Beispiel #1
0
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;
}
Beispiel #2
0
void
hDonFuncCalc(OpenBabel::OBMol* mol, Pharmacophore* pharmacophore)
{
   // Create for every hydrogen donor a pharmacophore point
   std::vector<OpenBabel::OBAtom*>::iterator ai;
   for (OpenBabel::OBAtom* a = mol->BeginAtom(ai); a; a = mol->NextAtom(ai))
   {
      if (a->GetAtomicNum() == 7 || a->GetAtomicNum() == 8)
      {
         if (a->GetFormalCharge() >= 0 && ((a->GetImplicitValence() - a->GetHvyValence()) !=0)) 
         {
            PharmacophorePoint p;
            p.func = HDON;
            p.point.x = a->x();
            p.point.y = a->y();
            p.point.z = a->z();
            p.hasNormal = true;
            p.alpha = funcSigma[HDON];
            p.normal = _hDonCalcNormal(a);
            pharmacophore->push_back(p);
         }
      }
   }
}