//
// Validate a single molecule.
//
bool Validator::Validate(OpenBabel::OBMol& validationMol)
{
    std::vector<unsigned int> validationFP;
    bool returnval = false;

    if (g_debug_output)
    {
        std::cerr << "Atoms: " << validationMol.NumAtoms() << std::endl;
        std::cerr << "Bonds: " << validationMol.NumBonds() << std::endl;
    }

    // Create the fingerprint for the validation molecule
    OpenBabel::OBFingerprint* fpType = OpenBabel::OBFingerprint::FindFingerprint("");

    // Acquire the fingerprint of the validation molecule so we can use it for
    // Tanimoto comparison.
    fpType->GetFingerprint(&validationMol, validationFP);

    if (g_debug_output)
    {
        std::cerr << "Validation: " << std::endl;
        foreach_uints(u_it, validationFP)
        {
            std::cerr << *u_it << "|";
        }
        std::cerr << std::endl;
    }
Esempio n. 2
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int main(int argc,char **argv)
{
   // Create a test molecule
   OpenBabel::OBMol mol;
   OpenBabel::OBAtom* a[5];
   a[0] = mol.NewAtom(); a[0]->SetAtomicNum(6);  a[0]->SetVector(-0.013,  1.086,  0.008);
   a[1] = mol.NewAtom(); a[1]->SetAtomicNum(1);  a[1]->SetVector( 0.002, -0.004,  0.002);
   a[2] = mol.NewAtom(); a[2]->SetAtomicNum(9);  a[2]->SetVector( 1.300,  1.570, -0.002);
   a[3] = mol.NewAtom(); a[3]->SetAtomicNum(35); a[3]->SetVector(-0.964,  1.737, -1.585);
   a[4] = mol.NewAtom(); a[4]->SetAtomicNum(17); a[4]->SetVector(-0.857,  1.667,  1.491);
   OpenBabel::OBBond* b;
   for (int i(1); i < 5; ++i)
   {
      b = mol.NewBond();
      b->SetBegin(a[0]); b->SetEnd(a[i]); b->SetBondOrder(1);
   }
   
   // Run the tests
   test01(&mol);
   test02(&mol);
   test03(&mol);
   test04(&mol);
   test05(&mol);
   test06(&mol);
   test07(&mol);
   test08(&mol);
   test09(&mol);
   
   // End
   return 0;
}
Esempio n. 3
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extern "C" int write_output_(char *out_filename, double *A, int *n)
{
  std::ofstream ofs(out_filename);
  OpenBabel::OBConversion ob(NULL, &ofs);
  OpenBabel::OBAtom atom;
  OpenBabel::OBMol mol;
  int i;

  ob.SetOutFormat("CML");

  /* Atom is Iridium */
  atom.SetAtomicNum(77);

  for (i = 0; i < *n; i++)
  {
    atom.SetVector(A[i*3], A[i*3+1], A[i*3+2]);
    mol.AddAtom(atom);
  }

  //for (i=0; i < *n; i++)
  //{
    //for (int j=i; j < *n; j++)
    //{
      //mol.AddBond(i+1, j+1, 0);
    //}
  //}

  ob.Write(&mol);
  ob.CloseOutFile();
}
Esempio n. 4
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  // Helper function -- handle SMARTS selections
  // Called by performAction()
  void SelectExtension::selectSMARTS(GLWidget *widget)
  {
    bool ok;
    QString pattern = QInputDialog::getText(qobject_cast<QWidget*>(parent()),
        tr("SMARTS Selection"),
        tr("SMARTS pattern to select"),
        QLineEdit::Normal,
        "", &ok);
    if (ok && !pattern.isEmpty()) {
      OBSmartsPattern smarts;
      smarts.Init(pattern.toStdString());
      OpenBabel::OBMol obmol = m_molecule->OBMol();
      smarts.Match(obmol);

      // if we have matches, select them
      if(smarts.NumMatches() != 0) {
        QList<Primitive *> matchedAtoms;

        vector< vector <int> > mapList = smarts.GetUMapList();
        vector< vector <int> >::iterator i; // a set of matching atoms
        vector<int>::iterator j; // atom ids in each match
        for (i = mapList.begin(); i != mapList.end(); ++i) {
          for (j = i->begin(); j != i->end(); ++j) {
            matchedAtoms.append(m_molecule->atom(obmol.GetAtom(*j)->GetIdx()-1));
          }
        }

        widget->clearSelected();
        widget->setSelected(matchedAtoms, true);
        widget->update();
      } // end matches
    }
    return;
  }
Esempio n. 5
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int spectrophoretest(int argc, char* argv[])
{
  int defaultchoice = 1;
  
  int choice = defaultchoice;

  if (argc > 1) {
    if(sscanf(argv[1], "%d", &choice) != 1) {
      printf("Couldn't parse that input as a number\n");
      return -1;
    }
  }

   // Create a test molecule
   OpenBabel::OBMol mol;
   OpenBabel::OBAtom* a[5];
   a[0] = mol.NewAtom(); a[0]->SetAtomicNum(6);  a[0]->SetVector(-0.013,  1.086,  0.008);
   a[1] = mol.NewAtom(); a[1]->SetAtomicNum(1);  a[1]->SetVector( 0.002, -0.004,  0.002);
   a[2] = mol.NewAtom(); a[2]->SetAtomicNum(9);  a[2]->SetVector( 1.300,  1.570, -0.002);
   a[3] = mol.NewAtom(); a[3]->SetAtomicNum(35); a[3]->SetVector(-0.964,  1.737, -1.585);
   a[4] = mol.NewAtom(); a[4]->SetAtomicNum(17); a[4]->SetVector(-0.857,  1.667,  1.491);
   OpenBabel::OBBond* b;
   for (int i(1); i < 5; ++i)
   {
      b = mol.NewBond();
      b->SetBegin(a[0]); b->SetEnd(a[i]); b->SetBondOrder(1);
   }
   
  switch(choice) {
  case 1:
    test01(&mol);
    test02(&mol);
    break;
  case 2:
    test03(&mol);
    test04(&mol);
    break;
  case 3:
    test05(&mol);
    test06(&mol);
    break;
  case 4:
    test07(&mol);
    test08(&mol);
    break;
  case 5:
    test09(&mol);
    break;
  default:
    std::cout << "Test number " << choice << " does not exist!\n";
    return -1;
  }

  return 0;
}
Esempio n. 6
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int main(int argc, char *argv[])
{
  if (argc != 2) {
    // Exit - we expect the name of an input file and output to the standard out
    std::cerr << "Error: expect one argument - path of input file." << std::endl;
    return 1;
  }

  OpenBabel::OBFormat *inFormat = NULL;
  OpenBabel::OBConversion conv(&std::cin, &std::cout);
  OpenBabel::OBMol mol;
  inFormat = conv.FormatFromExt(argv[1]);
  conv.SetInFormat(inFormat);
  std::ifstream in;
  in.open(argv[1]);
  conv.Read(&mol, &in);
  in.close();

  // Write out a few parameters.
  std::cout << "[Formula]\n" << mol.GetSpacedFormula() << std::endl;
  std::cout << "[Molecular weight]\n" << mol.GetMolWt() << std::endl;

  // Write out our file formats.
  std::cout << "[smiles]\n";
  conv.SetOutFormat("smi");
  conv.Write(&mol);
  std::cout << "[canonical smiles]\n";
  conv.SetOutFormat("can");
  conv.Write(&mol);
  std::cout << "[inchi]\n";
  conv.SetOutFormat("inchi");
  conv.Write(&mol);
  std::cout << "[inchikey]\n";
  conv.SetOptions("K", conv.OUTOPTIONS);
  conv.Write(&mol);
  std::cout << "[XYZ]\n";
  conv.SetOutFormat("xyz");
  conv.Write(&mol);
  std::cout << "[end]\n";
  std::cout << "[CML]\n";
  conv.SetOutFormat("cml");
  conv.Write(&mol);
  std::cout << "[end]\n";
  //std::cout << "[SVG]\n";
  //conv.SetOutFormat("svg");
  //conv.Write(&mol);
  //std::cout << "[end]\n";

