Molecule * OpenbabelWrapper::openFile(const QString &fileName,
const QString &fileType,
const QString &fileOptions)
{
// Check that the file can be read from disk
if (!canOpen(fileName, QFile::ReadOnly | QFile::Text))
return 0;
// Construct the OpenBabel objects, set the file type
OBConversion conv;
OBFormat *inFormat;
if (!fileType.isEmpty() && !conv.SetInFormat(fileType.toAscii().data()))
// Input format not supported
return 0;
else {
inFormat = conv.FormatFromExt(fileName.toAscii().data());
if (!conv.SetInFormat(inFormat))
// Input format not supported
return 0;
}
// set any options
if (!fileOptions.isEmpty()) {
foreach(const QString &option,
fileOptions.split('\n', QString::SkipEmptyParts)) {
conv.AddOption(option.toAscii().data(), OBConversion::INOPTIONS);
}
}
void testPdbOccupancies()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test08.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("HETATM 1 NA UNL 1 0.325 0.000 4.425 0.36") != string::npos);
OB_ASSERT(pdb.find("HETATM 17 O UNL 8 1.954 8.956 3.035 1.00") != string::npos);
OBMol mol_pdb;
conv.SetInFormat("pdb");
conv.ReadFile(&mol_pdb, GetFilename("test09.pdb"));
pdb = conv.WriteString(&mol_pdb);
OB_ASSERT(pdb.find("HETATM 1 NA UNL 1 0.325 0.000 4.425 0.36") != string::npos);
OB_ASSERT(pdb.find("HETATM 2 NA UNL 1 0.002 8.956 1.393 0.10") != string::npos);
OB_ASSERT(pdb.find("HETATM 17 O UNL 8 1.954 8.956 3.035 1.00") != string::npos);
}
void testSpaceGroupClean()
{
// See https://github.com/openbabel/openbabel/pull/254
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test02.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
OB_ASSERT( pSG != NULL );
// Check also for errors and warnings
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("error") == string::npos);
OB_ASSERT( summary.find("warning") == string::npos);
OB_ASSERT( pSG->GetId() == 166 );
string pdb = conv.WriteString(&mol);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("H -3 m") != string::npos);
}
void testIsomorphism1()
{
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
conv.ReadString(&mol, "CC1CCC(C)CC1");
OBQuery *query = CompileMoleculeQuery(&mol);
OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
OBIsomorphismMapper::Mappings maps;
mapper->MapAll(&mol, maps);
OB_ASSERT( maps.size() == 4 );
delete query;
delete mapper;
query = CompileSmilesQuery("C1(C)CCC(C)CC1");
mapper = OBIsomorphismMapper::GetInstance(query);
OBIsomorphismMapper::Mapping map;
mapper->MapFirst(&mol, map);
OB_ASSERT( map.size() == 8 );
mapper->MapUnique(&mol, maps);
OB_ASSERT( maps.size() == 1 );
mapper->MapAll(&mol, maps);
OB_ASSERT( maps.size() == 4 );
delete query;
delete mapper;
}
void LinMorphExtension::loadFile(QString file)
{
qDebug("LinMorphExtension::loadFile()");
if (file.isEmpty())
return;
if (!m_secondMolecule)
m_secondMolecule = new Molecule;
OBConversion conv;
OBFormat *inFormat = OBConversion::FormatFromExt(( file.toAscii() ).data() );
if ( !inFormat || !conv.SetInFormat( inFormat ) ) {
QMessageBox::warning( NULL, tr( "Avogadro" ),
tr( "Cannot read file format of file %1." )
.arg( file ) );
return;
}
if (!conv.ReadFile(m_secondMolecule, file.toStdString())) {
QMessageBox::warning( NULL, tr( "Avogadro" ),
tr( "Read mol file %1 failed." )
.arg( file ) );
return;
}
qDebug("LinMorphExtension::loadFile complete");
computeConformers(m_secondMolecule);
m_linMorphDialog->setFrame(1);
m_timeLine->setFrameRange(1, m_frameCount);
setDuration(m_linMorphDialog->fps());
}
bool MakeQueriesFromMolInFile(vector<OBQuery*>& queries, const std::string& filename, int* pnAtoms, bool noH)
{
OBMol patternMol;
patternMol.SetIsPatternStructure();
OBConversion patternConv;
OBFormat* pFormat;
//Need to distinguish between filename and SMARTS. Not infallable...
if( filename.empty() ||
filename.find('.')==string::npos ||
!(pFormat = patternConv.FormatFromExt(filename.c_str())) ||
!patternConv.SetInFormat(pFormat) ||
!patternConv.ReadFile(&patternMol, filename) ||
patternMol.NumAtoms()==0)
return false;
if(noH)
patternMol.DeleteHydrogens();
do
{
*pnAtoms = patternMol.NumHvyAtoms();
queries.push_back(CompileMoleculeQuery(&patternMol));
}while(patternConv.Read(&patternMol));
return true;
}
// Helper function to read molecule from file
shared_ptr<OBMol> GetMol(const std::string &filename)
{
// Create the OBMol object.
shared_ptr<OBMol> mol(new OBMol);
// Create the OBConversion object.
