; - BOOST_LOG(rdInfoLog) << "---" << std::endl; - BOOST_LOG(rdInfoLog) << MolToMolBlock(*m) << std::endl; - BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl; -#endif for (unsigned int i = 0; i < nat; i++) { RDGeom::Point3D pt1i = conf1.getAtomPos(i); RDGeom::Point3D pt2i = conf2.getAtomPos(i); @@ -147,7 +140,6 @@ void test2() { int cid; unsigned int nat = mol->getNumAtoms(); -#if 1 bm.reset(new DistGeom::BoundsMatrix(nat)); DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0); DGeomHelpers::setTopolBounds(*mol, bm); @@ -221,7 +213,6 @@ void test2() { delete mol; delete dmat; -#endif std::cerr << "-------------------------------------\n\n"; smi = "C/C=C/C"; mol = SmilesToMol(smi, 0, 1); @@ -296,46 +287,6 @@ void test2() { delete mol; delete dmat; -#if 0 - // this next block of tests all handle the special case that led to Issue284 - smi = "COC=O"; - mol = SmilesToMol(smi, 0, 1); - nat = mol->getNumAtoms(); - bm.reset(new DistGeom::BoundsMatrix(nat)); - DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0); - DGeomHelpers::setTopolBounds(*mol, bm); - cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1); - TEST_ASSERT(cid>-1); - dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0); - computeMolDmat(*mol, *dmat); - //TEST_ASSERT( (bm->getUpperBound(0,3) - bm->getLowerBound(0,3)) < .13); - double x,y,z; - x = bm->getUpperBound(0,3); - y = bm->getLowerBound(0,3); - z = dmat->getVal(0,3); - //TEST_ASSERT( (bm->getUpperBound(0,3) - dmat->getVal(0,3) > -0.1) - // && (bm->getLowerBound(0,3) - dmat->getVal(0,3) < 0.10 )); - - delete mol; - delete dmat; - - smi = "C[NH]C=O"; - mol = SmilesToMol(smi, 0, 1); - nat = mol->getNumAtoms(); - bm.reset(new DistGeom::BoundsMatrix(nat)); - DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0); - DGeomHelpers::setTopolBounds(*mol, bm); - cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1); - TEST_ASSERT(cid>-1); - dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0); - computeMolDmat(*mol, *dmat); - TEST_ASSERT( (bm->getUpperBound(0,3) - bm->getLowerBound(0,3)) < .13); - //TEST_ASSERT( (bm->getUpperBound(0,3) - dmat->getVal(0,3) > -0.1) - // && (bm->getLowerBound(0,3) - dmat->getVal(0,3) < 0.10)); - - delete mol; - delete dmat; -#endif boost::logging::enable_logs("rdApp.warning"); } @@ -627,7 +578,6 @@ void testOrdering() { delete m2; } -#if 1 void testIssue227() { std::string smi = "CCOP1(OCC)=CC(c2ccccc2)=C(c2ccc([N+]([O-])=O)cc2)N=C1c1ccccc1"; @@ -652,7 +602,6 @@ void testIssue227() { TEST_ASSERT(ok); delete m; } -#endif void testIssue236() { std::string smi = @@ -731,18 +680,6 @@ void testIssue276() { DistGeom::BoundsMatPtr bm(mat); DGeomHelpers::initBoundsMat(bm); DGeomHelpers::setTopolBounds(*m, bm); -#if 0 - for(unsigned int i=0;igetUpperBound(i,j) << " "; - else if(i>j) std::cout << bm->getLowerBound(i,j) << " "; - else std::cout << "0.00000" << " "; - } - std::cout << std::endl; - } - std::cout << std::endl; -#endif - ok = DistGeom::triangleSmoothBounds(bm); TEST_ASSERT(ok); @@ -916,7 +853,6 @@ void testRandomCoords() { CHECK_INVARIANT(cid >= 0, ""); // writer.write(*m); // writer.flush(); -#if 1 m2 = static_cast(sdsup.next()); // ROMol *m2 = NULL; if (m2) { @@ -925,13 +861,6 @@ void testRandomCoords() { const Conformer &conf1 = m->getConformer(0); const Conformer &conf2 = m2->getConformer(0); -#if 0 - BOOST_LOG(rdWarningLog) << "-----------------------" << std::endl; - BOOST_LOG(rdWarningLog) << MolToMolBlock(*m2) << std::endl; - BOOST_LOG(rdWarningLog) << "---" << std::endl; - BOOST_LOG(rdWarningLog) << MolToMolBlock(*m) << std::endl; - BOOST_LOG(rdWarningLog) << "-----------------------" << std::endl; -#endif for (unsigned int i = 0; i < nat; i++) { RDGeom::Point3D pt1i = conf1.getAtomPos(i); RDGeom::Point3D pt2i = conf2.getAtomPos(i); @@ -949,7 +878,6 @@ void testRandomCoords() { } } delete m2; -#endif delete m; } } @@ -998,7 +926,6 @@ void testConstrainedEmbedding() { coords[3] = ref->getConformer().getAtomPos(3); coords[4] = ref->getConformer().getAtomPos(4); -#if 1 int cid = DGeomHelpers::EmbedMolecule(*test, 30, 22, true, false, 2., true, 1, &coords); TEST_ASSERT(cid > -1); @@ -1012,7 +939,6 @@ void testConstrainedEmbedding() { double ssd = MolAlign::alignMol(*test, *ref, -1, -1, &alignMap); BOOST_LOG(rdInfoLog) << "ssd: " << ssd << std::endl; TEST_ASSERT(ssd < 0.1); -#endif delete test; } @@ -1100,7 +1026,6 @@ void testIssue2091974() { void testIssue2835784() { boost::logging::disable_logs("rdApp.warning"); -#if 1 { std::string smi = "C1C=C1"; RWMol *m = SmilesToMol(smi); @@ -1133,7 +1058,6 @@ void testIssue2835784() { TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end()); delete m; } -#endif { std::string smi = "C12=CCC1C2"; ROMol *m = SmilesToMol(smi); @@ -2352,41 +2276,6 @@ void testForceTransAmides() { mol->addBond(3, 5, Bond::BondType::SINGLE); MolOps::sanitizeMol(*mol); MolOps::addHs(*mol); -#if 0 - // worth leaving this here just to allow looking at the conformers if anything goes wrong later - { - DGeomHelpers::EmbedParameters params; - params.forceTransAmides = true; - params.randomSeed = 0xf00d; - params.useExpTorsionAnglePrefs = false; - params.useBasicKnowledge = true; - auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 10, params); - SDWriter w("amide.sdf"); - for (auto cid : cids) { - TEST_ASSERT(cid >= 0); - auto conf = mol->getConformer(cid); - auto tors = MolTransforms::getDihedralDeg(conf, 0, 1, 3, 4); - if (fabs(fabs(tors) - 180) > 5) { - w.write(*mol, cid); - std::cerr << cid << " TORS: " << tors << std::endl; - if (fabs(fabs(tors) - 180) > 40) { - std::cerr << "---------- DM " << std::endl; - double *dm = MolOps::get3DDistanceMat(*mol, cid); - auto nAtoms = mol->getNumAtoms(); - for (unsigned int i = 0; i < nAtoms; ++i) { - for (unsigned int j = 0; j < nAtoms; ++j) { - std::cerr << " " << std::setprecision(3) << std::setw(5) - << dm[i * nAtoms + j]; - } - std::cerr << std::endl; - } - } - } - // TEST_ASSERT(fabs(fabs(tors) - 180) < 5); - } - w.flush(); - } -#endif { DGeomHelpers::EmbedParameters params; params.forceTransAmides = true; @@ -2482,7 +2371,6 @@ int main() { << "********************************************************\n"; BOOST_LOG(rdInfoLog) << "Testing DistGeomHelpers\n"; -#if 1 BOOST_LOG(rdInfoLog) << "\t---------------------------------\n"; BOOST_LOG(rdInfoLog) << "\t test2 \n\n"; test2(); @@ -2679,7 +2567,6 @@ int main() { BOOST_LOG(rdInfoLog) << "\t Using symmetry in conformation pruning.