  // Let them know we are finished, should be done after all output is complete.
  std::cout << "[complete]" << std::endl;

  return 0;
}
void ReadFileThread::detectConformers(unsigned int c,
                                      const OpenBabel::OBMol &first,
                                      const OpenBabel::OBMol &current)
{
  if (!c) {
    // this is the first molecule read
    m_moleculeFile->setConformerFile(true);
    addConformer(current);
    return;
  }

  if (!m_moleculeFile->isConformerFile())
    return;

  // as long as we are not sure if this really is a
  // conformer/trajectory file, add the conformers
  addConformer(current);

  // performance: check only certain molecule 1-10,20,50
  switch (c) {
  case 1:
  case 2:
  case 3:
  case 4:
  case 5:
  case 6:
  case 7:
  case 8:
  case 9:
  case 10:
  case 20:
  case 50:
    break;
  default:
    return;
  }

  if (first.NumAtoms() != current.NumAtoms()) {
    m_moleculeFile->setConformerFile(false);
    m_moleculeFile->m_conformers.clear();
    return;
  }

  for (unsigned int i = 0; i < first.NumAtoms(); ++i) {
    OpenBabel::OBAtom *firstAtom = first.GetAtom(i+1);
    OpenBabel::OBAtom *currentAtom = current.GetAtom(i+1);
    if (firstAtom->GetAtomicNum() != currentAtom->GetAtomicNum()) {
      m_moleculeFile->setConformerFile(false);
      m_moleculeFile->m_conformers.clear();
      return;
    }
  }
}
Esempio n. 8
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  void StereoCenterItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *widget)
  {
    Molecule *mol = molecule();
    
    painter->save();
    painter->setPen(Qt::green);

    if (!mol) {
      // not connected: default behaviour (draw connectable box)
      MolInputItem::paint(painter, option, widget);
      painter->restore();
      return;
    }

    const QList<Atom*> &atoms = mol->atoms();
    OpenBabel::OBMol *obmol = mol->OBMol();
    QPointF offset(-5.0, 5.0);

#ifdef OPENBABEL2_TRUNK
    // need to calculate symmetry first
    std::vector<unsigned int> symmetry_classes;
    OpenBabel::OBGraphSym graphsym(obmol);
    graphsym.GetSymmetry(symmetry_classes);

    //std::vector<unsigned long> atomIds = FindTetrahedralAtoms(obmol, symmetry_classes);
    std::vector<OpenBabel::StereogenicUnit> units = FindStereogenicUnits(obmol, symmetry_classes);
    
    for (unsigned int i = 0; i < units.size(); ++i) {
      if (units.at(i).type == OpenBabel::OBStereo::Tetrahedral) {
        OpenBabel::OBAtom *obatom = obmol->GetAtomById(units.at(i).id);
        painter->drawEllipse(mapFromItem(mol, atoms[obatom->GetIndex()]->pos()), 10, 10);
      } else 
      if (units.at(i).type == OpenBabel::OBStereo::CisTrans) {
        OpenBabel::OBBond *obbond = obmol->GetBondById(units.at(i).id);
        OpenBabel::OBAtom *obatom1 = obbond->GetBeginAtom();
        OpenBabel::OBAtom *obatom2 = obbond->GetEndAtom();
        painter->drawEllipse(mapFromItem(mol, atoms[obatom1->GetIndex()]->pos()), 10, 10);
        painter->drawEllipse(mapFromItem(mol, atoms[obatom2->GetIndex()]->pos()), 10, 10);
      } 
 
    }
#else
    using OpenBabel::OBMolAtomIter;
    FOR_ATOMS_OF_MOL(atom, obmol)
      if (atom->IsChiral())
        painter->drawEllipse(mapFromItem(mol, atoms[atom->GetIdx()-1]->pos()), 10, 10);
#endif

    // default behavious (draw the label())
    MolInputItem::paint(painter, option, widget);
    painter->restore();
  }
Esempio n. 9
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  bool CDSpectra::checkForData(Molecule * mol) {
    OpenBabel::OBMol obmol = mol->OBMol();
    OpenBabel::OBElectronicTransitionData *etd = static_cast<OpenBabel::OBElectronicTransitionData*>(obmol.GetData("ElectronicTransitionData"));

    if (!etd) return false;
    if ( etd->GetRotatoryStrengthsVelocity().size() == 0 &&
         etd->GetRotatoryStrengthsLength().size() == 0 ) return false;

    // OK, we have valid data, so store them for later
    std::vector<double> wavelengths = etd->GetWavelengths();
    std::vector<double> rotl = etd->GetRotatoryStrengthsLength();
    std::vector<double> rotv = etd->GetRotatoryStrengthsVelocity();

    ui.combo_rotatoryType->clear();
    if (rotl.size() != 0) ui.combo_rotatoryType->addItem("Length");
    if (rotv.size() != 0) ui.combo_rotatoryType->addItem("Velocity");

    // Store in member vars
    m_xList.clear();
    m_yList.clear();
    for (uint i = 0; i < wavelengths.size(); i++)
      m_xList.append(wavelengths.at(i));
    for (uint i = 0; i < rotl.size(); i++)
      m_yListLength->append(rotl.at(i));
    for (uint i = 0; i < rotv.size(); i++)
      m_yListVelocity->append(rotv.at(i));


    rotatoryTypeChanged(ui.combo_rotatoryType->currentText());

    return true;
  }
Esempio n. 10
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OpenBabel::OBMol
Schuffenhauer::Rule_1(OpenBabel::OBMol& oldMol)
{
   	if (oldMol.GetSSSR().size() <= _ringsToBeRetained)
	{
		return oldMol;
	}
   
   	OpenBabel::OBMol newMol(oldMol);
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	OpenBabel::OBBondIterator bi;
   	OpenBabel::OBAtom* atom;
   	OpenBabel::OBAtom* nbrAtom[2];
   	for (atom = newMol.BeginAtom(avi); atom; atom = newMol.NextAtom(avi))
   	{
      	if ((atom->MemberOfRingSize() == 3) &&
          	(atom->IsNitrogen() || atom->IsOxygen()) &&
          	(atom->MemberOfRingCount() == 1) &&
          	(atom->GetHvyValence() == 2))
      	{
         	nbrAtom[0] = atom->BeginNbrAtom(bi);
         	nbrAtom[1] = atom->NextNbrAtom(bi);
			if (nbrAtom[0] && nbrAtom[1])
			{
         		newMol.DeleteAtom(atom);
         		newMol.GetBond(nbrAtom[0], nbrAtom[1])->SetBondOrder(2);
			}
      	}
   	}
   	return newMol;
}
Esempio n. 11
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bool IRSpectra::checkForData(Molecule * mol) {
    OpenBabel::OBMol obmol = mol->OBMol();
    OpenBabel::OBVibrationData *vibrations = static_cast<OpenBabel::OBVibrationData*>(obmol.GetData(OpenBabel::OBGenericDataType::VibrationData));
    if (!vibrations) return false;

    // Setup signals/slots
    connect(this, SIGNAL(plotDataChanged()),
            m_dialog, SLOT(regenerateCalculatedSpectra()));
    connect(ui.cb_labelPeaks, SIGNAL(toggled(bool)),
            m_dialog, SLOT(regenerateCalculatedSpectra()));
    connect(ui.spin_scale, SIGNAL(valueChanged(double)),
            this, SLOT(setScale(double)));
    connect(ui.spin_FWHM, SIGNAL(valueChanged(double)),
            m_dialog, SLOT(regenerateCalculatedSpectra()));
    connect(ui.combo_yaxis, SIGNAL(currentIndexChanged(QString)),
            this, SLOT(updateYAxis(QString)));

    // OK, we have valid vibrations, so store them for later
    vector<double> wavenumbers = vibrations->GetFrequencies();
    vector<double> intensities = vibrations->GetIntensities();

    // Case where there are no intensities, set all intensities to an arbitrary value, i.e. 1.0
    if (wavenumbers.size() > 0 && intensities.size() == 0) {
        // Warn user
        QMessageBox::information(m_dialog, tr("No intensities"), tr("The vibration data in the molecule you have loaded does not have any intensity data. Intensities have been set to an arbitrary value for visualization."));
        for (uint i = 0; i < wavenumbers.size(); i++) {
            intensities.push_back(1.0);
        }
    }