OBConversion conv;
OBFormat *format = conv.FormatFromExt(filename.c_str());
if (!format || !conv.SetInFormat(format)) {
std::cout << "Could not find input format for file " << filename << std::endl;
return mol;
}
// Open the file.
std::ifstream ifs(filename.c_str());
if (!ifs) {
std::cout << "Could not open " << filename << " for reading." << std::endl;
return mol;
}
// Read the molecule.
if (!conv.Read(mol.get(), &ifs)) {
std::cout << "Could not read molecule from file " << filename << std::endl;
return mol;
}
return mol;
}
void testTetrahedralStereo1()
{
cout << "testTetrahedralStereo1()" << endl;
// read a smiles string
OBMol mol;
OBConversion conv;
OB_REQUIRE( conv.SetInFormat("smi") );
cout << "smiles: C[C@H](O)N" << endl;
OB_REQUIRE( conv.ReadString(&mol, "C[C@H](O)N") );
// get the stereo data
OB_REQUIRE( mol.HasData(OBGenericDataType::StereoData) );
std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);
OB_REQUIRE( stereoData.size() == 1 );
// convert to tetrahedral data
OB_REQUIRE( ((OBStereoBase*)stereoData[0])->GetType() == OBStereo::Tetrahedral );
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(stereoData[0]);
OB_REQUIRE( ts );
// print the configuration
cout << *ts << endl;
// construct a valid configuration here
//
// C[C@H](O)N
// 0 1 2 3 4 <- ids
//
OBTetrahedralStereo::Config cfg(1, 0, OBStereo::MakeRefs(4, 3, 2), OBStereo::Clockwise);
// compare stereochemistry
OB_REQUIRE( ts->GetConfig() == cfg );
cout << endl;
}
void InputFileExtension::readOutputFile(const QString filename)
{
QApplication::setOverrideCursor(Qt::WaitCursor);
OBConversion conv;
OBFormat *inFormat = conv.FormatFromExt( filename.toAscii() );
if ( !inFormat || !conv.SetInFormat( inFormat ) ) {
QApplication::restoreOverrideCursor();
QMessageBox::warning(m_widget, tr("Avogadro"),
tr("Cannot read file format of file %1.").arg(filename));
return;
}
// TODO: Switch to MoleculeFile
ifstream ifs;
ifs.open(QFile::encodeName(filename));
if (!ifs) { // shouldn't happen, already checked file above
QApplication::restoreOverrideCursor();
QMessageBox::warning(m_widget, tr("Avogadro"),
tr("Cannot read file %1.").arg( filename ) );
return;
}
OBMol *obmol = new OBMol;
if (conv.Read(obmol, &ifs)) {
Molecule *mol = new Molecule;
mol->setOBMol(obmol);
mol->setFileName(filename);
emit moleculeChanged(mol, Extension::DeleteOld);
m_molecule = mol;
}
QApplication::restoreOverrideCursor();
}
void ColoredMol::color()
{
OBConversion conv;
std::string ext = boost::filesystem::extension(ligName);
if(ext.compare(".pdb") == 0)
{
conv.SetInFormat("PDB");
}
else if(ext.compare(".pdbqt") == 0)
{
conv.SetInFormat("PDBQT");
}
else
{
std::cout << "File extension not supported: " << ligName << '\n';
std::cout << "Please use .pdb or .pdbqt for ligand\n";
exit(0);
}
conv.ReadFile(&ligMol, ligName);
ext = boost::filesystem::extension(recName);
if(ext.compare(".pdb") == 0)
{
conv.SetInFormat("PDB");
}
else
{
std::cout << "File extension not supported: " << recName << '\n';
std::cout << "Please use .pdb for receptor\n";
exit(0);
}
conv.ReadFile(&recMol, recName);
addHydrogens();
ligCenter();
removeResidues();
removeEachAtom();
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
char *FileIn = NULL;
if (argc != 2) {
cerr << " Usage: " << program_name << " <input file>\n";
exit(-1);
}
else {
FileIn = argv[1];
}
// Find Input filetype
OBConversion conv;
OBFormat *inFormat = conv.FormatFromExt(FileIn);
if (!inFormat || !conv.SetInFormat(inFormat)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBPointGroup pg;
for (c = 1;; ++c)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
