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C++ openbabel::OBAtom类代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了C++中openbabel::OBAtom类的典型用法代码示例。如果您正苦于以下问题：C++ OBAtom类的具体用法？C++ OBAtom怎么用？C++ OBAtom使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。



在下文中一共展示了OBAtom类的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的C++代码示例。

示例1: nbrBonds

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;
}
开发者ID:UnixJunkie，项目名称:pharao，代码行数:34，代码来源:hDonFuncCalc.cpp


示例2: rings

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;
   }
}
开发者ID:UnixJunkie，项目名称:sieve，代码行数:35，代码来源:filterRings.cpp


示例3: ofs

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();
}
开发者ID:enikulenkov，项目名称:magistracy-proj，代码行数:30，代码来源:ga_utils_f.cpp


示例4: rings

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;
   }
}
开发者ID:UnixJunkie，项目名称:filter-it，代码行数:58，代码来源:filterNonaromaticRingFraction.cpp


示例5: rings

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;
   }  
}
开发者ID:UnixJunkie，项目名称:sieve，代码行数:58，代码来源:filterCores.cpp


示例6: detectConformers

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;
    }
  }
}
开发者ID:AlbertDeFusco，项目名称:avogadro，代码行数:53，代码来源:readfilethread_p.cpp


示例7: paint

  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();
  }
开发者ID:timvdm，项目名称:Molsketch，代码行数:52，代码来源:stereocenteritem.cpp


示例8: parent

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;
}
开发者ID:UnixJunkie，项目名称:align-it，代码行数:30，代码来源:hAccFuncCalc.cpp


示例9: newMol

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;
}
开发者ID:UnixJunkie，项目名称:stripper，代码行数:31，代码来源:schuffenhauer.cpp


示例10: bo

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);
   }
}
开发者ID:UnixJunkie，项目名称:filter-it，代码行数:45，代码来源:fingerprint.cpp


示例11: 

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);
         }
      }
   }
}
开发者ID:UnixJunkie，项目名称:align-it，代码行数:28，代码来源:hAccFuncCalc.cpp


示例12: GetPathAndIdentBond

    //--
    // [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;
    }
开发者ID:mbostwick，项目名称:semanticwebopenbabel，代码行数:20，代码来源:RelationBond.cpp


示例13: rings

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;
   }
}
开发者ID:UnixJunkie，项目名称:filter-it，代码行数:44，代码来源:filterAtomsInLargestNonaromaticRing.cpp


示例14: GetObjectPropertyPathAndIdentBond

    // [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;
    }
开发者ID:mbostwick，项目名称:semanticwebopenbabel，代码行数:20，代码来源:RelationBond.cpp


示例15: n

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;
}
开发者ID:UnixJunkie，项目名称:stripper，代码行数:24，代码来源:schuffenhauer.cpp


示例16: 

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);
         }
      }
   }
}
开发者ID:UnixJunkie，项目名称:pharao，代码行数:24，代码来源:hDonFuncCalc.cpp


示例17: extract_thermo

static int extract_thermo(OpenBabel::OBMol *mol,string method,double temperature,
                          double ezpe,double Hcorr,double Gcorr,double E0,double CV,
                          int RotSymNum,std::vector<double> Scomponents)
{
    // Initiate correction database
    OpenBabel::OBAtomicHeatOfFormationTable *ahof = new OpenBabel::OBAtomicHeatOfFormationTable();
    OpenBabel::OBAtomIterator OBai;
    OpenBabel::OBAtom *OBa;
    OpenBabel::OBElementTable *OBet;
    char valbuf[128];
    int ii,atomid,atomicnumber,found,foundall;
    double dhofM0, dhofMT, S0MT, DeltaSMT;
    double eFactor = HARTEE_TO_KCALPERMOL;

    OBet = new OpenBabel::OBElementTable();

