C++ openbabel::OBAtom类代码示例

Coordinate
_hDonCalcNormal(OpenBabel::OBAtom* a)
{
   int nbrBonds(0);
   Coordinate normal;

   std::vector<OpenBabel::OBBond*>::iterator bi;
   for (OpenBabel::OBBond* b = a->BeginBond(bi); b; b = a->NextBond(bi))
   {
      OpenBabel::OBAtom* aa = b->GetNbrAtom(a);
      if (aa->GetAtomicNum() == 1)
      {
         continue;
      }
      ++nbrBonds;
      normal.x += (aa->x() - a->x());
      normal.y += (aa->y() - a->y());
      normal.z += (aa->z() - a->z());
   }
   double length(sqrt(normal.x*normal.x + normal.y*normal.y + normal.z*normal.z));
   normal.x /= length;
   normal.y /= length;
   normal.z /= length;
  
   normal.x = -normal.x;
   normal.y = -normal.y;
   normal.z = -normal.z;
  
   normal.x += a->x();
   normal.y += a->y();
   normal.z += a->z();
  
   return normal;
}

void
FilterRings::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)
   {
      std::vector<OpenBabel::OBRing* > nrings = mol->GetSSSR();
      _result = nrings.size();
   }
   else
   {
      _result = 0;
   }
   
   if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
   {
      _passed = false;
   }
   else
   {
      _passed = true;
   }
}

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();
}

void
FilterNonaromaticRingFraction::Calculate(OpenBabel::OBMol* mol)
{
   // Are there atoms and rings?
   unsigned int rings(0);
   unsigned int natoms(0);
   OpenBabel::OBAtom* atom;
   std::vector<OpenBabel::OBAtom*>::iterator i;
   for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
   {
      if (atom->IsHydrogen()) continue;
      if (atom->IsInRing()) ++rings;
      ++natoms;
   }
   if (!natoms)
   {
      _result = 0.0;
      _passed = false;
      return;
   }
   
   std::set<int> uniqRingIdx;
   if (rings)
   {
      std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
      uniqRingIdx.clear();
      std::vector<int>::iterator path;
      std::vector<OpenBabel::OBRing*>::iterator ri;
      for (ri = nrings.begin(); ri != nrings.end(); ++ri)
      {
         if (!(*ri)->IsAromatic())
         {
            for (path = (*ri)->_path.begin(); path != (*ri)->_path.end(); ++path)
            {
               uniqRingIdx.insert(*path);
            }
         }
      }
   }
   unsigned int ar(uniqRingIdx.size());
   if (ar)
   {
      _result = (double) ar / (double) natoms;
   }
   else
   {
      _result = 0.0;
   }
   
   if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
   {
      _passed = false;
   }
   else
   {
      _passed = true;
   }
}

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;
   }  
}

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;
    }
  }
}

  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();
  }

std::list<OpenBabel::OBAtom*>
_hAccGetNeighbors(OpenBabel::OBAtom* a)
{
   std::list<OpenBabel::OBAtom*> aList;
   OpenBabel::OBMol* parent(a->GetParent());

   double r;
   OpenBabel::OBElementTable et;
   std::vector<OpenBabel::OBAtom*>::iterator ai;
   for (OpenBabel::OBAtom* aa = parent->BeginAtom(ai); aa; aa = parent->NextAtom(ai))
   {
      if (*aa == a)
      {
         continue;
      }
    
      r = et.GetVdwRad(aa->GetAtomicNum());
      double delta(H_BOND_DIST + H_RADIUS + r);
      double maxDistSq(delta*delta);
      double distSq((a->x() - aa->x()) * (a->x() - aa->x()) +
                    (a->y() - aa->y()) * (a->y() - aa->y()) +
                    (a->z() - aa->z()) * (a->z() - aa->z()));
    
      if (distSq <= maxDistSq)
      {
         aList.push_back(aa);
      }
   }
   return aList;
}