    // Normalize intensities into transmittances
    double maxIntensity=0;
    for (unsigned int i = 0; i < intensities.size(); i++) {
        if (intensities.at(i) >= maxIntensity) {
            maxIntensity = intensities.at(i);
        }
    }

    vector<double> transmittances;

    for (unsigned int i = 0; i < intensities.size(); i++) {
        double t = intensities.at(i);
        t = t / maxIntensity; 	// Normalize
        t = 0.97 * t;		// Keeps the peaks from extending to the limits of the plot
        t = 1.0 - t; 		// Simulate transmittance
        t *= 100.0;		// Convert to percent
        transmittances.push_back(t);
    }

    // Store in member vars
    m_xList->clear();
    m_yList->clear();
    for (uint i = 0; i < wavenumbers.size(); i++) {
        m_xList->append(wavenumbers.at(i));
        m_yList->append(transmittances.at(i));
    }

    return true;
}
Esempio n. 12
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void Geometry::computeGasteigerCharges()
{
// This is returning zero charges for some reason
return;
    qDebug() << "Geometry::computeGasteigerCharges() not working correctly";
    OpenBabel::OBAtom* obAtom(0);
    OpenBabel::OBMol obMol;

    obMol.BeginModify();
    obMol.UnsetPartialChargesPerceived();
    for (int i = 0; i < m_atoms.size(); ++i) {
        obAtom = obMol.NewAtom();
        obAtom->SetAtomicNum(m_atoms[i]->atomicNumber());
        obAtom->SetVector(m_coordinates[i].x, m_coordinates[i].y, m_coordinates[i].z);
    }
    obMol.SetTotalCharge(m_charge);
    obMol.SetTotalSpinMultiplicity(m_multiplicity);
    obMol.EndModify();
    
    OpenBabel::OBMolAtomIter iter(&obMol);
    for (int i = 0; i < m_atoms.size(); ++i, ++iter) {
        int index(iter->GetIdx());
        qDebug() << "Setting Gasteiger Charge for" << index << "to" << iter->GetPartialCharge();
        GasteigerCharge& charge(m_atoms[i]->getProperty<GasteigerCharge>());
        charge.setValue(iter->GetPartialCharge());
    }
}
Esempio n. 13
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void
FilterCores::Calculate(OpenBabel::OBMol* mol)
{
   // Any rings?
   OpenBabel::OBAtom* atom;
   std::vector<OpenBabel::OBAtom*>::iterator i;
   bool rings(false);
   for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
   {
      if (atom->IsInRing())
      {
         rings = true;
         break;
      }
   }
   
   if (rings)
   {
      // Make workcopy of original mol
      OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
   
      // Iteratively remove all endstanding atoms until none are left
      OpenBabel::OBAtom* atom;
      std::vector<OpenBabel::OBAtom*>::iterator i;
      bool endstanding(true);
      while (endstanding && m.NumAtoms())
      {
         endstanding = false;
         for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
         {
            if (atom->GetValence() < 2)
            {
               if (m.DeleteAtom(atom))
               {
                  endstanding = true;
                  break;
               }
            }
         }
      }

      if (m.NumAtoms()) _result = 1;
      else _result = 0;
   }
   else
   {
      _result = 0;
   }
   
   if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
   {
      _passed = false;
   }
   else
   {
      _passed = true;
   }  
}
Esempio n. 14
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  bool DOSSpectra::checkForData(Molecule * mol)
  {
    OpenBabel::OBMol obmol = mol->OBMol();
    //OpenBabel::OBDOSData *dos = static_cast<OpenBabel::OBDOSData*>(obmol.GetData(OpenBabel::OBGenericDataType::DOSData));
    OpenBabel::OBDOSData *dos = static_cast<OpenBabel::OBDOSData*>(obmol.GetData("DOSData"));
    if (!dos) return false;

    // OK, we have valid DOS, so store them for later
    std::vector<double> energies = dos->GetEnergies();
    std::vector<double> densities= dos->GetDensities();
    if (m_intDOS) delete m_intDOS;
    m_intDOS = new std::vector<double> (dos->GetIntegration());

    if (energies.size() == 0 || energies.size() != densities.size())
      return false;

    // Store in member vars
    m_numAtoms = mol->numAtoms();
    m_fermi = dos->GetFermiEnergy();
    ui.label_fermi->setText(QString::number(m_fermi));
    m_xList.clear();
    m_yList.clear();
    bool generateInt = false;
    if (m_intDOS->size() == 0) generateInt = true;
    for (uint i = 0; i < energies.size(); i++){
      m_xList.append(energies.at(i));
      double d = densities.at(i);
      m_yList.append(d);
      if (generateInt) {
        if (i == 0)
          m_intDOS->push_back(d);
        else
          m_intDOS->push_back(m_intDOS->at(i-1) + d);
      }
    }

    setImportedData(m_xList,
                    QList<double>::fromVector(QVector<double>::fromStdVector(*m_intDOS)));

    return true;
  }
Esempio n. 15
0
  bool NMRSpectra::checkForData(Molecule * mol)
  {
    OpenBabel::OBMol obmol = mol->OBMol();
    qDeleteAll(*m_NMRdata);
    m_NMRdata->clear();
    // Test for "NMR Isotropic Shift" in first atom
    bool hasNMR = false;
    if (obmol.NumAtoms() > 0)
      if (obmol.GetFirstAtom()->HasData("NMR Isotropic Shift"))
        hasNMR = true;

    if (!hasNMR) return false;
    // Setup signals/slots
    connect(this, SIGNAL(plotDataChanged()),
            m_dialog, SLOT(regenerateCalculatedSpectra()));
    connect(ui.combo_type, SIGNAL(currentIndexChanged(QString)),
            this, SLOT(setAtom(QString)));
    connect(ui.spin_ref, SIGNAL(valueChanged(double)),
            this, SLOT(setReference(double)));
    connect(ui.push_resetAxes, SIGNAL(clicked()),
            this, SLOT(updatePlotAxes()));
    connect(ui.spin_FWHM, SIGNAL(valueChanged(double)),
            m_dialog, SLOT(regenerateCalculatedSpectra()));
    connect(ui.cb_labelPeaks, SIGNAL(toggled(bool)),
            m_dialog, SLOT(regenerateCalculatedSpectra()));

    // Extract data from obmol
    FOR_ATOMS_OF_MOL(atom,obmol) {
      QString symbol = QString(OpenBabel::etab.GetSymbol(atom->GetAtomicNum()));
      double shift   = QString(atom->GetData("NMR Isotropic Shift")->GetValue().c_str()).toFloat();
      QList<double> *list = new QList<double>;
      if (m_NMRdata->contains(symbol)) {
        list	= m_NMRdata->value(symbol);
      }
      else {
        // Dump symbol into NMR Type list
        ui.combo_type->addItem(symbol);
      }
      list->append(shift);
      m_NMRdata->insert(symbol, list);
    }
Esempio n. 16
0
int main(int argc,char **argv){

if(argc<2){
cout << "Usage: ProgrameName InputFileName";
return 1;
}

ifstream ifs(argv[1]);
if(!ifs){
cout << "Cannot open input file";
return 1;
}

OpenBabel::OBConversion conv(&ifs, &cout);
if(conv.SetInAndOutFormats("mol","sdf")){
  OpenBabel::OBMol mol;
  if(conv.Read(&mol)){
    cout << "Mol.wt: "<<mol.GetMolWt()<<endl;//works even with implicit hydrogen
    mol.AddHydrogens(false,false); //ensure that hydrogens are all explicit
    cout << "No. of atoms: " << mol.NumAtoms()<<endl;
    cout << "No. of hvy atoms: " << mol.NumHvyAtoms() << endl;
    cout << "No. of bonds: " << mol.NumBonds() << endl;
    double exactMass = 0.0;
    FOR_ATOMS_OF_MOL(a, mol){
      cout << "iterating..."<<endl;
      exactMass += a->GetExactMass();
    }
  void GAMESSUKInputDialog::setMolecule(Molecule *molecule)
  {
    // Disconnect the old molecule first...
    if (m_molecule)
      disconnect(m_molecule, 0, this, 0);

    m_molecule = molecule;

