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);
}
}
extern "C" char *
ob_strip_salts (char *smiles, int neutralize_residue)
{
OBAtom atom;
OBMol mol, largestFragment;
OBConversion conv;
string tmpStr (smiles);
string outstring;
istringstream molstream1 (tmpStr);
ostringstream molstream2;
vector<OBMol> fragments;
vector <OBMol>::const_iterator i;
char *tmpMolfile;
int max = 0;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream1);
fragments = mol.Separate();
for( i = fragments.begin(); i != fragments.end(); i++ ) {
if (i->NumAtoms() > max) {
max=i->NumAtoms();
largestFragment = *i;
}
}
if(neutralize_residue != 0) {
largestFragment.ConvertDativeBonds();
FOR_ATOMS_OF_MOL(atom, largestFragment) {
atom->SetFormalCharge(0);
}
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 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());
}
void DoOption(const char* p, OBConversion& Conv,
OBConversion::Option_type typ, int& arg, int argc, char *argv[])
{
while(p && *p) //can have multiple single char options
{
char ch[2]="?";
*ch = *p++;
const char* txt=NULL;
//Get the option text if needed
int nParams = Conv.GetOptionParams(ch, typ);
if(nParams)
{
if(*p)
{
txt = p; //use text immediately following the option letter
p=NULL; //no more single char options
}
else if(arg<argc-1)
{
txt = argv[++arg]; //use text from next arg
if(*txt=='-')
{
//...unless it is another option
cerr << "Option -" << ch << " takes a parameter" << endl;
exit(0);
}
}
}
Conv.AddOption(ch, typ, txt);
}
}
// 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;
}
int main() {
OBAtom a, b, c;
a.SetAtomicNum(8);
b.SetAtomicNum(6);
c.SetAtomicNum(8);
OBMol mol;
mol.AddAtom(a);
mol.AddAtom(b);
mol.AddAtom(c);
mol.AddBond(1,2,2);
mol.AddBond(2,3,2);
OBConversion conv;
conv.SetOutFormat("SMI");
cout << conv.WriteString(&mol,1) << endl;
OBSmartsPattern sp;
sp.Init ("C~*");
sp.Match (mol,false);
cout << sp.NumMatches() << endl;
cout << sp.GetUMapList().size() << endl;
return EXIT_SUCCESS;
}
bool OpExtraOut::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
/*
OptionText contains an output filename with a format extension.
Make an OBConversion object with this as output destination.
Make a copy the current OBConversion and replace the output format by
an instance of ExtraFormat. This then does all the subsequent work.
*/
if(!pConv || !OptionText || *OptionText=='\0')
return true; //silent no-op. false would prevent the main output
if(pConv->IsFirstInput())
{
OBConversion* pExtraConv = new OBConversion(*pConv); //copy ensures OBConversion::Index>-1
std::ofstream* ofs;
if( (ofs = new std::ofstream(OptionText)) ) // extra parens to indicate truth value
pExtraConv->SetOutStream(ofs);
if(!ofs || !pExtraConv->SetOutFormat(OBConversion::FormatFromExt(OptionText)))
{
obErrorLog.ThrowError(__FUNCTION__, "Error setting up extra output file", obError);
return true;
}
OBConversion* pOrigConv = new OBConversion(*pConv);
//Make an instance of ExtraFormat and divert the output to it. It will delete itself.
