void testUFFBuilderSpecialCases(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF special cases." << std::endl;
RWMol *mol;
std::string key;
int needMore;
RDGeom::Point3D v1,v2;
ForceFields::ForceField *field;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
// ----------
// Trigonal bipyramid
// ----------
mol = MolFileToMol(pathName+"/tbp.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
const Conformer &conf = mol->getConformer();
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200,1e-8,1e-4);
TEST_ASSERT(!needMore);
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(1));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
TEST_ASSERT(feq(v1.dotProduct(v2),-1.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
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 test3CubeFiles () {
std::string path = getenv ("RDBASE");
path += "/Code/GraphMol/MIF/test_data/";
RWMol mol = *MolFileToMol(path + "HCl.mol", true, false);
RealValueVect *data = new RealValueVect (0.0, 125);
UniformRealValueGrid3D grd (5.0, 5.0, 5.0, 1.0, new Point3D (0.0, 0.0, 0.0),
data);
for (unsigned int i = 0; i < grd.getSize (); i++) {
grd.setVal (i, double (i / 10.0));
}
writeToCubeFile (grd, mol, path + "test3.cube");
UniformRealValueGrid3D grd2;
RWMol mol2 = *readFromCubeFile (grd2, path + "test3.cube");
CHECK_INVARIANT(grd.getSize() == grd2.getSize(),
"I/O: grid sizes are not the same.");
for (unsigned int i = 0; i < grd2.getSize (); i++) {
CHECK_INVARIANT(feq(grd2.getVal(i), double(i / 10.0)),
"I/O: values in grid are not correct.");
}
CHECK_INVARIANT(grd.getNumX() == grd2.getNumX(), "I/O: grids are not the same.");
CHECK_INVARIANT(grd.getNumY() == grd2.getNumY(), "I/O: grids are not the same.");
CHECK_INVARIANT(grd.getNumZ() == grd2.getNumZ(), "I/O: grids are not the same.");
CHECK_INVARIANT(feq(grd.getOffset().x, grd2.getOffset().x), "I/O: grids are not the same.");
CHECK_INVARIANT(feq(grd.getSpacing(), grd2.getSpacing()), "I/O: grids are not the same.");
CHECK_INVARIANT(grd.compareVectors(grd2), "I/O: grids are not the same.");
CHECK_INVARIANT(grd.compareParams(grd2), "I/O: grids are not the same.");
CHECK_INVARIANT(grd.compareGrids(grd2), "I/O: grids are not the same.");
CHECK_INVARIANT(mol.getNumAtoms() == mol2.getNumAtoms(),
"I/O: number of atoms are not the same.");
for (unsigned int i = 0; i < mol.getNumAtoms (); i++) {
CHECK_INVARIANT(mol.getAtomWithIdx (i)->getAtomicNum ()
== mol2.getAtomWithIdx (i)->getAtomicNum (),
"I/O: atoms are not the same");
CHECK_INVARIANT(feq (mol.getConformer ().getAtomPos (i).x,
mol2.getConformer ().getAtomPos (i).x),
"I/O: atom positions are not the same");
CHECK_INVARIANT(feq (mol.getConformer ().getAtomPos (i).y,
mol2.getConformer ().getAtomPos (i).y),
"I/O: atom positions are not the same");
CHECK_INVARIANT(feq (mol.getConformer ().getAtomPos (i).z,
mol2.getConformer ().getAtomPos (i).z),
"I/O: atom positions are not the same");
}
}
void test4Coulomb () {
std::string path = getenv("RDBASE");
path += "/Code/GraphMol/MIF/test_data/";
RWMol mol = *MolFileToMol(path + "HCl.mol", true, false);
computeGasteigerCharges(mol);
std::vector<double> charges;
std::vector<Point3D> pos;
Conformer conf = mol.getConformer(0);
for (int i = 0; i < mol.getNumAtoms(); ++i) {
charges.push_back(mol.getAtomWithIdx (i)->getProp<double> ("_GasteigerCharge"));
pos.push_back(conf.getAtomPos(i));
}
UniformRealValueGrid3D grd = *constructGrid(mol);
UniformRealValueGrid3D grd2 = *constructGrid(mol);
Coulomb coul(mol);
calculateDescriptors<Coulomb>(grd, coul);
calculateDescriptors<Coulomb>(grd2, Coulomb (charges, pos));
CHECK_INVARIANT(grd.compareGrids(grd2),
"Coulomb: Different constructors do not yield the same descriptor.");
CHECK_INVARIANT(feq (coul(0.0,0.0,0.0, 1000), 0.0),
"Coulomb: Potential between atoms wrong.(should be 0)");
CHECK_INVARIANT(coul(2.0,0.0,0.0, 1000) < 0,
"Coulomb: Potential between positive charges not positive.");
CHECK_INVARIANT(coul(-2.0,0.0,0.0, 1000) > 0,
"Coulomb: Potential between positive and negative charges not negative.");
CHECK_INVARIANT(feq(coul(0.0,0.0,0.0, 0.1), 0.0),
"Coulomb: Small threshold dist does not give 0.");
calculateDescriptors<Coulomb>(grd, Coulomb(mol, 0, 1.0, true));
for (unsigned int i = 0; i < grd.getSize(); i++) {
CHECK_INVARIANT(grd.getVal (i) <= 0.0, "Coulomb: Absolute value field not negative");
