/// <summary> Makes an array containing the morgan numbers of the atoms of atomContainer.
///
/// </summary>
/// <param name="atomContainer"> The atomContainer to analyse.
/// </param>
/// <returns> The morgan numbers value.
/// </returns>
public static int[] getMorganNumbers(IAtomContainer atomContainer)
{
int[] morganMatrix;
int[] tempMorganMatrix;
int N = atomContainer.AtomCount;
morganMatrix = new int[N];
tempMorganMatrix = new int[N];
IAtom[] atoms = null;
for (int f = 0; f < N; f++)
{
morganMatrix[f] = atomContainer.getBondCount(f);
tempMorganMatrix[f] = atomContainer.getBondCount(f);
}
for (int e = 0; e < N; e++)
{
for (int f = 0; f < N; f++)
{
morganMatrix[f] = 0;
atoms = atomContainer.getConnectedAtoms(atomContainer.getAtomAt(f));
for (int g = 0; g < atoms.Length; g++)
{
morganMatrix[f] += tempMorganMatrix[atomContainer.getAtomNumber(atoms[g])];
}
}
Array.Copy(morganMatrix, 0, tempMorganMatrix, 0, N);
}
return tempMorganMatrix;
}
public virtual void saturateRingSystems(IAtomContainer atomContainer)
{
IRingSet rs = new SSSRFinder(atomContainer.Builder.newMolecule(atomContainer)).findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(rs);
IAtomContainer ac = null;
IAtom atom = null;
int[] temp;
for (int f = 0; f < ringSets.Count; f++)
{
rs = (IRingSet)ringSets[f];
ac = RingSetManipulator.getAllInOneContainer(rs);
temp = new int[ac.AtomCount];
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
temp[g] = atom.getHydrogenCount();
atom.setHydrogenCount(atomContainer.getBondCount(atom) - ac.getBondCount(atom) - temp[g]);
}
saturate(ac);
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
atom.setHydrogenCount(temp[g]);
}
}
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="ac"> The AtomContainer to be searched
/// </param>
/// <param name="pathes"> A vectoring storing all the pathes
/// </param>
/// <param name="ringSet"> A ringset to be extended while we search
/// </param>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
private void doSearch(IAtomContainer ac, System.Collections.ArrayList pathes, IRingSet ringSet)
{
IAtom atom = null;
/*
* First we convert the molecular graph into a a path graph by
* creating a set of two membered pathes from all the bonds in the molecule
*/
initPathGraph(ac, pathes);
if (debug)
{
System.Console.Out.WriteLine("BondCount: " + ac.getBondCount() + ", PathCount: " + pathes.Count);
}
do
{
atom = selectAtom(ac);
if (atom != null)
{
remove(atom, ac, pathes, ringSet);
}
}while (pathes.Count > 0 && atom != null);
if (debug)
{
System.Console.Out.WriteLine("pathes.size(): " + pathes.Count);
}
if (debug)
{
System.Console.Out.WriteLine("ringSet.size(): " + ringSet.AtomContainerCount);
}
}
/// <summary>
/// Count bonds connecting two heavy atoms
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static int GetHeavyBondCount(IAtomContainer mol)
{
int hbCnt = 0;
for (int bi = 0; bi < mol.getBondCount(); bi++)
{
IBond b = mol.getBond(bi);
if (b.getAtomCount() != 2)
{
continue;
}
IAtom a = b.getAtom(0); // first atom
if (a.getAtomicNumber().intValue() == 1 || // do not count hydrogens
a.getSymbol().Equals("H"))
{
a = b.getAtom(1); // second atom
}
if (a.getAtomicNumber().intValue() == 1 || // do not count hydrogens
a.getSymbol().Equals("H"))
{
continue;
}
hbCnt++;
}
return(hbCnt);
}
/// <summary>
/// Remove the following features from a molecule
/// - Atom non-standard mass
/// - Stereo chemistry
/// - explicit hydrogens
/// </summary>
/// <param name="src"></param>
/// <returns>Modified mol</returns>
public static IAtomContainer RemoveIsotopesStereoExplicitHydrogens(
IAtomContainer src)
{
IAtom[] atoms = new IAtom[src.getAtomCount()];
IBond[] bonds = new IBond[src.getBondCount()];
IChemObjectBuilder builder = src.getBuilder();
