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C++ OBAtom::GetValence方法代码示例

本文整理汇总了C++中openbabel::OBAtom::GetValence方法的典型用法代码示例。如果您正苦于以下问题：C++ OBAtom::GetValence方法的具体用法？C++ OBAtom::GetValence怎么用？C++ OBAtom::GetValence使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类openbabel::OBAtom的用法示例。


在下文中一共展示了OBAtom::GetValence方法的6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，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: 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2: m

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;
}
开发者ID:UnixJunkie，项目名称:stripper，代码行数:98，代码来源:oprea_1.cpp

示例3: m


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

示例4: rings

void
FilterBridgeFraction::Calculate(OpenBabel::OBMol* mol)
{
   // Are there 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();
      unsigned int natoms(m.NumAtoms());
      if (!natoms)
      {
         _result = 0.0;
         _passed = false;
         return;
      }
   
      // 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;
               }
            }
         }
      }

      // Now remove all ring atoms
      rings = true;
      while (rings && m.NumAtoms())
      {
         rings = false;
         for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
         {
            if (atom->IsInRing())
            {
               if (m.DeleteAtom(atom))
               {
                  rings = true;
                  break;
               }
            }
         }
      }
   
      _result = (double) m.NumAtoms() / (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:82，代码来源:filterBridgeFraction.cpp

示例5: rings

void
FilterAtomsInSmallestBridge::Calculate(OpenBabel::OBMol* mol)
{
   // Are there 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;
               }
            }
         }
      }

      // Now remove all ring atoms
      rings = true;
      while (rings && m.NumAtoms())
      {
         rings = false;
         for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
         {
            if (atom->IsInRing())
            {
               if (m.DeleteAtom(atom))
               {
                  rings = true;
                  break;
               }
            }
         }
      }
   
      // Separate into fragments
      if (m.NumAtoms())
      {
         std::vector<std::vector<int> > bridges;
         m.ContigFragList(bridges);
         _result = bridges[0].size();
         for (unsigned int i(1); i < bridges.size(); ++i)
         {
            if (bridges[i].size() < _result) _result = bridges[i].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:sieve，代码行数:86，代码来源:filterAtomsInSmallestBridge.cpp

示例6: notaromatic

OpenBabel::OBMol
Schuffenhauer::Rule_11(OpenBabel::OBMol& oldMol)
{
   	// Return if the molecule contains an acyclic linker
   	std::vector<OpenBabel::OBAtom*>::iterator avi;
   	OpenBabel::OBAtom* atom;
   	for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
   	{
      	if (!atom->IsInRing() && atom->GetValence() >= 2)
      	{
         	return oldMol;
      	}
   	}
   
   	// Make sure we are dealing with a mixed aromatic/nonaromatic system
   	bool notaromatic(false);
   	bool aromatic(false);
   	for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
   	{
      	if (atom->IsAromatic())
      	{
         	aromatic = true;
      	}
      	else
      	{
         	notaromatic = true;
      	}
   	}
   	if (aromatic && notaromatic)
   	{
      	std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
     	if (allrings.size() <= _ringsToBeRetained)
      	{
         	return oldMol;
      	}
      
      	std::vector<OpenBabel::OBMol> mols;
      	std::vector<unsigned int> aromaticRings;
      	for (unsigned int i(0); i < allrings.size(); ++i)
      	{
         	if (allrings[i]->IsAromatic())
         	{
            	mols.push_back(oldMol);
            	aromaticRings.push_back(i);
         	}
      	}
   
      	std::vector<OpenBabel::OBMol> validMols;
      	for (unsigned int i(0); i < aromaticRings.size(); ++i)
      	{
         	mols[i] = RemoveRing(mols[i], allrings, aromaticRings[i]);
         	if (!mols[i].Empty())
         	{
            	validMols.push_back(mols[i]);
         	}
      	}

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

   	return oldMol;
}
开发者ID:UnixJunkie，项目名称:stripper，代码行数:65，代码来源:schuffenhauer.cpp


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