}
Coulomb coul1(mol, 0, -1.0, false, "_GasteigerCharge", 0.0, 0.01);
CHECK_INVARIANT(coul1(-2.0, 0.0, 0.0, 1000) < 0, "Coulomb: Potential between negative charges not positive.");
CHECK_INVARIANT(coul1(2.0, 0.0, 0.0, 1000) > 0, "Coulomb: Potential between positive and negative charges not negative.");
Coulomb coul2 = Coulomb(mol, 0, -.5, false, "_GasteigerCharge", 0.0, 0.01);
CHECK_INVARIANT(coul1(-2.0, 0.0, 0.0, 1000) < coul2 (-2.0, 0.0, 0.0, 1000),
"Coulomb: Higher probecharge does not result in stronger forces.");
Coulomb coul3(mol, 0, 1.0, false, "_GasteigerCharge", 0.01, 1.0);
CHECK_INVARIANT(coul3(0.0, 0.0, 0.0, 1000) > coul3(0.1, 0.0, 0.0, 1000),
"Coulomb: Softcore interaction wrong.");
CHECK_INVARIANT(coul3(0.66, 0.0, 0.0, 1000) > coul3(0.68, 0.0, 0.0, 1000),
"Coulomb: Softcore interaction wrong.");
CHECK_INVARIANT(coul3(0.70, 0.0, 0.0, 1000) > coul3(0.68, 0.0, 0.0, 1000),
"Coulomb: Softcore interaction wrong.");
CHECK_INVARIANT(feq(coul3(0.0,0.0,0.0, 0.1), 0.0),
"Coulomb: Small threshold dist does not give 0.");
}
void test1ConstructGrid() {
std::string path = getenv("RDBASE");
path += "/Code/GraphMol/MIF/test_data/";
// //Generate Molecule with 3D Coordinates and Partial Charges
// RWMol mol=*SmilesToMol("Cl");
// MolOps::addHs(mol);
// DGeomHelpers::EmbedMolecule(mol);
// MolToMolFile(mol, path + "HCl.mol");
RWMol mol = *MolFileToMol(path + "HCl.mol", true, false);
UniformRealValueGrid3D grd = *constructGrid(mol, 0, 5.0, 0.5);
Point3D bond = mol.getConformer().getAtomPos(1) - mol.getConformer().getAtomPos(0);
CHECK_INVARIANT(feq(grd.getSpacing (), 0.5),
"Spacing of grid is not correct.");
CHECK_INVARIANT(feq(grd.getNumX (), std::floor ((fabs (bond.x) + 10.0) / 0.5 + 0.5)),
"X length of grid is incorrect.");
CHECK_INVARIANT(feq(grd.getNumY (), std::floor ((fabs (bond.y) + 10.0) / 0.5 + 0.5)),
"Y length of grid is incorrect.");
CHECK_INVARIANT(feq(grd.getNumZ (), std::floor ((fabs (bond.z) + 10.0) / 0.5 + 0.5)),
"Z length of grid is incorrect.");
}
void testGetSetBondLength() {
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 1.36));
setBondLength(conf, 0, 19, 2.5);
dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 2.5));
setBondLength(conf, 19, 0, 3.0);
dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 3.0));
}
void testGetSetAngle() {
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(RDKit::round(angle * 10) / 10, 109.7));
setAngleDeg(conf, 0, 19, 21, 125.0);
angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, 125.0));
setAngleRad(conf, 21, 19, 0, M_PI / 2.);
angle = getAngleRad(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, M_PI / 2.));
angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, 90.0));
}
void testGetSetDihedral() {
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double dihedral = getDihedralDeg(conf, 0, 19, 21, 24);
TEST_ASSERT(RDKit::feq(RDKit::round(dihedral * 100) / 100, 176.05));
setDihedralDeg(conf, 8, 0, 19, 21, 65.0);
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, 65.0));
setDihedralDeg(conf, 8, 0, 19, 21, -130.0);
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -130.0));
setDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * M_PI);
dihedral = getDihedralRad(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -2. / 3. * M_PI));
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -120.0));
}
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;
}
void testGithub774() {
std::cout << " ----------------- Test Github774" << std::endl;
{
std::string smiles =
"Cc1c(C(=O)NCC[NH3+])[n+](=O)c2cc(CC[C@](F)(Cl)Br)ccc2n1[O-]";
std::string nameBase = "test774_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
Point2D ocoords(1.0, 2.0);
Point2D dcoords =
drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y));
Point2D acoords = drawer.getDrawCoords(dcoords);
TEST_ASSERT(feq(acoords.x, 1.0));
TEST_ASSERT(feq(acoords.y, 2.0));
}
// m->setProp("_Name","mol");
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
{
std::string smiles =
"CC(=O)\\C=C\\CC1[C@H]2N([C@@H](C(=O)O)C(C)(C)S2(=O)=O)C1=O";
std::string nameBase = "test774_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
// m->setProp("_Name","mol");
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
std::cerr << " Done" << std::endl;
}
