public virtual IAtomContainer getSpanningTree()
{
IAtomContainer ac = molecule.Builder.newAtomContainer();
for (int a = 0; a < V; a++)
{
ac.addAtom(molecule.getAtomAt(a));
}
for (int b = 0; b < E; b++)
{
if (bondsInTree[b])
{
ac.addBond(molecule.getBondAt(b));
}
}
return(ac);
}
/// <summary> Kruskal algorithm</summary>
/// <param name="atomContainer">
/// </param>
public virtual void buildSpanningTree(IAtomContainer atomContainer)
{
disconnected = false;
molecule = atomContainer;
V = atomContainer.AtomCount;
E = atomContainer.getBondCount();
sptSize = 0; edrSize = 0;
fastFindInit(V);
for (int i = 0; i < V; i++)
{
(atomContainer.getAtomAt(i)).setProperty("ST_ATOMNO", System.Convert.ToString(i + 1));
}
IBond bond;
int v1, v2;
bondsInTree = new bool[E];
for (int b = 0; b < E; b++)
{
bondsInTree[b] = false;
bond = atomContainer.getBondAt(b);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
v1 = System.Int32.Parse((bond.getAtomAt(0)).getProperty("ST_ATOMNO").ToString());
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
v2 = System.Int32.Parse((bond.getAtomAt(1)).getProperty("ST_ATOMNO").ToString());
//this below is a little bit slower
//v1 = atomContainer.getAtomNumber(bond.getAtomAt(0))+1;
//v2 = atomContainer.getAtomNumber(bond.getAtomAt(1))+1;
if (fastfind(v1, v2, true))
{
bondsInTree[b] = true;
sptSize++;
//System.out.println("ST : includes bond between atoms "+v1+","+v2);
}
if (sptSize >= (V - 1))
break;
}
// if atomcontainer is connected then the number of bonds in the spanning tree = (No atoms-1)
//i.e. edgesRings = new Bond[E-V+1];
//but to hold all bonds if atomContainer was disconnected then edgesRings = new Bond[E-sptSize];
if (sptSize != (V - 1))
disconnected = true;
for (int b = 0; b < E; b++)
if (!bondsInTree[b])
{
// edgesRings[edrSize] = atomContainer.getBondAt(b);
edrSize++;
}
cb = new int[edrSize][];
for (int i2 = 0; i2 < edrSize; i2++)
{
cb[i2] = new int[E];
}
for (int i = 0; i < edrSize; i++)
for (int a = 0; a < E; a++)
cb[i][a] = 0;
}
/// <summary> Checks some simple heuristics for whether the subgraph query can
/// realistically be a subgraph of the supergraph. If, for example, the
/// number of nitrogen atoms in the query is larger than that of the supergraph
/// it cannot be part of it.
///
/// </summary>
/// <param name="ac1"> the supergraph to be checked
/// </param>
/// <param name="ac2"> the subgraph to be tested for
/// </param>
/// <returns> true if the subgraph ac2 has a chance to be a subgraph of ac1
///
/// </returns>
private static bool testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
{
int ac1SingleBondCount = 0;
int ac1DoubleBondCount = 0;
int ac1TripleBondCount = 0;
int ac1AromaticBondCount = 0;
int ac2SingleBondCount = 0;
int ac2DoubleBondCount = 0;
int ac2TripleBondCount = 0;
int ac2AromaticBondCount = 0;
int ac1SCount = 0;
int ac1OCount = 0;
int ac1NCount = 0;
int ac1FCount = 0;
int ac1ClCount = 0;
int ac1BrCount = 0;
int ac1ICount = 0;
int ac1CCount = 0;
int ac2SCount = 0;
int ac2OCount = 0;
int ac2NCount = 0;
int ac2FCount = 0;
int ac2ClCount = 0;
int ac2BrCount = 0;
int ac2ICount = 0;
int ac2CCount = 0;
IBond bond;
IAtom atom;
for (int i = 0; i < ac1.getBondCount(); i++)
{
bond = ac1.getBondAt(i);
if (bond.getFlag(CDKConstants.ISAROMATIC))
{
ac1AromaticBondCount++;
}
else if (bond.Order == 1)
{
ac1SingleBondCount++;
}
else if (bond.Order == 2)
{
ac1DoubleBondCount++;
}
else if (bond.Order == 3)
{
ac1TripleBondCount++;
}
}
for (int i = 0; i < ac2.getBondCount(); i++)
{
bond = ac2.getBondAt(i);
if (bond is IQueryBond)
{
continue;
}
if (bond.getFlag(CDKConstants.ISAROMATIC))
{
ac2AromaticBondCount++;
}
else if (bond.Order == 1)
{
ac2SingleBondCount++;
}
else if (bond.Order == 2)
{