// not needed by OBPointGroup, but useful for external programs
mol.Center();
mol.ToInertialFrame();
pg.Setup(&mol);
cout << "Point Group: " << pg.IdentifyPointGroup() << endl;
} // end for loop
return(1);
}
// Reading an InChI and then adding hydrogens messed up the structure
void test_Issue134_InChI_addH()
{
OBConversion conv;
conv.SetInFormat("inchi");
OBMol mol;
conv.ReadString(&mol, "InChI=1S/C2H7NO/c1-2(3)4/h2,4H,3H2,1H3/t2-/m0/s1");
OB_ASSERT(!mol.HasData(OBGenericDataType::VirtualBondData));
mol.AddHydrogens();
conv.SetOutFormat("smi");
std::string res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C[C@@H](N)O");
}
int main(int argc, char **argv)
{
OBFunctionFactory *factory = OBFunctionFactory::GetFactory("MMFF94");
OBFunction *function = factory->NewInstance();
if (!function) {
cout << "ERROR: could not find MMFF94 function" << endl;
return -1;
}
if (argc < 2) {
cout << "Usage: " << argv[0] << " <filename>" << endl;
return -1;
}
OBMol mol;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(argv[1]);
if (!format || !conv.SetInFormat(format)) {
cout << "ERROR: could not find format for file " << argv[1] << endl;
return -1;
}
std::ifstream ifs;
ifs.open(argv[1]);
conv.Read(&mol, &ifs);
ifs.close();
cout << "# atoms = " << mol.NumAtoms() << endl;
function->GetLogFile()->SetOutputStream(&std::cout);
function->GetLogFile()->SetLogLevel(OBLogFile::Low);
// read options file
if (argc == 3) {
std::ifstream cifs;
cifs.open(argv[2]);
std::stringstream options;
std::string line;
while (std::getline(cifs, line))
options << line << std::endl;
function->SetOptions(options.str());
}
function->Setup(mol);
OBMinimize minimize(function);
minimize.SteepestDescent(50);
}
void testAutomorphismMask() {
// read file: 3 6-rings
//
// /\ /\ /\
// | | | |
// \/ \/ \/
//
cout << "testAutomorphismMask" << endl;
OBMol mol;
OBConversion conv;
conv.SetInFormat("cml");
std::ifstream ifs(OBTestUtil::GetFilename("isomorphism1.cml").c_str());
OB_REQUIRE( ifs );
conv.Read(&mol, &ifs);
OBIsomorphismMapper::Mappings maps;
// First of all, how many automorphisms are there without any mask?
// This takes about 20 seconds, so you may want to comment this out while debugging
FindAutomorphisms(&mol, maps);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 4 );
// Now, let's remove the bridge (atomId 6) of the central ring.
//
// /\ /\ /\
// | | | |
// \/ \/
// both rings can be flipped around exocyclic bond, the whole molecule can be mirrored
// horizontally, this results in 2 x 2 x 2 = 8 automorphisms
OBBitVec mask;
mask.SetRangeOn(1, mol.NumAtoms());
mask.SetBitOff(6+1);
FindAutomorphisms(&mol, maps, mask);
cout << maps.size() << endl;
for (unsigned int i = 0; i < maps.size(); ++i) {
OBIsomorphismMapper::Mapping::const_iterator j;
for (j = maps[i].begin(); j != maps[i].end(); ++j)
cout << j->second << " ";
cout << endl;
}
OB_ASSERT( maps.size() == 8 );
// Verify that atom Id 6 does not occur anywhere in the mappings
OBIsomorphismMapper::Mappings::const_iterator a;
OBIsomorphismMapper::Mapping::const_iterator b;
for (a = maps.begin(); a != maps.end(); ++a)
for (b = a->begin(); b!= a->end(); ++b) {
OB_ASSERT( b->first != 6 );
OB_ASSERT( b->second != 6 );
}
}
void testCIFMolecules()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("smi"); // check for disconnected fragments
conv.ReadFile(&mol, GetFilename("1519159.cif"));
string smi = conv.WriteString(&mol);
// never, never disconnected fragments from a molecule
OB_ASSERT(smi.find(".") == string::npos);
}
void testAutomorphismPreMapping()
{
