Example #1
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;
}
Example #2
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;
}
Example #3
0
OpenBabel::OBMol
Schuffenhauer::Rule_7(OpenBabel::OBMol& oldMol)
{
   	std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
   	if (allrings.size() <= _ringsToBeRetained)
   	{
      	return oldMol;
   	}

   	// Are all atoms and bonds aromatic?
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	OpenBabel::OBAtom* atom;
   	for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
   	{
      	if (!atom->IsAromatic())
      	{
         	return oldMol;
      	}
   	}
   	std::vector<OpenBabel::OBBond*>::iterator bvi;
   	OpenBabel::OBBond* bond;
   	for (bond = oldMol.BeginBond(bvi); bond; bond = oldMol.NextBond(bvi))
   	{
      	if (!bond->IsAromatic())
      	{
         	return oldMol;
      	}
   	}

   	std::vector<OpenBabel::OBMol> mols;
   	for (unsigned int i(0); i < allrings.size(); ++i)
   	{
      	mols.push_back(oldMol);
   	}
   
   	std::vector<OpenBabel::OBMol> validMols;
   	for (unsigned int i(0); i < mols.size(); ++i)
   	{
      	mols[i] = RemoveRing(mols[i], allrings, i);
      	if (!mols[i].Empty())
      	{
         	// Has aromaticity been broken?
         	bool broken(false);
         	for (atom = mols[i].BeginAtom(avi); atom; atom = mols[i].NextAtom(avi))
         	{
            	if (atom->IsInRing() && !atom->IsAromatic())
            	{
               		broken = true;
               		break;
            	}
         	}
         	if (!broken)
         	{
            	validMols.push_back(mols[i]);
         	}
      	}
   	}

	if (validMols.size() == 1)
   	{
      	return validMols[0];
   	}

   	return oldMol;
}
Example #4
0
void
FilterRingsystems::Calculate(OpenBabel::OBMol* mol)
{
   // Are there rings?
   bool rings(false);
   OpenBabel::OBAtom* atom;
   std::vector<OpenBabel::OBAtom*>::iterator i;
   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();
   
      // Remove all atoms that are not part of ring
      std::vector<OpenBabel::OBAtom*> nonRingAtoms;
      nonRingAtoms.clear();
      for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
      {
         if (!atom->IsInRing()) nonRingAtoms.push_back(atom);
      }
      for (unsigned int i(0); i < nonRingAtoms.size(); ++i)
      {
         m.DeleteAtom(nonRingAtoms[i]);
      }
      
      // Remove all bonds that are not part of a ring
      std::vector<OpenBabel::OBBond*> nonRingBonds;
      nonRingBonds.clear();
      OpenBabel::OBBond* bond;
      std::vector<OpenBabel::OBBond*>::iterator j;
      for (bond = m.BeginBond(j); bond; bond = m.NextBond(j))
      {
         if (!bond->IsInRing()) nonRingBonds.push_back(bond);
      }
      for (unsigned int i(0); i < nonRingBonds.size(); ++i)
      {
         m.DeleteBond(nonRingBonds[i]);
      }
      
      // Count ringsystems
      std::vector<std::vector< int > > ringsystems;
      m.ContigFragList(ringsystems);
      _result = ringsystems.size();

   }
   else
   {
      _result = 0;
   }
   
   if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
   {
      _passed = false;
   }
   else
   {
      _passed = true;
   }
}