ac2DoubleBondCount++;
}
else if (bond.Order == 3)
{
ac2TripleBondCount++;
}
}
if (ac2SingleBondCount > ac1SingleBondCount)
{
return(false);
}
if (ac2AromaticBondCount > ac1AromaticBondCount)
{
return(false);
}
if (ac2DoubleBondCount > ac1DoubleBondCount)
{
return(false);
}
if (ac2TripleBondCount > ac1TripleBondCount)
{
return(false);
}
for (int i = 0; i < ac1.AtomCount; i++)
{
atom = ac1.getAtomAt(i);
if (atom.Symbol.Equals("S"))
{
ac1SCount++;
}
else if (atom.Symbol.Equals("N"))
{
ac1NCount++;
}
else if (atom.Symbol.Equals("O"))
{
ac1OCount++;
}
else if (atom.Symbol.Equals("F"))
{
ac1FCount++;
}
else if (atom.Symbol.Equals("Cl"))
{
ac1ClCount++;
}
else if (atom.Symbol.Equals("Br"))
{
ac1BrCount++;
}
else if (atom.Symbol.Equals("I"))
{
ac1ICount++;
}
else if (atom.Symbol.Equals("C"))
{
ac1CCount++;
}
}
for (int i = 0; i < ac2.AtomCount; i++)
{
atom = ac2.getAtomAt(i);
if (atom is IQueryAtom)
{
continue;
}
if (atom.Symbol.Equals("S"))
{
ac2SCount++;
}
else if (atom.Symbol.Equals("N"))
{
ac2NCount++;
}
else if (atom.Symbol.Equals("O"))
{
ac2OCount++;
}
else if (atom.Symbol.Equals("F"))
{
ac2FCount++;
}
else if (atom.Symbol.Equals("Cl"))
{
ac2ClCount++;
}
else if (atom.Symbol.Equals("Br"))
{
ac2BrCount++;
}
else if (atom.Symbol.Equals("I"))
{
ac2ICount++;
}
else if (atom.Symbol.Equals("C"))
{
ac2CCount++;
}
}
if (ac1SCount < ac2SCount)
{
return(false);
}
if (ac1NCount < ac2NCount)
{
return(false);
}
if (ac1OCount < ac2OCount)
{
return(false);
}
if (ac1FCount < ac2FCount)
{
return(false);
}
if (ac1ClCount < ac2ClCount)
{
return(false);
}
if (ac1BrCount < ac2BrCount)
{
return(false);
}
if (ac1ICount < ac2ICount)
{
return(false);
}
if (ac1CCount < ac2CCount)
{
return(false);
}
return(true);
}
/// <summary> Kruskal algorithm</summary>
/// <param name="atomContainer">
/// </param>
public virtual void buildSpanningTree(IAtomContainer atomContainer)
{
disconnected = false;
molecule = atomContainer;
V = atomContainer.AtomCount;
E = atomContainer.getBondCount();
sptSize = 0; edrSize = 0;
fastFindInit(V);
for (int i = 0; i < V; i++)
{
(atomContainer.getAtomAt(i)).setProperty("ST_ATOMNO", System.Convert.ToString(i + 1));
}
IBond bond;
int v1, v2;
bondsInTree = new bool[E];
for (int b = 0; b < E; b++)
{
bondsInTree[b] = false;
bond = atomContainer.getBondAt(b);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
v1 = System.Int32.Parse((bond.getAtomAt(0)).getProperty("ST_ATOMNO").ToString());
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
v2 = System.Int32.Parse((bond.getAtomAt(1)).getProperty("ST_ATOMNO").ToString());
//this below is a little bit slower
//v1 = atomContainer.getAtomNumber(bond.getAtomAt(0))+1;
//v2 = atomContainer.getAtomNumber(bond.getAtomAt(1))+1;
if (fastfind(v1, v2, true))
{
bondsInTree[b] = true;
sptSize++;
//System.out.println("ST : includes bond between atoms "+v1+","+v2);
}
if (sptSize >= (V - 1))
{
break;
}
}
// if atomcontainer is connected then the number of bonds in the spanning tree = (No atoms-1)
//i.e. edgesRings = new Bond[E-V+1];
//but to hold all bonds if atomContainer was disconnected then edgesRings = new Bond[E-sptSize];
if (sptSize != (V - 1))
{
disconnected = true;
}
for (int b = 0; b < E; b++)
{
if (!bondsInTree[b])
{
// edgesRings[edrSize] = atomContainer.getBondAt(b);
edrSize++;
}
}
cb = new int[edrSize][];
for (int i2 = 0; i2 < edrSize; i2++)
{
cb[i2] = new int[E];
}
for (int i = 0; i < edrSize; i++)
{
for (int a = 0; a < E; a++)
{
cb[i][a] = 0;
}
}
}
/// <summary> Checks some simple heuristics for whether the subgraph query can
/// realistically be a subgraph of the supergraph. If, for example, the
/// number of nitrogen atoms in the query is larger than that of the supergraph
/// it cannot be part of it.