    // Set multiplicity to the OB value
    OpenBabel::OBMol obmol = m_molecule->OBMol();
    setMultiplicity(obmol.GetTotalSpinMultiplicity());

    // Update the preview text whenever primitives are changed
    connect(m_molecule, SIGNAL(atomRemoved(Atom *)),
            this, SLOT(updatePreviewText()));
    connect(m_molecule, SIGNAL(atomAdded(Atom *)),
            this, SLOT(updatePreviewText()));
    connect(m_molecule, SIGNAL(atomUpdated(Atom *)),
            this, SLOT(updatePreviewText()));
    // Add atom coordinates
    updatePreviewText();
  }
Esempio n. 18
0
unsigned int
Schuffenhauer::CalculateAcyclicBonds(OpenBabel::OBMol& mol)
{
   	unsigned int nbonds(0);
   	OpenBabel::OBAtom* nbratom[2];
   	OpenBabel::OBBond* bond;
   	std::vector<OpenBabel::OBBond*>::iterator bvi;
   	for (bond = mol.BeginBond(bvi); bond; bond = mol.NextBond(bvi))
   	{
      	nbratom[0] = bond->GetBeginAtom();
      	nbratom[1] = bond->GetEndAtom();
		if (nbratom[0] && nbratom[1])
		{
      		if (!bond->IsInRing() && 
				(nbratom[0]->GetValence() > 1) && 
				(nbratom[1]->GetValence() > 1))
      		{
         		++nbonds;
      		}
		}
   	}
   	return nbonds;
}
Esempio n. 19
0
  bool RamanSpectra::checkForData(Molecule * mol) {
    OpenBabel::OBMol obmol = mol->OBMol();
    OpenBabel::OBVibrationData *vibrations = static_cast<OpenBabel::OBVibrationData*>(obmol.GetData(OpenBabel::OBGenericDataType::VibrationData));
    if (!vibrations) return false;

    // OK, we have valid vibrations, so store them for later
    vector<double> wavenumbers = vibrations->GetFrequencies();
    vector<double> intensities = vibrations->GetRamanActivities();

    if (wavenumbers.size() == 0 || intensities.size() == 0)
      return false;

    /* Case where there are no intensities, set all intensities to an arbitrary value, i.e. 1.0
    if (wavenumbers.size() > 0 && intensities.size() == 0) {
      // Warn user
      //QMessageBox::information(m_dialog, tr("No intensities"), tr("The vibration data in the molecule you have loaded does not have any intensity data. Intensities have been set to an arbitrary value for visualization."));
      for (uint i = 0; i < wavenumbers.size(); i++) {
        intensities.push_back(1.0);
      }
    }*/

    // 
    double maxIntensity=0;
    for (unsigned int i = 0; i < intensities.size(); i++) {
      if (intensities.at(i) >= maxIntensity) {
        maxIntensity = intensities.at(i);
      }
    }

    /*vector<double> transmittances;*/

    for (unsigned int i = 0; i < intensities.size(); i++) {
      intensities[i] = intensities.at(i) / maxIntensity; 	// Normalize
    }

    // Store in member vars
    m_xList.clear();
    m_xList_orig.clear();
    m_yList.clear();
    m_yList_orig.clear();
    for (uint i = 0; i < wavenumbers.size(); i++){
      double w = wavenumbers.at(i);
      m_xList.append(w*scale(w));
      m_xList_orig.append(w);
      m_yList.append(intensities.at(i));
      m_yList_orig.append(intensities.at(i));
    }

    return true;
  }
Esempio n. 20
0
unsigned int
Schuffenhauer::CalculateHeteroAtoms(OpenBabel::OBMol& mol, OpenBabel::OBRing* ring, int a = 0)
{
   	unsigned int n(0);
   	OpenBabel::OBAtom* atom;
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	for (atom = mol.BeginAtom(avi); atom; atom = mol.NextAtom(avi))
   	{
      	if (ring->IsMember(atom) && (atom->GetAtomicNum() == a))
      	{
         	++n;
      	}
      	if (!a && ring->IsMember(atom))
      	{
         	if ((atom->GetAtomicNum() == 7) ||
				(atom->GetAtomicNum() == 8) ||
				(atom->GetAtomicNum() == 16))
         	{
            	++n;
         	}
      	}
   	}
   	return n;
}
Esempio n. 21
0
bool
Schuffenhauer::HasLinkerToHeteroAtom(OpenBabel::OBMol& mol, OpenBabel::OBRing* ring)
{
   	std::vector<OpenBabel::OBBond*>::iterator bvi;
   	OpenBabel::OBBond* bond;
   	OpenBabel::OBAtom* nbrAtom[2];
   	for (bond = mol.BeginBond(bvi); bond; bond = mol.NextBond(bvi))
   	{
      	nbrAtom[0] = bond->GetBeginAtom();
      	nbrAtom[1] = bond->GetEndAtom();
      	if
		(
			// Neighbours are real
			nbrAtom[0] &&
			nbrAtom[1] &&
			
			// Bond should be acyclic
			!bond->IsInRing() &&
			
			// Both atoms have to be ring atoms
			nbrAtom[0]->IsInRing() && 
			nbrAtom[1]->IsInRing() && 
			
			// At least one of the atoms should be hetero
			(nbrAtom[0]->IsHeteroatom() || nbrAtom[1]->IsHeteroatom()) &&
			
			// One of the atoms, but not both, should be part of this ring	
			((ring->IsMember(nbrAtom[0]) && !ring->IsMember(nbrAtom[1])) ||
			(ring->IsMember(nbrAtom[1]) && !ring->IsMember(nbrAtom[0])))
		)
		{
         	return true;
     	}
   	}
   	return false;
}
Esempio n. 22
0
List Factory::convert(Data::Geometry& geometry)
{
   List list;
   Atoms* atoms(new Atoms());
   Bonds* bonds(new Bonds());
   list.append(atoms);
   list.append(bonds);

   unsigned nAtoms(geometry.nAtoms());
   OpenBabel::OBMol obMol;
   obMol.BeginModify();
   AtomMap atomMap;
   
   for (unsigned i = 0; i < nAtoms; ++i) {
       unsigned Z(geometry.atomicNumber(i));
       qglviewer::Vec position(geometry.position(i));

       Atom* atom(new Atom(geometry.atomicNumber(i)));
       atom->setPosition(geometry.position(i));
       atoms->appendLayer(atom);

       OpenBabel::OBAtom* obAtom(obMol.NewAtom());
       obAtom->SetAtomicNum(Z);
       obAtom->SetVector(position.x, position.y, position.z);
       atomMap.insert(obAtom, atom);
   }

   obMol.SetTotalCharge(geometry.charge());
   obMol.SetTotalSpinMultiplicity(geometry.multiplicity());
   obMol.EndModify();
   obMol.ConnectTheDots();
   obMol.PerceiveBondOrders();

   for (OpenBabel::OBMolBondIter obBond(&obMol); obBond; ++obBond) {
       Atom* begin(atomMap.value(obBond->GetBeginAtom()));
       Atom* end(atomMap.value(obBond->GetEndAtom()));
       Bond* bond(new Bond(begin, end));
       bond->setOrder(obBond->GetBondOrder());
       bonds->appendLayer(bond);
   }

   return list;
}
Esempio n. 23
0
  bool UVSpectra::checkForData(Molecule * mol) {
    OpenBabel::OBMol obmol = mol->OBMol();
    OpenBabel::OBElectronicTransitionData *etd = static_cast<OpenBabel::OBElectronicTransitionData*>(obmol.GetData("ElectronicTransitionData"));

    if (!etd) return false;
    if (etd->GetEDipole().size() == 0) return false;

    // OK, we have valid data, so store them for later
    std::vector<double> wavelengths = etd->GetWavelengths();
    std::vector<double> edipole= etd->GetEDipole();