\n"; testSymmetryPruning(); -#endif BOOST_LOG(rdInfoLog) << "\t---------------------------------\n"; BOOST_LOG(rdInfoLog) << "\t Force trans amides.\n"; testForceTransAmides(); diff --git a/Code/GraphMol/FileParsers/MolFileWriter.cpp b/Code/GraphMol/FileParsers/MolFileWriter.cpp index 4e8e372c2..f9d50a71a 100644 --- a/Code/GraphMol/FileParsers/MolFileWriter.cpp +++ b/Code/GraphMol/FileParsers/MolFileWriter.cpp @@ -621,16 +621,6 @@ const std::string GetMolFileAtomLine(const Atom *atom, const Conformer *conf, rxnComponentNumber); std::string symbol = AtomGetMolFileSymbol(atom, true, queryListAtoms); -#if 0 - const boost::format fmter( - "%10.4f%10.4f%10.4f %3s%2d%3d%3d%3d%3d%3d 0%3d%3d%3d%3d%3d"); - std::stringstream ss; - ss << boost::format(fmter) % x % y % z % symbol.c_str() % massDiff % chg % - parityFlag % hCount % stereoCare % totValence % rxnComponentType % - rxnComponentNumber % atomMapNumber % inversionFlag % - exactChangeFlag; - res += ss.str(); -#else // it feels ugly to use snprintf instead of boost::format, but at least of the // time of this writing (with boost 1.55), the snprintf version runs in 20% of // the time. @@ -654,7 +644,6 @@ const std::string GetMolFileAtomLine(const Atom *atom, const Conformer *conf, #endif res += dest; -#endif return res; }; diff --git a/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp b/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp index 7c8a2a200..648aaba59 100644 --- a/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp +++ b/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp @@ -42,7 +42,7 @@ TEST_CASE("Github #5863: failure in WedgeMolBonds") { TEST_CASE("translating the chiral flag to stereo groups") { SECTION("basics") { auto withFlag = R"CTAB( - Mrv2211 03302308372D + Mrv2211 03302308372D 5 4 0 0 1 0 999 V2000 -6.5625 3.9286 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 @@ -103,7 +103,7 @@ M END SECTION("explicit zero chiral flag") { auto zeroFlag = R"CTAB( - Mrv2211 03302308372D + Mrv2211 03302308372D 5 4 0 0 o 0 999 V2000 -6.5625 3.9286 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 @@ -240,11 +240,10 @@ void testStereoExample(const std::string &mb, unsigned int aidx, } TEST_CASE("IUPAC recommendations") { -#if 1 SECTION("simple examples") { std::vector mbs = { R"CTAB( - Mrv2211 06082308462D + Mrv2211 06082308462D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -266,7 +265,7 @@ M V30 END CTAB M END )CTAB", R"CTAB( - Mrv2211 06082309052D + Mrv2211 06082309052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -288,7 +287,7 @@ M V30 END CTAB M END )CTAB", R"CTAB( - Mrv2211 06082309052D + Mrv2211 06082309052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -310,7 +309,7 @@ M V30 END CTAB M END )CTAB", R"CTAB(IUPAC does not like this one - Mrv2211 06082309142D + Mrv2211 06082309142D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -332,7 +331,7 @@ M V30 END CTAB M END )CTAB", R"CTAB(IUPAC does not like this one2 - Mrv2211 06082309142D + Mrv2211 06082309142D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -347,7 +346,7 @@ M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 -M