///
/// </summary>
/// <param name="ac1"> the supergraph to be checked
/// </param>
/// <param name="ac2"> the subgraph to be tested for
/// </param>
/// <returns> true if the subgraph ac2 has a chance to be a subgraph of ac1
///
/// </returns>
private static bool testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
{
int ac1SingleBondCount = 0;
int ac1DoubleBondCount = 0;
int ac1TripleBondCount = 0;
int ac1AromaticBondCount = 0;
int ac2SingleBondCount = 0;
int ac2DoubleBondCount = 0;
int ac2TripleBondCount = 0;
int ac2AromaticBondCount = 0;
int ac1SCount = 0;
int ac1OCount = 0;
int ac1NCount = 0;
int ac1FCount = 0;
int ac1ClCount = 0;
int ac1BrCount = 0;
int ac1ICount = 0;
int ac1CCount = 0;
int ac2SCount = 0;
int ac2OCount = 0;
int ac2NCount = 0;
int ac2FCount = 0;
int ac2ClCount = 0;
int ac2BrCount = 0;
int ac2ICount = 0;
int ac2CCount = 0;
IBond bond;
IAtom atom;
for (int i = 0; i < ac1.getBondCount(); i++)
{
bond = ac1.getBondAt(i);
if (bond.getFlag(CDKConstants.ISAROMATIC))
ac1AromaticBondCount++;
else if (bond.Order == 1)
ac1SingleBondCount++;
else if (bond.Order == 2)
ac1DoubleBondCount++;
else if (bond.Order == 3)
ac1TripleBondCount++;
}
for (int i = 0; i < ac2.getBondCount(); i++)
{
bond = ac2.getBondAt(i);
if (bond is IQueryBond)
continue;
if (bond.getFlag(CDKConstants.ISAROMATIC))
ac2AromaticBondCount++;
else if (bond.Order == 1)
ac2SingleBondCount++;
else if (bond.Order == 2)
ac2DoubleBondCount++;
else if (bond.Order == 3)
ac2TripleBondCount++;
}
if (ac2SingleBondCount > ac1SingleBondCount)
return false;
if (ac2AromaticBondCount > ac1AromaticBondCount)
return false;
if (ac2DoubleBondCount > ac1DoubleBondCount)
return false;
if (ac2TripleBondCount > ac1TripleBondCount)
return false;
for (int i = 0; i < ac1.AtomCount; i++)
{
atom = ac1.getAtomAt(i);
if (atom.Symbol.Equals("S"))
ac1SCount++;
else if (atom.Symbol.Equals("N"))
ac1NCount++;
else if (atom.Symbol.Equals("O"))
ac1OCount++;
else if (atom.Symbol.Equals("F"))
ac1FCount++;
else if (atom.Symbol.Equals("Cl"))
ac1ClCount++;
else if (atom.Symbol.Equals("Br"))
ac1BrCount++;
else if (atom.Symbol.Equals("I"))
ac1ICount++;
else if (atom.Symbol.Equals("C"))
ac1CCount++;
}
for (int i = 0; i < ac2.AtomCount; i++)
{
atom = ac2.getAtomAt(i);
if (atom is IQueryAtom)
continue;
if (atom.Symbol.Equals("S"))
ac2SCount++;
else if (atom.Symbol.Equals("N"))
ac2NCount++;
else if (atom.Symbol.Equals("O"))
ac2OCount++;
else if (atom.Symbol.Equals("F"))
ac2FCount++;
else if (atom.Symbol.Equals("Cl"))
ac2ClCount++;
else if (atom.Symbol.Equals("Br"))
ac2BrCount++;
else if (atom.Symbol.Equals("I"))
ac2ICount++;
else if (atom.Symbol.Equals("C"))
ac2CCount++;
}
if (ac1SCount < ac2SCount)
return false;
if (ac1NCount < ac2NCount)
return false;
if (ac1OCount < ac2OCount)
return false;
if (ac1FCount < ac2FCount)
return false;
if (ac1ClCount < ac2ClCount)
return false;
if (ac1BrCount < ac2BrCount)
return false;
if (ac1ICount < ac2ICount)
return false;
if (ac1CCount < ac2CCount)
return false;
return true;
}
/// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
/// The new molecule is a deep copy.