    // Store in member vars
    m_xList.clear();
    m_yList.clear();
    for (uint i = 0; i < wavelengths.size(); i++){
      m_xList.append(wavelengths.at(i));
      m_yList.append(edipole.at(i));
    }

    return true;
  }
Esempio n. 24
0
OpenBabel::OBMol
Schuffenhauer::Rule_12(OpenBabel::OBMol& oldMol)
{
   	std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
   	if (allrings.size() <= _ringsToBeRetained)
   	{
      	return oldMol;
   	}
   	std::vector<OpenBabel::OBMol> mols;
   	std::vector<unsigned int> rings;
   	for (unsigned int i(0); i < allrings.size(); ++i)
   	{
      	if (HasLinkerToHeteroAtom(oldMol, allrings[i]))
      	{
         	mols.push_back(oldMol);
         	rings.push_back(i);
      	}
   	}

   	std::vector<OpenBabel::OBMol> validMols;
   	for (unsigned int i(0); i < mols.size(); ++i)
   	{
      	mols[i] = RemoveRing(mols[i], allrings, rings[i]);
      	if (!mols[i].Empty())
      	{
         	validMols.push_back(mols[i]);
      	}
   	}

   	if (validMols.size() == 1)
   	{
      	return validMols[0];
   	}
  
   	return oldMol;
}
Esempio n. 25
0
int main(int argc,char **argv)
{
	std::string ifile = "";
	OpenBabel::OBSpectrophore::AccuracyOption accuracy = OpenBabel::OBSpectrophore::AngStepSize20;
	OpenBabel::OBSpectrophore::StereoOption stereo = OpenBabel::OBSpectrophore::NoStereoSpecificProbes;
	OpenBabel::OBSpectrophore::NormalizationOption normalization = OpenBabel::OBSpectrophore::NoNormalization;
	double resolution = 3.0;
	int c;
	
	opterr = 0;
	std::string msg;
	
	while ((c = getopt(argc, argv, "ui:n:a:s:r:h")) != -1)
	{
		switch (c)
		{
			case 'u':
            showImplementationDetails(argv[0]);
            exit(1);
				break;
				
			case 'i':
				if (!isValidValue('i', optarg))
				{
					msg = "Option -i is followed by an invalid argument: ";
					msg += optarg;
					showError(msg);
					exit(1);
				}
				else
				{
					ifile = optarg;
				}
				break;
				
			case 'n':
				if (!isValidValue('n', optarg))
				{
					msg = "Option -n is followed by an invalid argument: ";
					msg += optarg;
					showError(msg);
					exit(1);
				}
				else normalization = stringToNormalizationOption(optarg);
				break;
				
			case 'a':
				if (!isValidValue('a', optarg))
				{
					msg = "Option -a is followed by an invalid argument: ";
					msg += optarg;
					showError(msg);
					exit(1);
				}
				else accuracy = stringToAccuracyOption(optarg);
				break;
				
			case 's':
				if (!isValidValue('s', optarg))
				{
					msg = "Option -s is followed by an invalid argument: ";
					msg += optarg;
					showError(msg);
					exit(1);
				}
				else stereo = stringToStereoOption(optarg);
				break;
				
			case 'r':
				if (!isValidValue('r', optarg))
				{
					msg = "Option -r is followed by an invalid argument: ";
					msg += optarg;
					showError(msg);
					exit(1);
				}
				else
				{
					resolution = atof(optarg);
					if (resolution <= 0)
					{
						msg = "Resolution -r should be larger than 0.0: ";
						msg += optarg;
						showError(msg);
						exit(1);
					}
				}
				break;
				
			case 'h':
				showHelp(argv[0]);
				exit(0);
				break;
				
			case '?':
				if ((optopt == 'i') || 
						(optopt == 'n') || 
						(optopt == 'a') || 
						(optopt == 's') || 
						(optopt == 'r'))
				{
					msg = "Option -";
					msg += optopt;
					msg += " requires an argument.";
					showError(msg);
					exit(1);
				}
				else
				{
					msg = "Unknown option -";
					msg += optopt;
					msg += ".";
					showError(msg);
					exit(1);
				}
				break;
				
			default:
				showError("Unknown option");
				exit(1);
				break;
		}
	}
	
	// The input file (-i) is the only required option
	if (ifile.empty())
	{
		msg = "Input file specification is required (option -i).";
		showError(msg);
		exit(1);
	}
	OpenBabel::OBConversion obconversion;
	OpenBabel::OBFormat *format = obconversion.FormatFromExt(ifile.c_str());
	if (!format)
	{
		msg = "Could not find file format for ";
		msg += ifile;
		showError(msg);
		exit(1);
	}
	obconversion.SetInFormat(format);
	std::ifstream ifs;
	ifs.open(ifile.c_str());
	obconversion.SetInStream(&ifs);
	
	// Start calculations
	OpenBabel::OBMol mol;
	OpenBabel::OBSpectrophore spec;
	spec.SetAccuracy(accuracy);
	spec.SetNormalization(normalization);
	spec.SetStereo(stereo);
	spec.SetResolution(resolution);
	showParameters(spec, ifile);
	unsigned int count(0);
	while (obconversion.Read(&mol))
	{
		std::vector<double> result = spec.GetSpectrophore(&mol);
		if (result.empty()) {
			std::cerr << "Error calculating Spectrophore from molecule number ";
			std::cerr << count;
			std::cerr << " (counting starts at 0)!";
			std::cerr << std::endl;
		}
		else
		{
			std::cout << mol.GetTitle() << "\t";
			for (unsigned int i(0); i < result.size(); ++i)
			{
				std::cout << result[i] << "\t";
			}
			std::cout << std::endl;
		}
		mol.Clear();
		++count;
	}
	return 0;
}
Esempio n. 26
0
//*--------------------------------------------------------------------------*//
//* MAIN                                                                MAIN *//
//*--------------------------------------------------------------------------*//
int main(int argc, char* argv[])
{  
   // Initialise random number generator
	srandom(time(NULL));
	clock_t t0 = clock();
   
   // Print header
   printHeader();
	
	// Read options
   Options uo = parseCommandLine(argc,argv);
   if(!uo.noHybrid)
   {
      if(uo.funcGroupVec[AROM] && uo.funcGroupVec[LIPO])
      {
         uo.funcGroupVec[HYBL] = true;
      }
      if(uo.funcGroupVec[HDON] && uo.funcGroupVec[HACC])
      {
         uo.funcGroupVec[HYBH] = true;
      }
   }
   std::cerr << uo.print() << std::endl;
   
   if (uo.version)
   {
		printHeader();
		exit(0);
	}
   
	if (uo.help)
   {
		printUsage();
		exit(0);
	}
	
	// Db file and pharmacophore out are mandatory elements
	if (uo.dbInpFile.empty())
   {
		mainErr("Missing database file. This is a required option (-d).");
	}
   
	if (uo.pharmOutFile.empty() && uo.molOutFile.empty() && uo.scoreOutFile.empty())
   {
		mainErr("No output file defined. So there is actually no use to compute anything at all.");
	}	
   
	if ((uo.pharmOutFile.empty() && uo.scoreOutFile.empty()) && !uo.molOutFile.empty())
   {
		mainErr("No file defined to write pharmacophore information.");
	}	
	
	if (uo.refInpFile.empty() && uo.pharmOutFile.empty() && uo.molOutFile.empty() && !uo.scoreOutFile.empty())
   {
		mainErr("Only score file requested when no reference is given. Unable to generate this output.");
	}	
  
	// Reference variables
   Pharmacophore refPharm;
   refPharm.clear();
   std::string refId;
   double refVolume(0.0);
   int refSize(0);
	int exclSize(0);
  
	// Database variables
   std::vector<Result*> resList;
   Pharmacophore dbPharm;
   std::string dbId;
   double dbVolume(0.0);
   int dbSize(0);
  
   //----------------------------------------------------------------------------
	//...(A).. Process the reference
   //----------------------------------------------------------------------------
  
	if (!uo.refInpFile.empty())
	{
      //-------------------------------------------------------
      //...(1).. get reference pharmacophore
      //-------------------------------------------------------
    
      if (uo.refInpType == UNKNOWN)
      {
         std::string ext(getExt(uo.refInpFile));
         if (ext == ".phar")
         {
            uo.refInpType = PHAR;
         }
         else 
         {
            uo.refInpType = MOL;
         }
      }
		
      if (uo.refInpType == MOL)
      {
         OpenBabel::OBMol m;
         OpenBabel::OBConversion* reader = new OpenBabel::OBConversion();
         reader->SetInFormat(reader->FormatFromExt(uo.refInpFile.c_str()));
         if (!reader->Read(&m, uo.refInpStream))
         {
            mainErr("Unable to read reference molecule");
         }
         calcPharm(&m, &refPharm, uo);
         refId = m.GetTitle();
         delete reader;
         reader = NULL;
      }
      else if (uo.refInpType == PHAR)
      {
         PharmacophoreReader* reader = new PharmacophoreReader();
         refPharm = reader->read(uo.refInpStream, refId);
         if (refPharm.empty())
         {
            mainErr("Error reading reference pharmacophore");
         }
         delete reader;
         reader = NULL;
      }
      else
      {
         mainErr("Unknown format of reference molecule.");
      }
		