pConv->SetOutFormat(new ExtraFormat(pOrigConv, pExtraConv));
}
return true;
}
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;
}
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);
}
extern "C" char *
ob_add_hydrogens (char *smiles, int polaronly, int correct4PH)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
string outstring;
istringstream molstream1 (tmpStr);
ostringstream molstream2;
char *tmpMolfile;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream1);
mol.AddHydrogens (polaronly != 0, correct4PH != 0);
conv.Write (&mol, &molstream2);
outstring = molstream2.str ();
// remove the trailling $$$$\n from the SDFile
if (outstring.find ("$$$$\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 5);
}
else if (outstring.find ("$$$$\r\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 6);
}
tmpMolfile = strdup (outstring.c_str ());
return (tmpMolfile);
}
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;
}
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");
}
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 );
}
}
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 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;
}
extern "C" unsigned int
ob_is_nostruct (char *molfile)
{
OBMol mol;
OBConversion conv;
string tmpStr (molfile);
istringstream molstream (tmpStr);
conv.SetInAndOutFormats ("MDL", "MDL");
conv.Read (&mol, &molstream);
return (mol.Empty ())? 1 : 0;
}
int main(int argc, char **argv)
{
if (argc < 2) {
std::cout << "Usage: " << argv[0] << " <filename>" << std::endl;
return 1;
}
// Read the file
shared_ptr<OBMol> mol = GetMol(argv[1]);
// Create the OBConformerSearch object
OBConformerSearch cs;
// Setup
std::cout << "Setting up conformer searching..." << std::endl
<< " conformers: 30" << std::endl
<< " children: 5" << std::endl
<< " mutability: 5" << std::endl
<< " convergence: 25" << std::endl;
cs.Setup(*mol.get(),
30, // numConformers
5, // numChildren
5, // mutability
25); // convergence
// Perform searching
cs.Search();
// Print the rotor keys
RotorKeys keys = cs.GetRotorKeys();
for (RotorKeys::iterator key = keys.begin(); key != keys.end(); ++key) {
for (unsigned int i = 1; i < key->size(); ++i)
std::cout << key->at(i) << " ";
std::cout << std::endl;
}
// Get the conformers
cs.GetConformers(*mol.get());
std::cout << mol->NumConformers() << std::endl;
OBConversion conv;
conv.SetOutFormat("sdf");
for (unsigned int c = 0; c < mol->NumConformers(); ++c) {
mol->SetConformer(c);
conv.Write(mol.get(), &std::cerr);
}
}
void CheckValidDipeptide(OBConversion &conv,
const string &test,
unsigned int testCount)
{
OBMol mol;
OBResidue *res;
ostringstream os;
mol.Clear();
conv.ReadString(&mol, test);
chainsparser.PerceiveChains(mol);
if (mol.NumResidues() != 2) {
os << "not ok " << testCount << " # expected 2 residues, but found "
<< mol.NumResidues() << '\n';
os << "# ";
FOR_RESIDUES_OF_MOL(res, mol)
os << res->GetName() << " ";
os << endl;
BOOST_CHECK_MESSAGE( 0, os.str().c_str() );
} else {
res = mol.GetResidue(0);
BOOST_CHECK_MESSAGE( res, "Get first AA from dipeptide" );
res = mol.GetResidue(1);
BOOST_CHECK_MESSAGE( res, "Get second AA from dipeptide" );
}
}
// 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);
}
extern "C" char *
ob_delete_hydrogens (char *smiles, int nonpolaronly)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
string outstring;
istringstream molstream1 (tmpStr);
ostringstream molstream2;
char *tmpMolfile;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream1);
if(mol.NumHvyAtoms () > 0) {
if (nonpolaronly != 0)
{
mol.DeleteNonPolarHydrogens ();
}
else
{
mol.DeleteHydrogens ();
}
} else {
cout << "Warning: Cannot remove hydrogens. Resulting molecule would be empty!" << endl;
}
conv.Write (&mol, &molstream2);
outstring = molstream2.str ();
// remove the trailling $$$$\n from the SDFile
if (outstring.find ("$$$$\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 5);
}
else if (outstring.find ("$$$$\r\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 6);
}
tmpMolfile = strdup (outstring.c_str ());
return (tmpMolfile);
}
/*****************************************************************
* This function Copyright (c) 2004
* by Bayer Business Services GmbH
*****************************************************************/
extern "C" double
ob_molweight (char *smiles)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
istringstream molstream (tmpStr);
double molweight = 0.0;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream);
molweight = mol.GetMolWt ();
return (molweight);
}
extern "C" int
ob_total_charge (char *smiles)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
istringstream molstream (tmpStr);
int totalcharge = 0;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream);
totalcharge = mol.GetTotalCharge ();
return (totalcharge);
}
extern "C" unsigned int
ob_num_rotatable_bonds (char *smiles)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
istringstream molstream (tmpStr);
unsigned int numrotors = 0;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream);
numrotors = mol.NumRotors ();
return (numrotors);
}
extern "C" unsigned int
ob_num_heavy_atoms (char *smiles)
{
OBMol mol;
OBConversion conv;
string tmpStr (smiles);
istringstream molstream (tmpStr);
unsigned int numheavyatoms = 0;
conv.SetInAndOutFormats ("SMI", "SMI");
conv.Read (&mol, &molstream);
numheavyatoms = mol.NumHvyAtoms ();
return (numheavyatoms);
}