///
/// </summary>
/// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
/// </param>
/// <returns> The molecule without Hs.
/// </returns>
/// <cdk.keyword> hydrogen, removal </cdk.keyword>
public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.
// Clone atoms except those to be removed.
IMolecule mol = atomContainer.Builder.newMolecule();
int count = atomContainer.AtomCount;
for (int i = 0; i < count; i++)
{
// Clone/remove this atom?
IAtom atom = atomContainer.getAtomAt(i);
if (!atom.Symbol.Equals("H"))
{
IAtom clonedAtom = null;
try
{
clonedAtom = (IAtom)atom.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clonedAtom.setHydrogenCount(0);
mol.addAtom(clonedAtom);
map[atom] = clonedAtom;
}
else
{
remove.Add(atom); // maintain list of removed H.
}
}
// Clone bonds except those involving removed atoms.
count = atomContainer.getBondCount();
for (int i = 0; i < count; i++)
{
// Check bond.
//UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
IBond bond = atomContainer.getBondAt(i);
IAtom[] atoms = bond.getAtoms();
bool removedBond = false;
//UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
int length = atoms.Length;
for (int k = 0; k < length; k++)
{
if (remove.Contains(atoms[k]))
{
removedBond = true;
break;
}
}
// Clone/remove this bond?
if (!removedBond)
// if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
{
IBond clone = null;
try
{
clone = (IBond)atomContainer.getBondAt(i).Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
mol.addBond(clone);
}
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext();)
{
// Process neighbours.
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext();)
{
//UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
IAtom neighb = (IAtom)map[n.Current];
neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
}
}
mol.Properties = atomContainer.Properties;
mol.Flags = atomContainer.Flags;
return(mol);
}
/// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
/// The new molecule is a deep copy.
///
/// </summary>
/// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
/// </param>
/// <returns> The molecule without Hs.
/// </returns>
/// <cdk.keyword> hydrogen, removal </cdk.keyword>
public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.
// Clone atoms except those to be removed.
IMolecule mol = atomContainer.Builder.newMolecule();
int count = atomContainer.AtomCount;
for (int i = 0; i < count; i++)
{
// Clone/remove this atom?
IAtom atom = atomContainer.getAtomAt(i);
if (!atom.Symbol.Equals("H"))
{
IAtom clonedAtom = null;
try
{
clonedAtom = (IAtom)atom.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clonedAtom.setHydrogenCount(0);
mol.addAtom(clonedAtom);
map[atom] = clonedAtom;
}
else
{
remove.Add(atom); // maintain list of removed H.
}
}
// Clone bonds except those involving removed atoms.
count = atomContainer.getBondCount();
for (int i = 0; i < count; i++)
{
// Check bond.
//UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
IBond bond = atomContainer.getBondAt(i);
IAtom[] atoms = bond.getAtoms();
bool removedBond = false;
//UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
int length = atoms.Length;
for (int k = 0; k < length; k++)
{
if (remove.Contains(atoms[k]))
{
removedBond = true;
break;
}
}
// Clone/remove this bond?
if (!removedBond)
// if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
{
IBond clone = null;
try
{
clone = (IBond)atomContainer.getBondAt(i).Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
mol.addBond(clone);
}
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext(); )
{
// Process neighbours.
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext(); )
{
//UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
IAtom neighb = (IAtom)map[n.Current];
neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
}
}
mol.Properties = atomContainer.Properties;
mol.Flags = atomContainer.Flags;
return (mol);
}