V30 3 1 2 4 +M V30 3 1 2 4 M V30 4 1 2 5 CFG=1 M V30 END BOND M V30 END CTAB @@ -369,7 +368,7 @@ M END } SECTION("three coordinate") { auto m = R"CTAB( - Mrv2108 01192209042D + Mrv2108 01192209042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -403,7 +402,6 @@ M END)CTAB"_ctab; CHECK(m->getAtomWithIdx(5)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } -#endif SECTION("this came up") { std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/test_data/github87.mol"; @@ -415,7 +413,7 @@ M END)CTAB"_ctab; SECTION("narrow angle") { auto m = R"CTAB( - Mrv2211 06092305312D + Mrv2211 06092305312D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -469,7 +467,7 @@ M END)CTAB"_ctab; SECTION("linear arrangements") { { auto m = R"CTAB( - Mrv2211 06102314502D + Mrv2211 06102314502D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -498,7 +496,7 @@ M END } { auto m = R"CTAB(opposing stereo - Mrv2211 06102314502D + Mrv2211 06102314502D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -528,7 +526,7 @@ M END { // std::cerr<<"11111111111111"< (1) +> (1) [1,2,] $$$$ - Mrv1810 06051911332D + Mrv1810 06051911332D 3 2 0 0 0 0 999 V2000 -10.3083 4.8496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -2692,7 +2690,7 @@ $$$$ 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M END -> (1) +> (1) [1,2,] )SDF"; { @@ -2717,7 +2715,7 @@ M END #ifdef RDK_BUILD_MAEPARSER_SUPPORT void testGitHub2881() { - std::string data = R"DATA(f_m_ct { + std::string data = R"DATA(f_m_ct { s_m_title s_m_entry_id s_m_entry_name @@ -2731,28 +2729,28 @@ void testGitHub2881() { b_m_subgroup_collapsed i_m_ct_format ::: - "Untitled Document-4" - 17 - newTemplates2.1 - /Users/nicola/schrodinger/coordgen_standalone - templates.mae + "Untitled Document-4" 17 - 3_S_4_6_2 - 7_S_8_9_6_10 - templates->templates->templates - templates->templates1->templates11 + newTemplates2.1 + /Users/nicola/schrodinger/coordgen_standalone + templates.mae + 17 + 3_S_4_6_2 + 7_S_8_9_6_10 + templates->templates->templates + templates->templates1->templates11 0 2 - m_depend[2] { + m_depend[2] { # First column is dependency index # i_m_depend_dependency s_m_depend_property ::: - 1 10 s_st_Chirality_1 - 2 10 s_st_Chirality_2 + 1 10 s_st_Chirality_1 + 2 10 s_st_Chirality_2 ::: - } - m_atom[15] { + } + m_atom[15] { # First column is atom index # i_m_mmod_type r_m_x_coord @@ -2764,24 +2762,24 @@ void testGitHub2881() { s_m_color_rgb s_m_atom_name ::: - 1 5 1.186400 1.035900 0.000000 900 2 6 A0A0A0 C1 - 2 5 0.370300 1.157000 0.000000 900 2 6 A0A0A0 C2 - 3 4 -0.326500 0.715300 0.000000 900 2 6 A0A0A0 C3 - 4 5 0.085100 0.000400 0.000000 900 2 6 A0A0A0 C4 - 5 26 -0.328300 -0.713600 0.000000 900 43 7 5757FF N5 - 6 5 -1.151500 0.716400 0.000000 900 2 6 A0A0A0 C6 - 7 5 -1.564900 0.002400 0.000000 900 2 6 A0A0A0 C7 - 8 5 -1.153300 -0.712600 0.000000 900 2 6 A0A0A0 C9 - 9 2 1.724800 0.410800 0.000000 900 2 6 A0A0A0 C12 - 10 2 1.723800 -0.414200 0.000000 900 2 6 A0A0A0 C13 - 11 5 1.183800 -1.037900 0.000000 900 2 6 A0A0A0 C14 - 12 5 0.367400 -1.157000 0.000000 900 2 6 A0A0A0 C15 - 13 7 2.508100 -0.670100 0.000000 900 2 6 A0A0A0 C16 - 14 7 2.993800 -0.003300 0.000000 900 2 6 A0A0A0 C17 - 15 29 2.509700 