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = src.getAtom(i);
IAtom atom2 = (IAtom)builder.newInstance(typeof(IAtom), atom.getSymbol());
SetImplicitHydrogenCount(atom2, GetImplicitHydrogenCount(atom));
atom2.setPoint2d(atom.getPoint2d());
atoms[i] = atom2;
}
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = src.getBond(i);
int u = src.getAtomNumber(bond.getAtom(0));
int v = src.getAtomNumber(bond.getAtom(1));
IBond bond2 = (IBond)builder.newInstance(typeof(IBond), atoms[u], atoms[v]);
bond2.setIsAromatic(bond.isAromatic());
bond2.setIsInRing(bond.isInRing());
bond2.setOrder(bond.getOrder());
bond2.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
bond2.setFlag(CDKConstants.SINGLE_OR_DOUBLE, bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE));
bonds[i] = bond2;
}
IAtomContainer dest = (IAtomContainer)builder.newInstance(typeof(IAtomContainer));
dest.setAtoms(atoms);
dest.setBonds(bonds);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(dest);
dest = AtomContainerManipulator.suppressHydrogens(dest);
GetHydrogenAdder().addImplicitHydrogens(dest);
return(dest);
}
/// <summary> Transforms an AtomContainer into a BitSet (which's size = number of bond
/// in the atomContainer, all the bit are set to true)
///
/// </summary>
/// <param name="ac"> AtomContainer to transform
/// </param>
/// <returns> The bitSet
/// </returns>
public static System.Collections.BitArray getBitSet(IAtomContainer ac)
{
System.Collections.BitArray bs;
int n = ac.getBondCount();
if (n != 0)
{
bs = new System.Collections.BitArray((n % 64 == 0 ? n / 64 : n / 64 + 1) * 64);
for (int i = 0; i < n; i++)
{
SupportClass.BitArraySupport.Set(bs, i);
}
}
else
{
bs = new System.Collections.BitArray(64);
}
return(bs);
}
/// <summary>
/// Creates a molecule graph for use with jgrapht.
/// Bond orders are not respected.
/// </summary>
/// <param name="molecule">the specified molecule</param>
/// <returns>a graph representing the molecule</returns>
static public SimpleGraph getMoleculeGraph(IAtomContainer molecule) {
SimpleGraph graph = new SimpleGraph();
for (int i=0; i<molecule.AtomCount; i++ ) {
IAtom atom = molecule.Atoms[i];
graph.addVertex(atom);
}
for (int i=0; i<molecule.getBondCount(); i++ ) {
IBond bond = molecule.Bonds[i];
/*
int order = (int) bond.getOrder();
for (int j=0; j<order; j++) {
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
*/
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
return graph;
}
/// <summary> Removes all external aliphatic chains by chopping them off from the
/// ends
///
/// </summary>
/// <param name="ac"> The AtomContainer to work with
/// </param>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
private void removeAliphatic(IAtomContainer ac)
{
bool removedSomething;
IAtom atom = null;
do
{
removedSomething = false;
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
for (System.Collections.IEnumerator e = ac.atoms(); e.MoveNext();)
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
atom = (IAtom)e.Current;
if (ac.getBondCount(atom) == 1)
{
ac.removeAtomAndConnectedElectronContainers(atom);
removedSomething = true;
}
}
}while (removedSomething);
}
/// <summary> Selects an optimal atom for removal
/// See {@cdk.cite HAN96} for details
///
/// </summary>
/// <param name="ac"> The AtomContainer to search
/// </param>
/// <returns> The selected Atom
/// </returns>
private IAtom selectAtom(IAtomContainer ac)
{
int minDegree = 999;
// :-)
int degree = minDegree;
IAtom minAtom = null;
IAtom atom = null;
for (int f = 0; f < ac.AtomCount; f++)
{
atom = ac.getAtomAt(f);
degree = ac.getBondCount(atom);
if (degree < minDegree)
{
minAtom = atom;
minDegree = degree;
}
}
return(minAtom);
}
/// <summary>
/// Creates a molecule graph for use with jgrapht.
/// Bond orders are not respected.