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;
}

void
Fingerprint::_getFragments(std::vector<int> levels, std::vector<int>curfrag, 
int level, OpenBabel::OBAtom* patom, OpenBabel::OBBond* pbond)
{
   const int MaxFragSize = 7;
   int bo(0);
   if (pbond) bo = pbond->IsAromatic() ? 5 : pbond->GetBondOrder();

   curfrag.push_back(bo);
   curfrag.push_back(patom->GetAtomicNum());
   levels[patom->GetIdx()] = level;

   std::vector<OpenBabel::OBBond*>::iterator i;
   OpenBabel::OBBond* pnewbond;
   for (pnewbond = patom->BeginBond(i); pnewbond; pnewbond = patom->NextBond(i))
   {
      if (pnewbond == pbond)
      {
         continue;
      }
      OpenBabel::OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
      int atlevel = levels[pnxtat->GetIdx()];
      if (atlevel)
      {
         if (atlevel == 1)
         {
            curfrag[0] = bo;
            _ringset.insert(curfrag);
         }
      }
      else
      {
         if (level < MaxFragSize)
         {
            _getFragments(levels, curfrag, level + 1, pnxtat, pnewbond);
         }
      }
   }
   
   if ((curfrag[0] == 0) &&
      ((level > 1) || (patom->GetAtomicNum() > 8) || (patom->GetAtomicNum() < 6)))
   {
      _fragset.insert(curfrag);
   }
}

void
hAccFuncCalc(OpenBabel::OBMol* mol, Pharmacophore* pharmacophore)
{
   // Create for every hydrogen acceptor a pharmacophore point
   std::vector<OpenBabel::OBAtom*>::iterator ai;
   for (OpenBabel::OBAtom* atom = mol->BeginAtom(ai); atom; atom = mol->NextAtom(ai))
   {
      if (atom->GetAtomicNum() == 7 || atom->GetAtomicNum() == 8)
      {
         if (atom->GetFormalCharge() <= 0)
         {        
            if(_hAccDelocalized(atom) || (_hAccCalcAccSurf(atom) < 0.02))
            {
               continue;
            }
            PharmacophorePoint p;
            p.func = HACC;
            p.point.x = atom->x();
            p.point.y = atom->y();
            p.point.z = atom->z();
            p.hasNormal = true;
            p.alpha = funcSigma[HACC];
            p.normal = _hAccCalcNormal(atom);
            pharmacophore->push_back(p);
         }
      }
   }
}

    //--
    // [rad] generate path and ident for bond
    void RelationBond::GetPathAndIdentBond(const std::string& refMoleculeId, std::string& refPath, std::string& refIdent)
    {
				
				refPath = m_vecSatisfiedClasses.front()->GetPrefix() + ":" + m_vecSatisfiedClasses.front()->GetName();

				std::stringstream ssConv;
				OpenBabel::OBBond* pBond = m_pBond;

				OpenBabel::OBAtom* pAtomStart = pBond->GetBeginAtom();
				OpenBabel::OBAtom* pAtomEnd = pBond->GetEndAtom();


				ssConv << m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
					pAtomStart->GetIdx() << "_"	<< pAtomEnd->GetIdx();

				refIdent = "";
				ssConv >> refIdent;
    }

void
FilterAtomsInLargestNonaromaticRing::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)
   {
      std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
      _result = 0;
      std::vector<OpenBabel::OBRing*>::iterator ri;
      for (ri = nrings.begin(); ri != nrings.end(); ++ri)
      {
         if ( !(*ri)->IsAromatic() && ((*ri)->Size() > _result))
         {
            _result = (*ri)->Size();
         }
      }
      
      if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
      {
         _passed = false;
      }
      else
      {
         _passed = true;
      }
   }
   else
   {
      _result = 0;
      _passed = true;
   }
}

    // [rad] generate path and ident for bond
    void RelationBond::GetObjectPropertyPathAndIdentBond(int iPosition, 
                                                            const std::string& refMoleculeId, 
                                                            std::string& refPath, 
                                                            std::string& refIdent)
    {
				refPath = m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetPrefix() + ":" + 
					m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetName();
				
				std::stringstream ssConv;
				
				OpenBabel::OBAtom* pAtomStart = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetBeginAtom();
				OpenBabel::OBAtom* pAtomEnd = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetEndAtom();

				ssConv << m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
					pAtomStart->GetIdx() << "_"	<< pAtomEnd->GetIdx();

				refIdent = "";
				ssConv >> refIdent;
    }

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;
}