      //-------------------------------------------------------
		//...(2).. process reference pharmacophore
      //-------------------------------------------------------
		
      if (uo.merge)
      {
         pharMerger.merge(refPharm);
      }
    
      refSize = refPharm.size();
      for (unsigned int i(0); i < refSize; ++i)
		{
         if (refPharm[i].func == EXCL)
         {
				// extract overlap with exclusion spheres
				for (unsigned int j(0); j < refPharm.size(); ++j)
            {
					if (refPharm[j].func != EXCL)
               {
						refVolume -= VolumeOverlap(refPharm[i], refPharm[j], !uo.noNormal);
					}
				}
				exclSize++;
			}
         else
         {
				// add point self-overlap
				refVolume += VolumeOverlap(refPharm[i], refPharm[i], !uo.noNormal);
			}
      }
      
      if(!uo.isQuiet)
      {
         std::cerr << "Reference pharmacophore " << refId << std::endl;
         std::cerr << "   number of points:            " << refSize - exclSize << std::endl;
			std::cerr << "   number of exclusion spheres: " << exclSize << std::endl;
         std::cerr << "   totalvolume:                 " << refVolume << std::endl;
      }
	}

   //----------------------------------------------------------------------------
	//...(B).. Process the database file
   //----------------------------------------------------------------------------

   // DB files
   if (uo.dbInpType == UNKNOWN)
   {
      std::string ext(getExt(uo.dbInpFile));
      if (ext==".phar")
      {
         uo.dbInpType = PHAR;
      }
      else
      {
         uo.dbInpType = MOL;
      }
   }
	
	// local storage of the rotation matrix
	SiMath::Matrix rotMat(3,3,0.0);

   unsigned int molCount(0);
   
   OpenBabel::OBConversion* molReader = NULL;
	PharmacophoreReader* pharmReader = NULL;
   
   if (uo.dbInpType == PHAR)
   {
      pharmReader = new PharmacophoreReader();
   }
   else if (uo.dbInpType == MOL)
   {
      molReader = new OpenBabel::OBConversion();
      molReader->SetInFormat(molReader->FormatFromExt(uo.dbInpFile.c_str()));
      molReader->SetInStream(uo.dbInpStream);
   }
   else
   {
      mainErr("Unknown format of db file.");
   }

   bool done(false);
   OpenBabel::OBMol m;
   while (!done)
   {	
      dbPharm.clear();
      m.Clear();

      if (uo.dbInpType == MOL)
      {
         if (!molReader->Read(&m))
         {
            done = true;
            break;
         }
         else
         {
            calcPharm(&m, &dbPharm, uo);
            dbId = m.GetTitle();
         }
      }
      else
      {
         if (uo.dbInpStream->eof())
         {
            done = true;
            break;
         }
         else
         {
            dbPharm = pharmReader->read(uo.dbInpStream, dbId);
         }
      }
      if (dbPharm.empty())
      {
         continue;
      }

      ++molCount;
      if (!uo.isQuiet )
      {
         if ((molCount % 10) == 0)
         {
            std::cerr << "." << std::flush;
         }
         if ((molCount % 500) == 0)
         {
            std::cerr << molCount << std::endl << std::flush;
         }
      }

			
      if (uo.merge)
      {
         pharMerger.merge(dbPharm);
      }
      
      if (uo.refInpFile.empty())
      {
         if (!(uo.isQuiet))
         {
            printProgress(molCount);
         } 
         if( !uo.pharmOutFile.empty())
         {
            uo.pharmOutWriter->write(dbPharm, uo.pharmOutStream, dbId);
         }
         continue;
      }

      //-------------------------------------------------------
      //...(1).. Alignment
      //-------------------------------------------------------
      
      dbSize = dbPharm.size();
      dbVolume = 0.0;
      for (unsigned int i(0); i < dbSize; ++i) 
      {
         if (dbPharm[i].func == EXCL)
         {
            continue;
         }
         dbVolume += VolumeOverlap(dbPharm[i], dbPharm[i], !uo.noNormal);
      }
			
      // Create a result structure
      Result res;
      res.refId           = refId;
      res.refVolume       = refVolume;
      res.dbId            = dbId;
      res.dbVolume        = dbVolume;
      res.overlapVolume   = 0.0;
      res.exclVolume      = 0.0;
      res.resMol          = m;
      res.resPharSize     = 0;
			
      if (uo.scoreOnly)
      {
         FunctionMapping funcMap(&refPharm, &dbPharm, uo.epsilon);
         PharmacophoreMap fMap = funcMap.getNextMap();
         double volBest(-9999.999);
         
         // loop over all reference points
         while (!fMap.empty())
         {
            double newVol(0.0);
            double exclVol(0.0);
            for (PharmacophoreMap::iterator itP = fMap.begin(); itP != fMap.end(); ++itP) 
            {
               if ((itP->first)->func == EXCL)
               {
                  exclVol += VolumeOverlap((itP->first), (itP->second), !uo.noNormal);					
               }
               else if (((itP->first)->func == (itP->second)->func ) || 
                       (((itP->first)->func == HYBH || 
                         (itP->first)->func == HDON || 
                         (itP->first)->func == HACC) 
                     && ((itP->second)->func == HDON || 
                         (itP->second)->func == HACC ||
                         (itP->second)->func == HYBH))
                     || (((itP->first)->func == HYBL || 
                          (itP->first)->func == AROM || 
                          (itP->first)->func == LIPO)
                      && ((itP->second)->func == AROM || 
                          (itP->second)->func == LIPO || 
                          (itP->second)->func == HYBL)))
               {
                  newVol += VolumeOverlap((itP->first),(itP->second), !uo.noNormal);
               }
            }
					
            if ((newVol - exclVol) > volBest)
            {
               res.resPhar.clear();
               res.resPharSize = 0;
               for (PharmacophoreMap::iterator itP = fMap.begin(); itP != fMap.end(); ++itP) 
               {
                  // add point to resulting pharmacophore
                  PharmacophorePoint p(itP->second);
                  (res.resPhar).push_back(p);
                  ++res.resPharSize;
               }						
               res.overlapVolume = newVol;
               res.exclVolume = exclVol;
               volBest = newVol - exclVol;
            }
            // get the next map
            fMap.clear();
            fMap = funcMap.getNextMap();
         }
      }
      else
      {
         FunctionMapping funcMap(&refPharm, &dbPharm, uo.epsilon);
         PharmacophoreMap fMap = funcMap.getNextMap();
         PharmacophoreMap bestMap;
				
         // default solution
         SolutionInfo best;
         best.volume = -999.9;
         
         // rotor is set to no rotation 
         best.rotor.resize(4);
         best.rotor = 0.0;
         best.rotor[0] = 1.0;
				
         double bestScore = -1000;
         int mapSize(fMap.size());
         int maxSize = mapSize - 3;
				
         while (!fMap.empty())
         {
            int msize = fMap.size();
            
            // add the exclusion spheres to the alignment procedure
            if (uo.withExclusion)
            {
               for (unsigned int i(0); i < refSize ; ++i)
               {
                  if (refPharm[i].func != EXCL)
                  {
                     continue;
                  }
                  for (unsigned int j(0); j < dbSize; ++j)
                  {
                     if (dbPharm[j].func == EXCL)
                     {
                        continue;
                     }
                     fMap.insert(std::make_pair(&(refPharm[i]), &(dbPharm[j])));
                  }
               }
            }
					