/// </summary>
/// <param name="molecule">the specified molecule</param>
/// <returns>a graph representing the molecule</returns>
static public SimpleGraph getMoleculeGraph(IAtomContainer molecule)
{
SimpleGraph graph = new SimpleGraph();
for (int i = 0; i < molecule.AtomCount; i++)
{
IAtom atom = molecule.Atoms[i];
graph.addVertex(atom);
}
for (int i = 0; i < molecule.getBondCount(); i++)
{
IBond bond = molecule.Bonds[i];
/*
* int order = (int) bond.getOrder();
* for (int j=0; j<order; j++) {
* graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
* }
*/
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
return(graph);
}
/// <summary>
/// Remove explicit and implicit hydrogens bonded to positive nitrogens
/// </summary>
/// <param name="org"></param>
/// <returns></returns>
public int RemoveHydrogensBondedToPositiveNitrogens(IAtomContainer org)
{
int chg, impHydCnt;
int implicitHydRemoved = 0;
HashSet <IAtom> atomsToRemove = new HashSet <IAtom>();
HashSet <IBond> bondsToRemove = new HashSet <IBond>();
int nOrgAtoms = org.getAtomCount();
int nOrgBonds = org.getBondCount();
// Get H atoms and their bonds to pos-charged Nitrogen, adjusting charge
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (bond.getAtomCount() != 2)
{
continue;
}
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
if (a1.getSymbol() == "H" && a2.getSymbol() == "N" && GetFormalCharge(a2) > 0)
{
chg = GetFormalCharge(a2) - 1;
SetFormalCharge(a2, chg);
atomsToRemove.Add(a1);
bondsToRemove.Add(bond);
}
else if (a2.getSymbol() == "H" && a1.getSymbol() == "N" && GetFormalCharge(a1) > 0)
{
chg = GetFormalCharge(a1) - 1;
SetFormalCharge(a1, chg);
atomsToRemove.Add(a2);
bondsToRemove.Add(bond);
}
}
// Check for implicit H attached to pos-charged N
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom a = org.getAtom(ai);
if (a.getSymbol() == "N" && GetFormalCharge(a) > 0 && GetImplicitHydrogenCount(a) > 0)
{
chg = GetFormalCharge(a) - 1;
SetFormalCharge(a, chg);
impHydCnt = GetImplicitHydrogenCount(a) - 1;
SetImplicitHydrogenCount(a, impHydCnt);
implicitHydRemoved++;
}
}
if (implicitHydRemoved > 0)
{
implicitHydRemoved = implicitHydRemoved; // debug
}
if (atomsToRemove.Count == 0)
{
return(implicitHydRemoved); // just return if no explicit H to remove
}
// Get list of atoms to keep
IAtom[] cpyAtoms = new IAtom[nOrgAtoms - atomsToRemove.Count];
int nCpyAtoms = 0;
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom atom = org.getAtom(ai);
if (!atomsToRemove.Contains(atom))
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
org.setAtoms(cpyAtoms);
// Get list of bonds to keep
IBond[] cpyBonds = new IBond[nOrgBonds - bondsToRemove.Count];
int nCpyBonds = 0;
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (!bondsToRemove.Contains(bond))
{
cpyBonds[nCpyBonds++] = bond;
}
}
org.setBonds(cpyBonds);
return(atomsToRemove.Count + implicitHydRemoved);
}
/// <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> 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);
}
public virtual void saturateRingSystems(IAtomContainer atomContainer)
{
IRingSet rs = new SSSRFinder(atomContainer.Builder.newMolecule(atomContainer)).findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(rs);
IAtomContainer ac = null;
IAtom atom = null;
int[] temp;
for (int f = 0; f < ringSets.Count; f++)
{
rs = (IRingSet) ringSets[f];
ac = RingSetManipulator.getAllInOneContainer(rs);
temp = new int[ac.AtomCount];
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
temp[g] = atom.getHydrogenCount();
atom.setHydrogenCount(atomContainer.getBondCount(atom) - ac.getBondCount(atom) - temp[g]);
}
saturate(ac);
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
atom.setHydrogenCount(temp[g]);
}
}
}
/// <summary> Removes all external aliphatic chains by chopping them off from the
/// ends
///
/// </summary>
/// <param name="ac"> The AtomContainer to work with
/// </param>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
private void removeAliphatic(IAtomContainer ac)
{
bool removedSomething;
IAtom atom = null;
do
{
removedSomething = false;
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' 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_javautilEnumerationhasMoreElements'"
for (System.Collections.IEnumerator e = ac.atoms(); e.MoveNext(); )
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' 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_javautilEnumerationnextElement'"
atom = (IAtom)e.Current;
if (ac.getBondCount(atom) == 1)
{