cout << "testAutomorphismPreMapping" << endl;
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
conv.ReadString(&mol, "c1(C)c(C)c(C)c(C)c(C)c1");
Automorphisms aut;
FindAutomorphisms((OBMol*)&mol, aut);
cout << aut.size() << endl;
OB_ASSERT( aut.size() == 2 );
}
void testIsomorphismMask()
{
// read file: 3 6-rings
//
// /\ /\ /\
// | | | |
// \/ \/ \/
//
OBMol mol;
OBConversion conv;
conv.SetInFormat("cml");
std::ifstream ifs(OBTestUtil::GetFilename("isomorphism1.cml").c_str());
OB_REQUIRE( ifs );
conv.Read(&mol, &ifs);
OBQuery *query = CompileSmilesQuery("C1CCCCC1");
OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
// no mask
OBIsomorphismMapper::Mappings maps;
mapper->MapUnique(&mol, maps);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 3 );
// mask first ring
OBBitVec mask;
for (int i = 0; i < 6; ++i)
mask.SetBitOn(i+1);
mapper->MapUnique(&mol, maps, mask);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 1 );
// mask second ring also
for (int i = 6; i < 10; ++i)
mask.SetBitOn(i+1);
mapper->MapUnique(&mol, maps, mask);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 2 );
// just mask last ring (atomIds 7-8, 10-13)
mask.Clear();
for (int i = 10; i < 14; ++i)
mask.SetBitOn(i+1);
mask.SetBitOn(7 + 1); mask.SetBitOn(8 + 1);
mapper->MapUnique(&mol, maps, mask);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 1 ); // Should be same result as masking just the first ring
delete query;
delete mapper;
}
// A segfault was occuring when a Universal SMILES was output after an InChIfied SMILES.
// This was due to short-circuit caching of InChIs on reading. The fix was to limit
// the situations when the cached value was used, but also to delete the cached value
// in this particular instance.
void test_Issue135_UniversalSmiles()
{
// Test writing U smiles after I smiles
OBConversion conv;
conv.SetInFormat("smi");
OBMol mol;
conv.ReadString(&mol, "C(=O)([O-])C(=O)O");
conv.SetOutFormat("smi");
conv.SetOptions("I", OBConversion::OUTOPTIONS);
std::string res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C(=O)(C(=O)O)[O-]");
conv.SetOptions("U", OBConversion::OUTOPTIONS);
res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C(=O)(C(=O)[O-])O");
}
void testPdbOutHexagonalAlternativeOrigin2()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test06.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("H -3 m") != string::npos);
}
void testPdbRemSpacesHMName()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test07.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("I41/amd:2") != string::npos);
}
// Delete hydrogens should not remove charged or isotopic hydrogens or [H][H] or [Cu][H][Cu]
// or hydrogens with assigned atom classes
void test_Issue178_DeleteHydrogens()
{
OBConversion conv;
conv.SetInFormat("smi");
OBMol mol;
// Test DeleteHydrogens() and DeleteNonPolarHydrogens()
static const char *smi[] = { "C[H]", "[H][H]", "C[1H]", "C[H]C", "C[H+]" };
int numHs[] = { 0, 2, 1, 1, 1 };
for (int i = 0; i < 5; ++i) {
for (int j = 0; j < 2; ++j) {
conv.ReadString(&mol, smi[i]);
if (j == 0)
mol.DeleteHydrogens();
else
mol.DeleteNonPolarHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, numHs[i]);
}
}
// Test DeletePolarHydrogens()
static const char *smiB[] = { "N[H]", "[H][H]", "N[1H]", "N[H]C", "N[H+]" };
int numHsB[] = { 0, 2, 1, 1, 1 };
for (int i = 0; i < 5; ++i) {
conv.ReadString(&mol, smiB[i]);
mol.DeletePolarHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, numHsB[i]);
}
// Test atom class
// Currently, the SMILES parser does not retain atom classes for hydrogens on reading so...
