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Fix undefined behavior in testCoordGen test (#3495)

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* Fix ROMol->RWMol static casts

* Fix accessing of end-iterator.

* Fix some test build issues I saw while compiling with Clang.

* Add build settings for sanitizers.

* Revert "Add build settings for sanitizers."

This reverts commit 5dc84374f0.
This commit is contained in:
Rocco Moretti
2020-10-16 21:26:13 -05:00
committed by GitHub
parent 7eda4708c1
commit 3cc2123637
3 changed files with 15 additions and 19 deletions
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3
Code/GraphMol/FileParsers/MolFileWriter.cpp
View File

@@ -1377,8 +1377,7 @@ std::string MolToMolBlock(const ROMol &mol, bool includeStereo, int confId,
bool kekulize, bool forceV3000) {
RDUNUSED_PARAM(includeStereo);
RDKit::Utils::LocaleSwitcher switcher;
ROMol tromol(mol);
auto &trwmol = static_cast<RWMol &>(tromol);
RWMol trwmol(mol);
// NOTE: kekulize the molecule before writing it out
// because of the way mol files handle aromaticity
if (trwmol.needsUpdatePropertyCache()) {

4
Code/GraphMol/FileParsers/testMolSupplier.cpp
View File

@@ -121,7 +121,7 @@ int testMolSup() {
TEST_ASSERT(nmol->getProp<std::string>("s_m_entry_name") ==
"NCI_aids_few.1");
TEST_ASSERT(nmol->hasProp("r_f3d_dummy"));
TEST_ASSERT(abs(nmol->getProp<double>("r_f3d_dummy") - 42.123) < 0.0001);
TEST_ASSERT(std::abs(nmol->getProp<double>("r_f3d_dummy") - 42.123) < 0.0001);
// Test atom properties
TEST_ASSERT(nmol->getNumAtoms() == 19);
@@ -144,7 +144,7 @@ int testMolSup() {
// The real property is only defined for i >= 10
if (i >= 10) {
TEST_ASSERT(atom->hasProp("r_f3d_dummy"));
TEST_ASSERT(abs(atom->getProp<double>("r_f3d_dummy") - (19.1 - i)) <
TEST_ASSERT(std::abs(atom->getProp<double>("r_f3d_dummy") - (19.1 - i)) <
0.0001);
} else {
TEST_ASSERT(!atom->hasProp("r_f3d_dummy"));

27
Code/GraphMol/MolOps.cpp
View File

@@ -442,10 +442,10 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
ownIt = true;
}
unsigned int nFrags = getMolFrags(mol, *mapping);
std::vector<ROMOL_SPTR> res;
std::vector<RWMOL_SPTR> res;
if (nFrags == 1) {
auto *tmp = new ROMol(mol);
ROMOL_SPTR sptr(tmp);
auto *tmp = new RWMol(mol);
RWMOL_SPTR sptr(tmp);
res.push_back(sptr);
if (fragsMolAtomMapping) {
INT_VECT comp;
@@ -460,17 +460,16 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
boost::dynamic_bitset<> copiedBonds(mol.getNumBonds(), 0);
res.reserve(nFrags);
for (unsigned int frag = 0; frag < nFrags; ++frag) {
auto *tmp = new ROMol();
ROMOL_SPTR sptr(tmp);
auto *tmp = new RWMol();
RWMOL_SPTR sptr(tmp);
res.push_back(sptr);
}
// copy atoms
INT_INT_VECT_MAP comMap;
for (unsigned int idx = 0; idx < mol.getNumAtoms(); ++idx) {
auto *tmp = static_cast<RWMol *>(res[(*mapping)[idx]].get());
const Atom *oAtm = mol.getAtomWithIdx(idx);
ids[idx] = tmp->addAtom(oAtm->copy(), false, true);
ids[idx] = res[(*mapping)[idx]]->addAtom(oAtm->copy(), false, true);
copiedAtoms[idx] = 1;
if (fragsMolAtomMapping) {
if (comMap.find((*mapping)[idx]) == comMap.end()) {
@@ -505,8 +504,7 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
}
ringStereoAtomsCopied.push_back(ridx);
}
auto *tmp = static_cast<RWMol *>(res[(*mapping)[idx]].get());
tmp->getAtomWithIdx(ids[idx])->setProp(
res[(*mapping)[idx]]->getAtomWithIdx(ids[idx])->setProp(
common_properties::_ringStereoAtoms, ringStereoAtomsCopied);
}
}
@@ -521,9 +519,8 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
continue;
}
Bond *nBond = bond->copy();
auto *tmp =
static_cast<RWMol *>(res[(*mapping)[nBond->getBeginAtomIdx()]].get());
nBond->setOwningMol(static_cast<ROMol *>(tmp));
RWMol *tmp = res[(*mapping)[nBond->getBeginAtomIdx()]].get();
nBond->setOwningMol( tmp );
nBond->setBeginAtomIdx(ids[nBond->getBeginAtomIdx()]);
nBond->setEndAtomIdx(ids[nBond->getEndAtomIdx()]);
nBond->getStereoAtoms().clear();
@@ -538,7 +535,7 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
if (mol.getRingInfo()->isInitialized()) {
for (const auto &i : mol.getRingInfo()->atomRings()) {
INT_VECT aids;
auto *tmp = static_cast<RWMol *>(res[(*mapping)[i[0]]].get());
auto tmp = res[(*mapping)[i[0]]].get();
if (!tmp->getRingInfo()->isInitialized()) {
tmp->getRingInfo()->initialize();
}
@@ -596,14 +593,14 @@ std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
if (sanitizeFrags) {
for (auto &re : res) {
sanitizeMol(*static_cast<RWMol *>(re.get()));
sanitizeMol( *re );
}
}
if (ownIt) {
delete mapping;
}
return res;
return std::vector<ROMOL_SPTR>( res.begin(), res.end() );
}
unsigned int getMolFrags(const ROMol &mol, INT_VECT &mapping) {