ac.removeAtomAndConnectedElectronContainers(atom);
removedSomething = true;
}
}
}
while (removedSomething);
}
/// <summary> Parse a branch
///
/// </summary>
/// <param name="v"> Description of Parameter
/// </param>
/// <param name="buffer"> Description of Parameter
/// </param>
/// <param name="container"> Description of Parameter
/// </param>
/// <param name="parent"> Description of Parameter
/// </param>
/// <param name="chiral"> Description of Parameter
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <param name="atomsInOrderOfSmiles"> Description of Parameter
/// </param>
private void parseChain(System.Collections.ArrayList v, System.Text.StringBuilder buffer, IAtomContainer container, IAtom parent, bool chiral, bool[] doubleBondConfiguration, System.Collections.ArrayList atomsInOrderOfSmiles)
{
int positionInVector = 0;
IAtom atom;
//System.out.println("in parse chain. Size of tree: " + v.size());
for (int h = 0; h < v.Count; h++)
{
System.Object o = v[h];
if (o is IAtom)
{
atom = (IAtom)o;
if (parent != null)
{
parseBond(buffer, atom, parent, container);
}
else
{
if (chiral && BondTools.isStereo(container, atom))
{
parent = (IAtom)((System.Collections.ArrayList)v[1])[0];
}
}
parseAtom(atom, buffer, container, chiral, doubleBondConfiguration, parent, atomsInOrderOfSmiles, v);
//System.out.println("in parseChain after parseAtom()");
/*
* The principle of making chiral smiles is quite simple, although the code is
* pretty uggly. The Atoms connected to the chiral center are put in sorted[] in the
* order they have to appear in the smiles. Then the Vector v is rearranged according
* to sorted[]
*/
if (chiral && BondTools.isStereo(container, atom) && container.getBond(parent, atom) != null)
{
//System.out.println("in parseChain in isChiral");
IAtom[] sorted = null;
System.Collections.IList chiralNeighbours = container.getConnectedAtomsVector(atom);
if (BondTools.isTetrahedral(container, atom, false) > 0)
{
sorted = new IAtom[3];
}
if (BondTools.isTetrahedral(container, atom, false) == 1)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
bool normalBindingIsLeft = false;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
if (BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom))
{
normalBindingIsLeft = true;
break;
}
}
}
}
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (normalBindingIsLeft)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
else
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 2)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[0] = atom2;
sorted[2] = atom1;
}
else
{
sorted[0] = atom1;
sorted[2] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 3)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = ohere.Length - 1; i > -1; i--)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[1] = atom2;
sorted[2] = atom1;
}
else
{
sorted[1] = atom1;
sorted[2] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 4)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = ohere.Length - 1; i > -1; i--)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
double angle1 = 0;
double angle2 = 0;
IAtom atom1 = null;
IAtom atom2 = null;
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
if (angle1 == 0)
{
angle1 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom1 = (IAtom)chiralNeighbours[i];
}
else
{
angle2 = BondTools.giveAngle(atom, parent, (IAtom)chiralNeighbours[i]);
atom2 = (IAtom)chiralNeighbours[i];
}
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
}
}
if (angle1 < angle2)
{
sorted[1] = atom2;
sorted[0] = atom1;
}
else
{
sorted[1] = atom1;
sorted[0] = atom2;
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 5)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
if (BondTools.isTetrahedral(container, atom, false) == 6)
{
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_NONE)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[2] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[1] = (IAtom)chiralNeighbours[i];
}
}
}
}
}
if (BondTools.isSquarePlanar(container, atom))
{
sorted = new IAtom[3];
//This produces a U=SP1 order in every case
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent && !isBondBroken((IAtom)chiralNeighbours[i], atom))
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0)
{
sorted = new IAtom[container.getConnectedAtoms(atom).Length - 1];
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
System.Collections.SortedList hm = new System.Collections.SortedList();
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[sorted.Length - 1] = (IAtom)chiralNeighbours[i];
