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();
}
Exemple #2
0
bool
Oprea_1::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
	OpenBabel::OBMol m(mol);
	OpenBabel::OBAtom* atom;
	OpenBabel::OBAtom* nbrAtom[2];
	OpenBabel::OBBondIterator bi;
	std::vector<OpenBabel::OBAtom*>::iterator avi;
	OpenBabel::OBBond* bond;
	std::vector<OpenBabel::OBBond*>::iterator bvi;
	bool removed(true);
	while (removed)
	{
		removed = false;
		for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
		{
			if (IsEndStanding(atom, false, false))
			{
				m.DeleteAtom(atom);
				removed = true;
				break;
			}
		}
	}

	// Make all atoms as neutral C and all bond orders equal to 1
 	m.BeginModify();
	for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
	{
		atom->SetAtomicNum(6);
		atom->SetFormalCharge(0);
	}
	for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
	{
		bond->SetBondOrder(1);
	}
	m.EndModify();
   
   	// Transform all neighbouring linker atoms into a single bond
   	removed = true;
   	while (removed)
   	{
		removed = false;
		for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
		{
			if (!atom->IsInRing() && (atom->GetValence() == 2))
			{
		        nbrAtom[0] = atom->BeginNbrAtom(bi);
		        nbrAtom[1] = atom->NextNbrAtom(bi);
				if (nbrAtom[0] && nbrAtom[1])
				{
					m.BeginModify();
		        	m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
		        	m.DeleteAtom(atom);
		      		m.EndModify();
					removed = true;
					break;
				}
			}
		}
   	}

   	// Shrink all rings to their minimum size
   	removed = true;
   	while (removed)
   	{
      	removed = false;
      	for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
      	{
         	if ((atom->MemberOfRingSize() > 3) &&
				(atom->GetValence() == 2))
         	{
            	nbrAtom[0] = atom->BeginNbrAtom(bi);
            	nbrAtom[1] = atom->NextNbrAtom(bi);
				if (nbrAtom[0] && nbrAtom[1])
				{
            		m.BeginModify();
            		m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
            		m.DeleteAtom(atom);
            		m.EndModify();
            		removed = true;
            		break;
				}
         	}
      	}
   	}
   
   	if (!m.Empty())
	{
 		_smiles = _mol2can.WriteString(&m, true);
	}
   	else
   	{
      	_smiles = "-";
      	return false;
   	}
   	return true;
}
Exemple #3
0
bool
Oprea_2::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
   	OpenBabel::OBMol m(mol);

   	// Tag all HBD
   	std::vector<bool> hbd(m.NumAtoms() + 1);
   	for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
   	{    
		if (atom->MatchesSMARTS("[NH,NH2,NH3,OH,nH]"))
      	{
         	hbd[atom->GetIdx()] = true;
      	}
      	else
      	{
         	hbd[atom->GetIdx()] = false;
      	}
   	}
   
   	// Tag all HBA
   	std::vector<bool> hba(m.NumAtoms() + 1);
   	for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
   	{   
 		if (!atom->IsAmideNitrogen() &&        // No amide nitrogen
			!atom->IsAromatic() &&             // Not aromatic
			(atom->GetFormalCharge() <= 0) &&    // No + charge
			atom->MatchesSMARTS("[NH0]"))        // No hydrogens
      	{
         	hba[atom->GetIdx()] = true;
      	}
      	else
		if (atom->IsNitrogen() &&              // Nitrogen
          	atom->IsAromatic() &&              // Aromatic
			atom->MatchesSMARTS("[nH0]") && 	   // No hydrogens
         	(atom->GetHvyValence() <= 2) &&    // Maximal two non-H atoms connected
         	(atom->GetFormalCharge() <= 0))    // No + charge
      	{     
         	hba[atom->GetIdx()] = true;
      	}
      	else
      	if (atom->IsOxygen() &&                // Oxygen
         	(atom->GetFormalCharge() <= 0))    // No + charge
      	{
         	hba[atom->GetIdx()] = true;
     	}
      	else
      	{
          	hba[atom->GetIdx()] = false;
      	}
   	}
   
   	// Mark the C(=O) or S(=O) also as HBA
   	for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
   	{   
		if (atom->MatchesSMARTS("C=O"))
		{
         	hba[atom->GetIdx()] = true;
		}
		else
		if (atom->MatchesSMARTS("S=O"))
		{
         	hba[atom->GetIdx()] = true;
		} 
	}

   	// Make all atoms as neutral C, N (HBD), or O (HBA)
   	m.BeginModify();
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	OpenBabel::OBAtom* atom;
   	for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
   	{
      	if (hba[atom->GetIdx()])
		{
			atom->SetAtomicNum(8);
		}
      	else
		if (hbd[atom->GetIdx()])
		{
			atom->SetAtomicNum(7);
		}
      	else
		{
			atom->SetAtomicNum(6);
		}
      	atom->SetFormalCharge(0);
   	}
   	m.EndModify();

	// Remove all endstanding atoms
   	OpenBabel::OBBondIterator bi;
  	OpenBabel::OBBond* bond;
   	std::vector<OpenBabel::OBBond*>::iterator bvi;
    bool removed(true);
   	while (removed)
   	{
      	removed = false;
      	for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
      	{
         	if (IsEndStanding(atom, false, false))
         	{
	         	m.DeleteAtom(atom);
            	removed = true;
				break;
         	}
      	}
   	}
   
   	// Set all bond orders equal to 1
   	m.BeginModify();
   	for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
   	{
      	bond->SetBondOrder(1);
   	}
   	m.EndModify();

   	// Transform all neighbouring linker atoms into a single bond
   	removed = true; 
	OpenBabel::OBAtom* nbrAtom[2];
   	while (removed)
   	{
		removed = false;
		for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
		{
			if (!atom->IsInRing() && (atom->GetValence() == 2))
			{
				m.BeginModify();
		        nbrAtom[0] = atom->BeginNbrAtom(bi);
		        nbrAtom[1] = atom->NextNbrAtom(bi);
				if (nbrAtom[0] && nbrAtom[1])
				{
		        	m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
		        	m.DeleteAtom(atom);
		      		m.EndModify();
					removed = true;
					break;
				}
			}
		}
   	}

   	// Shrink all rings to their minimum size
   	removed = true;
   	while (removed)
   	{
      	removed = false;
      	for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
      	{
         	if ((atom->MemberOfRingSize() > 3) && (atom->GetValence() == 2))
         	{
            	nbrAtom[0] = atom->BeginNbrAtom(bi);
            	nbrAtom[1] = atom->NextNbrAtom(bi);
				if (nbrAtom[0] && nbrAtom[1])
				{
            		if (nbrAtom[0]->GetAtomicNum() == atom->GetAtomicNum())
            		{
               			m.BeginModify();
               			m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
               			m.DeleteAtom(atom);
               			m.EndModify();
               			removed = true;
               			break;
            		}
            		else
					if (nbrAtom[1]->GetAtomicNum() == atom->GetAtomicNum())
            		{
               			m.BeginModify();
               			m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
               			m.DeleteAtom(atom);
               			m.EndModify();
               			removed = true;
               			break;
					}
            	}
         	}
      	}
   	}

   	if (!m.Empty())
	{
		_smiles = _mol2can.WriteString(&m, true);
	}
   	else
   	{
      	_smiles = "-";
      	return false;
   	}
   	return true;
}