            // Only align if the expected score has any chance of being larger 
            // than best score so far
            if ((msize > maxSize)
            && (((double) msize / (refSize - exclSize + dbSize - msize)) > bestScore))
            {
               Alignment align(fMap);
               SolutionInfo r = align.align(!uo.noNormal);

               if (best.volume < r.volume)
               {
                  best = r;
                  bestScore = best.volume / (refVolume + dbVolume - best.volume);
                  bestMap = fMap;
                  mapSize = msize;
               }
            }
            else
            {
               // Level of mapping site to low
               break;
            }
	
            if (bestScore > 0.98)
            {
               break;
            }
					
            // Get the next map
            fMap.clear();
            fMap = funcMap.getNextMap();
         }
				
         // Transform the complete pharmacophore and the molecule towards the 
         // best alignment
         rotMat = quat2Rotation(best.rotor);
         positionPharmacophore(dbPharm, rotMat, best);
         positionMolecule(&res.resMol, rotMat, best);
				
         // Update result
         res.info = best;

         // Compute overlap volume between exlusion spheres and pharmacophore 
         // points
         for (int i(0); i < refSize; ++i) 
         {
            if (refPharm[i].func != EXCL)
            {
               continue;
            }
            for (int j(0); j < dbSize; ++j)
            {
               res.exclVolume += VolumeOverlap(refPharm[i], dbPharm[j], !uo.noNormal);
            }
         }
				
         // make copy of the best map and compute the volume overlap
         for (PharmacophoreMap::iterator itP = bestMap.begin(); itP != bestMap.end(); ++itP) 
         {
            if(((itP->first)->func == EXCL) || ((itP->second)->func == EXCL))
            { 
               continue; 
            }
					
            // compute overlap
            res.overlapVolume += VolumeOverlap(itP->first, itP->second, !uo.noNormal);
					
            // add point to resulting pharmacophore
				PharmacophorePoint p(itP->second);
            (res.resPhar).push_back(p);
            ++res.resPharSize;
         }
      }
			
      // update scores
      res.info.volume = res.overlapVolume - res.exclVolume;
      if (res.info.volume > 0.0)
      {
         res.tanimoto = res.info.volume / (res.refVolume + res.dbVolume - res.info.volume);
         res.tversky_ref = res.info.volume / res.refVolume;
         res.tversky_db = res.info.volume / res.dbVolume;
      }

      switch (uo.rankby) 
      {
         case TANIMOTO:
            res.rankbyScore = res.tanimoto;
            break;
         case TVERSKY_REF:
            res.rankbyScore = res.tversky_ref;
            break;
         case TVERSKY_DB:
            res.rankbyScore = res.tversky_db;
            break;
      }

      //-------------------------------------------------------
      //...(5).. Generate output
      //-------------------------------------------------------
      if (uo.cutOff != 0.0)
      {
         if (res.rankbyScore < uo.cutOff)
         {
            continue;
         }
      }

      if (uo.best != 0)
      {
         addBest(res, uo, resList);
      }
      else 
      { 
         if (!uo.molOutFile.empty())
         { 
            logOut(&res, uo);
         }
         if (!uo.pharmOutFile.empty())
         {
            logPharmacophores(&res, uo);
         }
         if (!uo.scoreOutFile.empty())
         {
            logScores(&res, uo);
         }
      }
   }

   if (molReader)
   {
      delete molReader;
      molReader = NULL;
   }
   if (pharmReader)
   {
      delete pharmReader;
      pharmReader = NULL;
   }
  
   //----------------------------------------------------------------------------
   //...(C).. Process best list (if defined)
   //----------------------------------------------------------------------------

   if (uo.best != 0)
   {
      std::vector<Result*>::iterator itR;
      for (itR = resList.begin(); itR != resList.end(); ++itR) 
      {
         Result* res(*itR);
         if (!uo.molOutFile.empty())
         {
            logOut(res, uo);
         }
         if (!uo.pharmOutFile.empty())
         {
            logPharmacophores(res, uo);
         }
         if (!uo.scoreOutFile.empty())
         {
            logScores(res, uo);
         }
         delete res;
      }
   }

   // done processing database
   if (!uo.isQuiet)
   {
      if (uo.refInpFile.empty())
      {
         std::cerr << std::endl;
         std::cerr << "Processed " << molCount << " molecules";
         double tt = (double)(clock() - t0 )/CLOCKS_PER_SEC;
         std::cerr << " in " << tt << " seconds (";
         std::cerr << molCount/tt << " molecules per second)." << std::endl;
      }
      else
      {
         std::cerr << std::endl;
         std::cerr << "Processed " << molCount << " molecules" << std::endl;
         double tt = (double)(clock() - t0 )/CLOCKS_PER_SEC;
         std::cerr << molCount << " alignments in " << tt << " seconds (";
         std::cerr << molCount/tt << " alignments per second)." << std::endl;
      }
   }
	
   exit(0);

}
void
FilterBridgeFraction::Calculate(OpenBabel::OBMol* mol)
{
   // Are there rings?
   OpenBabel::OBAtom* atom;
   std::vector<OpenBabel::OBAtom*>::iterator i;
   bool rings(false);
   for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
   {
      if (atom->IsInRing())
      {
         rings = true;
         break;
      }
   }

   if (rings)
   {
      // Make workcopy of original mol
      OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
      unsigned int natoms(m.NumAtoms());
      if (!natoms)
      {
         _result = 0.0;
         _passed = false;
         return;
      }
   
      // Iteratively remove all endstanding atoms until none are left
      OpenBabel::OBAtom* atom;
      std::vector<OpenBabel::OBAtom*>::iterator i;
      bool endstanding(true);
      while (endstanding && m.NumAtoms())
      {
         endstanding = false;
         for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
         {
            if (atom->GetValence() < 2)
            {
               if (m.DeleteAtom(atom))
               {
                  endstanding = true;
                  break;
               }
            }
         }
      }

      // Now remove all ring atoms
      rings = true;
      while (rings && m.NumAtoms())
      {
         rings = false;
         for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
         {
            if (atom->IsInRing())
            {
               if (m.DeleteAtom(atom))
               {
                  rings = true;
                  break;
               }
            }
         }
      }
   
      _result = (double) m.NumAtoms() / (double) natoms;
   }
   else
   {
      _result = 0.0;
   }
   
   if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
   {
      _passed = false;
   }
   else
   {
      _passed = true;
   }
}
Esempio n. 28
0
void Molecule::addHydrogens(Atom *a,
                            const QList<unsigned long> &atomIds,
                            const QList<unsigned long> &bondIds)
{
    if (atomIds.size() != bondIds.size()) {
        qDebug() << "Error, addHydrogens called with atom & bond id lists of different size!";
    }

    // Construct an OBMol, call AddHydrogens and translate the changes
    OpenBabel::OBMol obmol = OBMol();
    if (a) {
        OpenBabel::OBAtom *obatom = obmol.GetAtom(a->index()+1);
        // Set implicit valence for unusual elements not handled by OpenBabel
        // PR#2803076
        switch (obatom->GetAtomicNum()) {
        case 3:
        case 11:
        case 19:
        case 37:
        case 55:
        case 85:
        case 87:
            obatom->SetImplicitValence(1);
            obatom->SetHyb(1);
            obmol.SetImplicitValencePerceived();
            break;

        case 4:
        case 12:
        case 20:
        case 38:
        case 56:
        case 88:
            obatom->SetImplicitValence(2);
            obatom->SetHyb(2);
            obmol.SetImplicitValencePerceived();
            break;

        case 84: // Po
            obatom->SetImplicitValence(2);
            obatom->SetHyb(3);
            obmol.SetImplicitValencePerceived();
            break;