    // Now loop over atoms in order to correct the Delta H formation
    OBai     = mol->BeginAtoms();
    atomid   = 0;
    foundall = 0;
    dhofM0   = E0*eFactor;
    dhofMT   = dhofM0+(Hcorr-ezpe)*eFactor;
    S0MT     = 0;
    if (temperature > 0)
    {
        // Multiply by 1000 to make the unit cal/mol K
        S0MT += 1000*eFactor*(Hcorr-Gcorr)/temperature;
    }

    // Check for symmetry
    OBPointGroup obPG;

    obPG.Setup(mol);
    const char *pg = obPG.IdentifyPointGroup();

    double Rgas = 1.9872041; // cal/mol K http://en.wikipedia.org/wiki/Gas_constant
    double Srot = -Rgas * log(RotSymNum);

    //printf("DHf(M,0) = %g, DHf(M,T) = %g, S0(M,T) = %g\nPoint group = %s RotSymNum = %d Srot = %g\n",
    //       dhofM0, dhofMT, S0MT, pg, RotSymNum, Srot);
    if (RotSymNum > 1)
    {
        // We assume Gaussian has done this correctly!
        Srot = 0;
    }
    S0MT     += Srot;
    DeltaSMT  = S0MT;

    for (OBa = mol->BeginAtom(OBai); (NULL != OBa); OBa = mol->NextAtom(OBai))
    {
        double dhfx0, dhfxT, S0xT;
        atomicnumber = OBa->GetAtomicNum();
        found = ahof->GetHeatOfFormation(OBet->GetSymbol(atomicnumber),
                                         0,
                                         method,
                                         temperature,
                                         &dhfx0, &dhfxT, &S0xT);
        if (1 == found)
        {
            dhofM0 += dhfx0;
            dhofMT += dhfxT;
            DeltaSMT += S0xT;
            foundall ++;
        }
        atomid++;
    }
    if (foundall == atomid)
    {
        std::string attr[5];
        double result[5];
        char buf[32];

        attr[0].assign("DeltaHform(0K)");
        result[0] = dhofM0;
        snprintf(buf, sizeof(buf), "DeltaHform(%gK)", temperature);
        attr[1].assign(buf);
        result[1] = dhofMT;
        snprintf(buf, sizeof(buf), "DeltaSform(%gK)", temperature);
        attr[2].assign(buf);
        result[2] = DeltaSMT;
        snprintf(buf, sizeof(buf), "DeltaGform(%gK)", temperature);
        attr[3].assign(buf);
        result[3] = dhofMT - temperature*result[2]/1000;
        snprintf(buf, sizeof(buf), "S0(%gK)", temperature);
        attr[4].assign(buf);
        result[4] = S0MT;

        add_unique_pairdata_to_mol(mol, "method", method, 0);
        for(ii=0; (ii<5); ii++)
        {
            // Add to molecule properties
            sprintf(valbuf,"%f", result[ii]);
            add_unique_pairdata_to_mol(mol, attr[ii], valbuf, 0);
        }
        sprintf(valbuf, "%f", CV);
        add_unique_pairdata_to_mol(mol, "cv", valbuf, 0);
        sprintf(valbuf, "%f", CV+Rgas);
        add_unique_pairdata_to_mol(mol, "cp", valbuf, 0);
        // Entropy components
        if (Scomponents.size() == 3)
//.........这里部分代码省略.........
开发者ID:dspoel，项目名称:openbabel，代码行数:101，代码来源:gaussformat.cpp


示例18: allrings

OpenBabel::OBMol
Schuffenhauer::Rule_4(OpenBabel::OBMol& oldMol)
{
   	std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
   	if (allrings.size() <= _ringsToBeRetained)
   	{
      	return oldMol;
   	}

