void prepareMolForDrawing(RWMol &mol, bool kekulize, bool addChiralHs,
bool wedgeBonds, bool forceCoords) {
if (kekulize) {
MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
}
if (addChiralHs) {
std::vector<unsigned int> chiralAts;
for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
++atIt) {
if ((*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
(*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW) {
chiralAts.push_back((*atIt)->getIdx());
}
}
if (chiralAts.size()) {
bool addCoords = false;
if (!forceCoords && mol.getNumConformers()) addCoords = true;
MolOps::addHs(mol, false, addCoords, &chiralAts);
}
}
if (forceCoords || !mol.getNumConformers()) {
RDDepict::compute2DCoords(mol);
}
if (wedgeBonds) {
WedgeMolBonds(mol, &mol.getConformer());
}
}
void prepareMolForDrawing(RWMol &mol, bool kekulize, bool addChiralHs,
bool wedgeBonds, bool forceCoords) {
if (kekulize) {
MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
}
if (addChiralHs) {
std::vector<unsigned int> chiralAts;
for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
++atIt) {
if (isAtomCandForChiralH(mol, *atIt)) {
chiralAts.push_back((*atIt)->getIdx());
}
}
if (chiralAts.size()) {
bool addCoords = false;
if (!forceCoords && mol.getNumConformers()) addCoords = true;
MolOps::addHs(mol, false, addCoords, &chiralAts);
}
}
if (forceCoords || !mol.getNumConformers()) {
// compute 2D coordinates in a standard orientation:
const bool canonOrient = true;
RDDepict::compute2DCoords(mol, NULL, canonOrient);
}
if (wedgeBonds) {
WedgeMolBonds(mol, &mol.getConformer());
}
}
void test2() {
BOOST_LOG(rdInfoLog) << "testing coordinate generation" << std::endl;
#if 1
{
RWMol *m = SmilesToMol("c1cccnc1");
TEST_ASSERT(m);
unsigned int confId = AvalonTools::set2DCoords(*m);
TEST_ASSERT(m->getNumConformers() == 1);
TEST_ASSERT(confId == 0);
delete m;
}
#endif
{
std::string molb = AvalonTools::set2DCoords("c1cccnc1", true);
TEST_ASSERT(molb != "");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGeneral(std::string rdbase){
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- testing general mol2 file parsing --" << std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/nonExistFile.mol2";
try{
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const BadFileException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyrazole_pyridine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
// this was sf.net issue 2727976:
TEST_ASSERT(m->getNumConformers()==1);
TEST_ASSERT(m->getConformer().is3D());
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).x,1.5019));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).y,1.0435));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).z,0.0000));
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/benzene.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
delete m;
}
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_noatoms.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const FileParseException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_nomol.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const FileParseException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/lonePairMol.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5 && m->getNumBonds()==4);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/symmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/highlySymmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(4)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(12)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/fusedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(13)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyridiniumPhenyl.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/sulfonAmide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineRWH.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineEC.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateCharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUncharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUnchargedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(2)->getFormalCharge()==0);
delete m;
}
#if 0
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Sulfonate.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
BOOST_LOG(rdInfoLog) <<MolToSmiles(*m)<<std::endl;
delete m;
}
#endif
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE general mol2 file parsing --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