0.664800 0.000000 900 43 7 5757FF N18 + 1 5 1.186400 1.035900 0.000000 900 2 6 A0A0A0 C1 + 2 5 0.370300 1.157000 0.000000 900 2 6 A0A0A0 C2 + 3 4 -0.326500 0.715300 0.000000 900 2 6 A0A0A0 C3 + 4 5 0.085100 0.000400 0.000000 900 2 6 A0A0A0 C4 + 5 26 -0.328300 -0.713600 0.000000 900 43 7 5757FF N5 + 6 5 -1.151500 0.716400 0.000000 900 2 6 A0A0A0 C6 + 7 5 -1.564900 0.002400 0.000000 900 2 6 A0A0A0 C7 + 8 5 -1.153300 -0.712600 0.000000 900 2 6 A0A0A0 C9 + 9 2 1.724800 0.410800 0.000000 900 2 6 A0A0A0 C12 + 10 2 1.723800 -0.414200 0.000000 900 2 6 A0A0A0 C13 + 11 5 1.183800 -1.037900 0.000000 900 2 6 A0A0A0 C14 + 12 5 0.367400 -1.157000 0.000000 900 2 6 A0A0A0 C15 + 13 7 2.508100 -0.670100 0.000000 900 2 6 A0A0A0 C16 + 14 7 2.993800 -0.003300 0.000000 900 2 6 A0A0A0 C17 + 15 29 2.509700 0.664800 0.000000 900 43 7 5757FF N18 ::: - } - m_bond[17] { + } + m_bond[17] { # First column is bond index # i_m_from i_m_to @@ -2805,8 +2803,8 @@ void testGitHub2881() { 16 13 14 2 17 14 15 1 ::: - } -} + } +} )DATA"; { auto *iss = new std::istringstream(data); @@ -2840,7 +2838,6 @@ void testGitHub3517() { int main() { RDLog::InitLogs(); -#if 1 BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n"; testMolSup(); BOOST_LOG(rdErrorLog) << "Finished: testMolSup()\n"; @@ -3014,7 +3011,6 @@ int main() { testGitHub2285(); BOOST_LOG(rdErrorLog) << "Finished: testGitHub2285()\n"; BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n"; -#endif BOOST_LOG(rdErrorLog) << "-----------------------------------------\n"; testGitHub2479(); diff --git a/Code/GraphMol/MolStandardize/testNormalize.cpp b/Code/GraphMol/MolStandardize/testNormalize.cpp index 986be156c..f5416826d 100644 --- a/Code/GraphMol/MolStandardize/testNormalize.cpp +++ b/Code/GraphMol/MolStandardize/testNormalize.cpp @@ -545,10 +545,8 @@ void testGithub4281() { int main() { RDLog::InitLogs(); -#if 1 test1(); test2(); -#endif testGithub2414(); testNormalizeMultipleAltSmarts(); testGithub3460(); diff --git a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp index dd524dfdb..3f6bc6c45 100644 --- a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +++ b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp @@ -512,7 +512,6 @@ void testGitHubIssue1705() { BOOST_LOG(rdInfoLog) << "test grouping substituents in chunks as large as possible" << std::endl; -#if 1 { RWMol *core = SmilesToMol("Oc1ccccc1"); RGroupDecompositionParameters params; @@ -566,8 +565,6 @@ Cl[*:2] TEST_ASSERT(ss.str() == expected); #endif } -#endif - // std::cerr<<"n\n\n\n\n\n--------------------------------------------------------------\n\n\n\n\n"; { RWMol *core = SmilesToMol("Cc1ccccc1"); RGroupDecompositionParameters params; @@ -4157,7 +4154,6 @@ int main() { << "********************************************************\n"; BOOST_LOG(rdInfoLog) << "Testing R-Group Decomposition \n"; -#if 1 testSymmetryMatching(FingerprintVariance); testSymmetryMatching(); testRGroupOnlyMatching(); @@ -4182,7 +4178,6 @@ int main() { testUnprocessedMapping(); testSingleAtomBridge(); -#endif testSymmetryPerformance(); testScorePermutations(); testMultiCorePreLabelled(); diff --git a/Code/GraphMol/SLNParse/SLNAttribs.cpp b/Code/GraphMol/SLNParse/SLNAttribs.cpp