	// Only focus on ringsystems with more than one ring
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	std::vector<OpenBabel::OBMol> mols;
   	OpenBabel::OBAtom* atom;
	std::vector<int> fusedRings;
	for (unsigned int i(0); i < allrings.size(); ++i)
	{
   		for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
		{
			if (allrings[i]->IsMember(atom) && (atom->MemberOfRingCount() > 1))
			{
				fusedRings.push_back(i);
		     	mols.push_back(oldMol);
				break;
			}
		}
	}
	if (fusedRings.empty())
	{
		return oldMol;
	}
  
   	std::vector<OpenBabel::OBMol> validMols;
   	for (unsigned int i(0); i < fusedRings.size(); ++i)
   	{
     	mols[i] = RemoveRing(mols[i], allrings, fusedRings[i]);
      	if (!mols[i].Empty())
      	{
         	validMols.push_back(mols[i]);
      	}
   	}
    	if (validMols.empty())
   	{
		return oldMol;
	}
    
	int delta;
	int absdelta;
	std::vector<int> score;
	for (unsigned int i(0); i < validMols.size(); ++i)
	{
		delta = CalculateDelta(validMols[i]);
		absdelta = abs(delta);
		score.push_back(1000 * absdelta + delta);
	}
	int maximum = score[0];
	for (unsigned int i(1); i < validMols.size(); ++i)
	{
		if (score[i] > maximum)
		{
			maximum = score[i];
		}
	}
	unsigned int oldMolecules = validMols.size();
	std::vector<OpenBabel::OBMol> remainingMols;
	for (unsigned int i(0); i < validMols.size(); ++i)
	{
		if (score[i] == maximum)
		{
			remainingMols.push_back(validMols[i]);
		}
	}
	if (remainingMols.size() == 1)
	{
		return remainingMols[0];
    }
   
   	return oldMol;
}
开发者ID:UnixJunkie，项目名称:stripper，代码行数:78，代码来源:schuffenhauer.cpp


示例19: m

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))
         	{
//.........这里部分代码省略.........
开发者ID:UnixJunkie，项目名称:stripper，代码行数:101，代码来源:oprea_2.cpp


示例20: if

bool
_hAccDelocalized(OpenBabel::OBAtom* a)
{
   if (a->GetAtomicNum() != 7)
   {
      return false;
   }
   if (a->IsAromatic() && a->GetImplicitValence() == 3)
   {
      return true;
   }
  
   std::vector<OpenBabel::OBBond*>::iterator bi1;
   for (OpenBabel::OBBond* b1 = a->BeginBond(bi1); b1; b1 = a->NextBond(bi1))
   {
      OpenBabel::OBAtom* aa = b1->GetNbrAtom(a);
    
      if (aa->IsAromatic() && a->GetImplicitValence() == 3)
      {
         return true;
      }
    
      if (aa->GetAtomicNum() == 6)
      {
         std::vector<OpenBabel::OBBond*>::iterator bi2;
         for (OpenBabel::OBBond* b2 = aa->BeginBond(bi2); b2; b2 = aa->NextBond(bi2))
         {
            OpenBabel::OBAtom* aaa = b2->GetNbrAtom(aa);
            
            if (aaa == a)
            {
               continue;
            }
            if (b2->GetBO() == 2)
            {
               if (aaa->GetAtomicNum() == 8)  return true;
               if (aaa->GetAtomicNum() == 7)  return true;
               if (aaa->GetAtomicNum() == 16) return true;
            }
         }
      }
      else if (aa->GetAtomicNum() == 16)
      {
         std::vector<OpenBabel::OBBond*>::iterator bi2;
         for (OpenBabel::OBBond* b2 = aa->BeginBond(bi2); b2; b2 = aa->NextBond(bi2))
         {
            OpenBabel::OBAtom* aaa = b2->GetNbrAtom(aa);
            
            if (aaa == a)
            {
               continue;
            }
            if ((b2->GetBO() == 2) && (aaa->GetAtomicNum() == 8))
            {
               return true;
            }
         }
      }
   }
   return false;
}
开发者ID:UnixJunkie，项目名称:align-it，代码行数:61，代码来源:hAccFuncCalc.cpp



注：本文中的openbabel::OBAtom类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。

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