conv.ReadString(&mol, "C[H]");
OBAtomClassData *ac = new OBAtomClassData;
ac->Add(2, 99); // Assign the hydrogen (atom 2) a class of 99
mol.SetData(ac);
mol.DeleteHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, 1);
}
void testAlternativeOrigin()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.ReadFile(&mol, GetFilename("test04.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("warning") == string::npos);
OB_ASSERT( pSG != NULL );
OB_ASSERT( pSG->GetOriginAlternative() == 1);
}
int main(int argc, char **argv)
{
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
std::ifstream ifs(GetFilename("canonstable.can").c_str());
OB_REQUIRE( ifs );
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
conv.SetOutFormat("can");
std::string line;
while (std::getline(ifs, line)) {
OB_REQUIRE( conv.ReadString(&mol, line.c_str()) );
std::vector<OBAtom*> atoms;
FOR_ATOMS_OF_MOL(atom, mol)
atoms.push_back(&*atom);
for (int i = 0; i < 5; ++i) {
// shuffle the atoms
std::random_shuffle(atoms.begin(), atoms.end());
mol.RenumberAtoms(atoms);
// get can smiles
mol.SetTitle("");
std::string cansmi = conv.WriteString(&mol, true);
// comapare with ref
if (cansmi != line) {
cout << "ref = " << line << endl;
cout << "can = " << cansmi << endl;
OB_ASSERT( cansmi == line );
}
}
}
return 0;
}
void testPdbOutAlternativeOrigin()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test04.cif"));
string pdb = conv.WriteString(&mol);
// ending space is needed to check that there is no origin set
OB_ASSERT(pdb.find("P 4/n b m ") != string::npos);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("P 4/n b m:1") != string::npos);
}
char *serializeMolecule(const char *molecule) {
string instring(molecule);
string outstring;
istringstream inStream(instring);
LibHandler ob_lib;
if (!ob_lib.isLoaded()) {
return NULL;
}
OBMol mol;
OBConversion conv;
conv.SetInFormat(MOLECULE_TYPE);
conv.Read(&mol,&inStream);
return serializeOBMol(mol);
}
int main(int argc, char **argv)
{
if (argc < 2) {
std::cerr << "Usage: " << argv[0] << " filename" << std::endl;
return -1;
}
// read a molecule
OBConversion conv;
OBFormat *format = conv.FormatFromExt(argv[1]);
conv.SetInFormat(format);
std::string filename(argv[1]);
std::ifstream ifs;
ifs.open(filename.c_str());
if (!ifs) {
std::cerr << "Could not open " << filename << std::endl;
return -1;
}
CairoPainter *painter = new CairoPainter;
OBDepict depictor(painter);
string::size_type pos = filename.find_last_of(".");
if (pos != string::npos)
filename = filename.substr(0, pos);
OBMol mol;
unsigned int count = 1;
while (conv.Read(&mol, &ifs)) {
// depict the molecule
depictor.DrawMolecule(&mol);
depictor.AddAtomLabels(OBDepict::AtomSymmetryClass);
std::stringstream ss;
ss << filename << count << ".png";
painter->WriteImage(ss.str());
count++;
}
return 0;
}
void testDecayToP1()
{
// See https://github.com/openbabel/openbabel/pull/261
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.ReadFile(&mol, GetFilename("test03.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
OB_ASSERT( pSG != NULL );
// Check also for errors and warnings
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("2 warnings") != string::npos);
OB_ASSERT( pSG->GetId() == 1 );
}
void testIsomorphism4()
{
cout << "testIsomorphism4" << endl;
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
conv.ReadString(&mol, "C12C(C2)C1");
OBQuery *query = CompileSmilesQuery("C1CC1");
OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
OBIsomorphismMapper::Mappings maps;
mapper->MapUnique(&mol, maps);
cout << maps.size() << endl;
OB_ASSERT( maps.size() == 2 );
delete query;
delete mapper;
}
int main()
{
// Create an OBConversion object.
OBConversion conv;
// Set the input format.
if (!conv.SetInFormat("smi")) {
// Handle error.
return 1;
}
// Create the OBMol object.
OBMol mol;
// Read the smiles string.
if (conv.ReadString(&mol, "CCCC")) {
// Handle error.
return 1;
}
// ...Use OBMol object...
}
bool verifyLSSR(const std::string &filename, const LSSR &ref)
{
cout << "Verify LSSR: " << filename << endl;
std::string file = OBTestUtil::GetFilename(filename);
// read a smiles string
OBMol mol;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(file.c_str());
OB_REQUIRE( format );
OB_REQUIRE( conv.SetInFormat(format) );
std::ifstream ifs;
ifs.open(file.c_str());
OB_REQUIRE( ifs );
OB_REQUIRE( conv.Read(&mol, &ifs) );
std::vector<int> ringSizeCount(20, 0);
std::vector<OBRing*> lssr = mol.GetLSSR();
for (unsigned int i = 0; i < lssr.size(); ++i) {
ringSizeCount[lssr[i]->_path.size()]++;
}
/*
cout << "ringSize: ringCount" << endl;
cout << "3: " << ringSizeCount[3] << endl;
cout << "4: " << ringSizeCount[4] << endl;
cout << "5: " << ringSizeCount[5] << endl;
cout << "6: " << ringSizeCount[6] << endl;
*/
bool fail = false;
for (unsigned int i = 0; i < ref.size_count.size(); ++i) {
const LSSR::Size_Count &size_count = ref.size_count[i];
OB_ASSERT( ringSizeCount[size_count.ringSize] == size_count.ringCount );
}
return true;
}