index 7300e5997..01f6f12fe 100644 --- a/Code/GraphMol/SLNParse/SLNAttribs.cpp +++ b/Code/GraphMol/SLNParse/SLNAttribs.cpp @@ -201,14 +201,6 @@ void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery) { BOOST_LOG(rdWarningLog) << "Chiral modifier m ignored, chiral spec " << attribVal[0] << " will be used\n"; } -#if 0 - } else if(attribVal=="r"){ - } else if(attribVal=="r*"){ - } else if(attribVal=="rm"){ - } else if(attribVal=="s"){ - } else if(attribVal=="s*"){ - } else if(attribVal=="sm"){ -#endif } else { BOOST_LOG(rdWarningLog) << "Unsupported stereochemistry specifier '" << attribVal << "' ignored.\n"; diff --git a/Code/GraphMol/catch_graphmol.cpp b/Code/GraphMol/catch_graphmol.cpp index 7c8a06943..7adb004fb 100644 --- a/Code/GraphMol/catch_graphmol.cpp +++ b/Code/GraphMol/catch_graphmol.cpp @@ -32,7 +32,6 @@ #include using namespace RDKit; -#if 1 TEST_CASE("SMILES Parsing works", "[molops]") { std::unique_ptr mol(SmilesToMol("C1CC1")); REQUIRE(mol); @@ -1151,7 +1150,7 @@ TEST_CASE("RemoveHsParameters", "[molops]") { } } } -#endif + TEST_CASE("github #2895: acepentalene aromaticity perception ", "[molops][bug][aromaticity]") { SECTION("acepentalene") { @@ -1679,7 +1678,7 @@ M END)CTAB"_ctab; } SECTION("a simpler system") { auto m = R"CTAB( - Mrv2014 03092106042D + Mrv2014 03092106042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -2607,7 +2606,7 @@ TEST_CASE("query moves") { TEST_CASE("moves with conformer") { auto m1 = R"CTAB( - Mrv2108 01192209042D + Mrv2108 01192209042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -3905,8 +3904,8 @@ TEST_CASE("atom output") { ss.str(""); } SECTION("chirality 2") { - // same as - // C[Pt@SP2]([H])(F)Cl which is stored internally as + // same as + // C[Pt@SP2]([H])(F)Cl which is stored internally as // C[Pt@SP3](F)(Cl)[H] auto m = "C[Pt@SP2H](F)Cl"_smiles; REQUIRE(m); @@ -3924,7 +3923,7 @@ TEST_CASE( "[RWMol]") { // This mols is made up, it probably doesn't make sense at all. auto m1 = R"CTAB( - Mrv2311 02062417062D + Mrv2311 02062417062D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -4198,7 +4197,7 @@ TEST_CASE("Try not to set wedged bonds as double in the kekulization") { // verify that in both cases the kekulization results in assigning // a single bond order to the wedged bonds. auto mblock1 = R"( - Mrv2311 05242408112D + Mrv2311 05242408112D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -4251,7 +4250,7 @@ M END Bond::BondType::DOUBLE); auto mblock2 = R"( - Mrv2311 05242408162D + Mrv2311 05242408162D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -4313,7 +4312,7 @@ M END // similar to the previous test case, but adding fused rings and // an O atom that wouldn't accept double bonds auto mblock1 = R"( - Mrv2311 05282412322D + Mrv2311 05282412322D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -4373,7 +4372,7 @@ M END Bond::BondType::DOUBLE); auto mblock2 = R"( - Mrv2311 05282412342D + Mrv2311 05282412342D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB @@ -4438,7 +4437,6 @@ M END pathName += "/Code/GraphMol/FileParsers/test_data/atropisomers/"; std::vector> prs = { -#if 1 {"BMS-986142_atrop8.sdf", 8}, {"Mrtx1719_atrop3.sdf", 