        default: // do nothing
            break;
        }
        obmol.AddHydrogens(obatom);
    }
    else
        obmol.AddHydrogens();
    // All new atoms in the OBMol must be the additional hydrogens
    unsigned int numberAtoms = numAtoms();
    int j = 0;
    for (unsigned int i = numberAtoms+1; i <= obmol.NumAtoms(); ++i, ++j) {
        if (obmol.GetAtom(i)->IsHydrogen()) {
            OpenBabel::OBAtom *obatom = obmol.GetAtom(i);
            Atom *atom;
            if (atomIds.isEmpty())
                atom = addAtom();
            else if (j < atomIds.size())
                atom = addAtom(atomIds.at(j));
            else {
                qDebug() << "Error - not enough unique ids in addHydrogens.";
                break;
            }
            atom->setOBAtom(obatom);
            // Get the neighbor atom
            OpenBabel::OBBondIterator iter;
            OpenBabel::OBAtom *next = obatom->BeginNbrAtom(iter);
            Bond *bond;
            if (bondIds.isEmpty())
                bond = addBond();
            else // Already confirmed by atom ids
                bond = addBond(bondIds.at(j));
            bond->setEnd(Molecule::atom(atom->index()));
            bond->setBegin(Molecule::atom(next->GetIdx()-1));
        }
    }
    for (unsigned int i = 1; i <= numberAtoms; ++i) {
        // Warning -- OB atom index off-by-one here
        atom(i-1)->setPartialCharge(obmol.GetAtom(i)->GetPartialCharge());
    }
}
Esempio n. 29
0
bool extract_thermochemistry(OpenBabel::OBMol  &mol,
                             bool    bVerbose,
                             int    *Nsymm,
                             int     Nrotbonds,
                             double  dBdT,
                             double *temperature,
                             double *DeltaHf0,
                             double *DeltaHfT,
                             double *DeltaGfT,
                             double *DeltaSfT,
                             double *S0T,
                             double *CVT,
                             double *CPT,
                             std::vector<double> &Scomponents,
                             double *ZPVE)
{
    enum kkTYPE {kkDH, kkDG, kkDS, kkS0, kkCV, kkSt, kkSr, kkSv, kkZP};
    typedef struct {
        std::string term;
        kkTYPE kk;
    } energy_unit;
    double St = 0, Sr = 0, Sv = 0, Sconf = 0, Ssymm = 0;
    double Rgas      = 1.9872041; 
    int    RotSymNum = 1;
    OpenBabel::OBRotationData* rd;
    
    rd = (OpenBabel::OBRotationData*)mol.GetData("RotationData");
    if (NULL != rd)
    {
        RotSymNum = rd->GetSymmetryNumber();
        if (bVerbose)
        {
            printf("Found symmetry number %d in input file.\n", RotSymNum);
        }
    }
    else if (bVerbose)
    {
        printf("Using default symmetry number %d\n", RotSymNum);
    }
    if ((*Nsymm > 0) && (*Nsymm != RotSymNum))
    {
        // Rgas in cal/mol K http://en.wikipedia.org/wiki/Gas_constant
        Ssymm = -Rgas*log((1.0* *Nsymm)/RotSymNum);
        RotSymNum = *Nsymm;
        if (bVerbose)
        {
            printf("Changing symmetry number to %d\n", RotSymNum);
        }
    }
    else if (*Nsymm == 0)
    {
        *Nsymm = RotSymNum;
    }
    if (Nrotbonds > 0) 
    {
        Sconf = Rgas*Nrotbonds*log(3.0);
    }
    energy_unit eu[] = {
        { "zpe",        kkZP },
        { "DeltaHform", kkDH },
        { "DeltaGform", kkDG },
        { "DeltaSform", kkDS },
        { "S0",         kkS0 },
        { "cv",         kkCV },
        { "Strans",     kkSt },
        { "Srot",       kkSr },
        { "Svib",       kkSv }
    };
#define NEU (sizeof(eu)/sizeof(eu[0]))
    int found = 0;
    std::vector<OpenBabel::OBGenericData*> obdata = mol.GetData();
    for(std::vector<OpenBabel::OBGenericData*>::iterator j = obdata.begin(); (j<obdata.end()); ++j)
    {
        std::string term  = (*j)->GetAttribute();
        double value = atof((*j)->GetValue().c_str());
        double T     = 0;
        {
            size_t lh = term.find("(");
            size_t rh = term.find("K)");
            double TT = atof(term.substr(lh+1,rh-lh-1).c_str());
            if (0 != TT)
            {
                if (0 == T)
                {
                    T            = TT;
                    *temperature = TT;
                }
                else
                {
                    std::cerr << "Different T in the input file, found " << T << " before and now " << TT << ". Output maybe inconsistent." << std::endl;
                    T = TT;
                }
            }
        }
        for(unsigned int i = 0; (i<NEU); i++)
        {
            if (strstr(term.c_str(), eu[i].term.c_str()) != 0)
            {
                switch (eu[i].kk)
                {
		            case kkZP:
		                {
		                    *ZPVE = value;
		                }
		                break;
                case kkDH:
                    if (0 == T)
                    {
                        *DeltaHf0 = value;
                    }
                    else
                    {
                        *DeltaHfT = value;
                    }
                    found ++;
                    break;
                case kkDG:
                    *DeltaGfT = value - T*(Ssymm+Sconf)/1000;
                    found ++;
                    break;
                case kkDS:
                    *DeltaSfT = value + Ssymm + Sconf;
                    found ++;
                    break;
                case kkS0:
                    *S0T = value + Ssymm + Sconf;
                    found ++;
                    break;
                case kkSt:
                    St = value;
                    found ++;
                    break;
                case kkSr:
                    Sr = value;
                    found ++;
                    break;
                case kkSv:
                    Sv = value;
                    found ++;
                    break;
                case kkCV:
                    *CVT = value;
                    found++;
                    break;
                default:
                    break;
                }
            }
        }
    }
    double P   = 16.605/4.184; // Convert pressure to kcal/mol
    *CPT       = *CVT + Rgas + (2*P*dBdT + pow(P*dBdT, 2.0)/Rgas);

    Scomponents.push_back(St);
    Scomponents.push_back(Sr);
    Scomponents.push_back(Sv);
    Scomponents.push_back(Ssymm);
    Scomponents.push_back(Sconf);
    if (bVerbose && (Ssymm != 0))
    {
        printf("Applyied symmetry correction to free energy of %g kcal/mol\n",
               -(*temperature*Ssymm)/1000);
    }
    if (bVerbose && (Sconf != 0))
    {
        printf("Applyied conformational correction to free energy of %g kcal/mol\n",
               -(*temperature*Sconf)/1000);
    }
    return (found == 9);
}
	//--
	bool DataProperty::Satisfy(OpenBabel::OBRing* pRing, 
								const std::string& refTo, 
								std::vector<Class*>& vecSatisfiedClasses, 
								std::string& refValue)
	{
		//bool bSatisfied = false;
		int iPosition = -1;

		// [rad] if we are default, we automatically satisfy		
		if(!IsDefault())
		{			
			if(!SatisfyCommon(vecSatisfiedClasses, iPosition))
			{
				// [rad] this property does not apply

				refValue = "";
				return(false);
			}
		}

		// [rad] go through possible data types..

		if(!refTo.compare("RING_SIZE"))
		{
			ConvertInt(pRing->Size(), refValue);
		}
		else if(!refTo.compare("RING_IS_AROMATIC"))
		{
			ConvertBool(pRing->IsAromatic(), refValue);
		}
		else if(!refTo.compare("RING_IS_HOMOCYCLIC"))
		{
			OpenBabel::OBMol* pMolecule = pRing->GetParent();
			OpenBabel::OBAtom* pAtom;

			bool bHomoCyclic = true;

			std::vector<int>::iterator iter_path = pRing->_path.begin();
			while(iter_path != pRing->_path.end())
			{
				pAtom = pMolecule->GetAtom((*iter_path));

				if(pAtom)
				{
					if(6 != pAtom->GetAtomicNum())
					{
						bHomoCyclic = false;
						break;
					}
				}

				iter_path++;
			}

			ConvertBool(bHomoCyclic, refValue);
		}
		else if(!refTo.compare("RING_IS_HETEROCYCLIC"))
		{
			OpenBabel::OBMol* pMolecule = pRing->GetParent();
			OpenBabel::OBAtom* pAtom;

			bool bHeteroCyclic = false;

			std::vector<int>::iterator iter_path = pRing->_path.begin();
			while(iter_path != pRing->_path.end())
			{
				pAtom = pMolecule->GetAtom((*iter_path));

				if(pAtom)
				{
					if(6 != pAtom->GetAtomicNum())
					{
						bHeteroCyclic = true;
						break;
					}
				}

				iter_path++;
			}

			ConvertBool(bHeteroCyclic, refValue);
		}
		else
		{
			// [rad] unknown datatype?
			refValue = "";
			return(false);
		}

		return(true);
	}