21}, {"AtropManyChiralsEnhanced2.sdf", 7}, @@ -4497,7 +4495,6 @@ M END {"RP-6306_atrop3.sdf", 3}, {"macrocycle-8-ortho-broken-hash.sdf", 14}, {"JDQ443_atrop3.sdf", 26}, -#endif {"JDQ443_3d.sdf", 26}, // keep }; @@ -4715,7 +4712,7 @@ TEST_CASE("Github #7873: monomer info segfaults and mem leaks", "[PDB]") { *deleted = true; } }; - + bool sanitize = true; int flavor = 0; std::unique_ptr mol(SequenceToMol("KY", sanitize, flavor)); @@ -4730,7 +4727,7 @@ TEST_CASE("Github #7873: monomer info segfaults and mem leaks", "[PDB]") { mol->getAtomWithIdx(0)->setMonomerInfo(res); mol->getAtomWithIdx(0)->setMonomerInfo(nullptr); CHECK(was_deleted == true); - - } + + } } diff --git a/Code/GraphMol/itertest.cpp b/Code/GraphMol/itertest.cpp index f6011ddc9..6ad731c39 100644 --- a/Code/GraphMol/itertest.cpp +++ b/Code/GraphMol/itertest.cpp @@ -246,7 +246,6 @@ void test5() { BOOST_LOG(rdInfoLog) << "test5 done" << endl; } -#if 1 void _test6Help(const ROMol *m) { Mol::ConstAtomIterator atIt; unsigned int idx = 0; @@ -312,11 +311,9 @@ void test6() { delete m; BOOST_LOG(rdInfoLog) << "test6 done" << endl; }; -#endif void test7() { string smi = "c1ccccc1C"; -#if 1 Mol *m = SmilesToMol(smi); Mol::AromaticAtomIterator atomIt; Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms()); @@ -346,13 +343,11 @@ void test7() { TEST_ASSERT(idx == 6); delete m; -#endif BOOST_LOG(rdInfoLog) << "test7 done" << endl; } void testIssue263() { string smi = "c1ccccc1C"; -#if 1 Mol *m = SmilesToMol(smi); Mol::AtomIterator atomIt; unsigned int idx = 0; @@ -371,7 +366,6 @@ void testIssue263() { CHECK_INVARIANT(idx == 7, "bad idx"); delete m; -#endif BOOST_LOG(rdInfoLog) << "testIssue263 done" << endl; } diff --git a/Code/PgSQL/rdkit/adapter.cpp b/Code/PgSQL/rdkit/adapter.cpp index 3083faaf9..4a60ca323 100644 --- a/Code/PgSQL/rdkit/adapter.cpp +++ b/Code/PgSQL/rdkit/adapter.cpp @@ -1032,11 +1032,7 @@ extern "C" bytea *makeLowSparseFingerPrint(CSfp data, int numInts) { n = iter->first % numInts; if (iterV > INTRANGEMAX) { -#if 0 - elog(ERROR, "sparse fingerprint is too big, increase INTRANGEMAX in rdkit.h"); -#else iterV = INTRANGEMAX; -#endif } if (s[n].low == 0 || s[n].low > iterV) { diff --git a/Code/RDGeneral/testDict.cpp b/Code/RDGeneral/testDict.cpp index d064300fb..5e95c8e05 100644 --- a/Code/RDGeneral/testDict.cpp +++ b/Code/RDGeneral/testDict.cpp @@ -491,29 +491,6 @@ void testConstReturns() { TEST_ASSERT(nv == "foo"); } -#if 0 - { - Dict d; - std::string v="foo"; - d.setVal("foo",v); - - double ls=0; - BOOST_LOG(rdErrorLog) << "copy" << std::endl; - for(int i=0;i<100000000;++i){ - std::string nv=d.getVal("foo"); - ls+= nv.size(); - } - BOOST_LOG(rdErrorLog) << "done: "<("foo"); - ls+= nv.size(); - } - BOOST_LOG(rdErrorLog) << "done: "<("foo"); - } -#else { // int nreps=100000000; int nreps = 100000; @@ -590,8 +567,6 @@ void testConstReturns() { // std::string nv=d.getVal("foo"); } -#endif - BOOST_LOG(rdErrorLog) << "\tdone" << std::endl; } @@ -726,7 +701,6 @@ int main() { RDLog::InitLogs(); testGithub940(); -#if 1 testRDAny(); Dict d; INT_VECT fooV; @@ -812,7 +786,6 @@ int main() { testStringVals(); testVectToString(); -#endif testConstReturns(); testUpdate(); testCustomProps();