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)BondTools.giveAngle(atom, parent, ((IAtom)chiralNeighbours[i]))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[sorted.Length - 1] = (IAtom)chiralNeighbours[i];
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
for (int i = 0; i < ohere.Length; i++)
{
sorted[i] = ((IAtom)chiralNeighbours[((System.Int32)ohere[i])]);
}
}
if (container.getBond(parent, atom).Stereo == 0)
{
for (int i = 0; i < chiralNeighbours.Count; i++)
{
if (chiralNeighbours[i] != parent)
{
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == 0)
{
hm[(double)(BondTools.giveAngleFromMiddle(atom, parent, ((IAtom)chiralNeighbours[i])))] = (System.Int32)i;
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_UP)
{
sorted[0] = (IAtom)chiralNeighbours[i];
}
if (container.getBond(atom, (IAtom)chiralNeighbours[i]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
sorted[sorted.Length - 2] = (IAtom)chiralNeighbours[i];
}
}
}
//UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
sorted[sorted.Length - 1] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 1])]);
if (ohere.Length == 2)
{
sorted[sorted.Length - 3] = ((IAtom)chiralNeighbours[((System.Int32)ohere[0])]);
if (BondTools.giveAngleFromMiddle(atom, parent, ((IAtom)chiralNeighbours[((System.Int32)ohere[1])])) < 0)
{
IAtom dummy = sorted[sorted.Length - 2];
sorted[sorted.Length - 2] = sorted[0];
sorted[0] = dummy;
}
}
if (ohere.Length == 3)
{
sorted[sorted.Length - 3] = sorted[sorted.Length - 2];
sorted[sorted.Length - 2] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 2])]);
sorted[sorted.Length - 4] = ((IAtom)chiralNeighbours[((System.Int32)ohere[ohere.Length - 3])]);
}
}
}
//This builds an onew[] containing the objects after the center of the chirality in the order given by sorted[]
if (sorted != null)
{
int numberOfAtoms = 3;
if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0)
{
numberOfAtoms = container.getConnectedAtoms(atom).Length - 1;
}
System.Object[] omy = new System.Object[numberOfAtoms];
System.Object[] onew = new System.Object[numberOfAtoms];
for (int k = getRingOpenings(atom, null).Count; k < numberOfAtoms; k++)
{
if (positionInVector + 1 + k - getRingOpenings(atom, null).Count < v.Count)
{
omy[k] = v[positionInVector + 1 + k - getRingOpenings(atom, null).Count];
}
}
for (int k = 0; k < sorted.Length; k++)
{
if (sorted[k] != null)
{
for (int m = 0; m < omy.Length; m++)
{
if (omy[m] is IAtom)
{
if (omy[m] == sorted[k])
{
onew[k] = omy[m];
}
}
else
{
if (omy[m] == null)
{
onew[k] = null;
}
else
{
if (((System.Collections.ArrayList)omy[m])[0] == sorted[k])
{
onew[k] = omy[m];
}
}
}
}
}
else
{
onew[k] = null;
}
}
//This is a workaround for 3624.MOL.2 I don't have a better solution currently
bool doubleentry = false;
for (int m = 0; m < onew.Length; m++)
{
for (int k = 0; k < onew.Length; k++)
{
if (m != k && onew[k] == onew[m])
{
doubleentry = true;
}
}
}
if (!doubleentry)
{
//Make sure that the first atom in onew is the first one in the original smiles order. This is important to have a canonical smiles.
if (positionInVector + 1 < v.Count)
{
System.Object atomAfterCenterInOriginalSmiles = v[positionInVector + 1];
int l = 0;
while (onew[0] != atomAfterCenterInOriginalSmiles)
{
System.Object placeholder = onew[onew.Length - 1];
for (int k = onew.Length - 2; k > -1; k--)
{
onew[k + 1] = onew[k];
}
onew[0] = placeholder;
l++;
if (l > onew.Length)
{
break;
}
}
}
//This cares about ring openings. Here the ring closure (represendted by a figure) must be the first atom. In onew the closure is null.
if (getRingOpenings(atom, null).Count > 0)
{
int l = 0;
while (onew[0] != null)
{
System.Object placeholder = onew[0];
for (int k = 1; k < onew.Length; k++)
{
onew[k - 1] = onew[k];
}
onew[onew.Length - 1] = placeholder;
l++;
if (l > onew.Length)
{
break;
}
}
}
//The last in onew is a vector: This means we need to exchange the rest of the original smiles with the rest of this vector.
if (onew[numberOfAtoms - 1] is System.Collections.ArrayList)
{
for (int i = 0; i < numberOfAtoms; i++)
{
if (onew[i] is IAtom)
{
System.Collections.ArrayList vtemp = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
vtemp.Add(onew[i]);
for (int k = positionInVector + 1 + numberOfAtoms; k < v.Count; k++)
{
vtemp.Add(v[k]);
}
onew[i] = vtemp;
for (int k = v.Count - 1; k > positionInVector + 1 + numberOfAtoms - 1; k--)
{
v.RemoveAt(k);
}
for (int k = 1; k < ((System.Collections.ArrayList)onew[numberOfAtoms - 1]).Count; k++)
{
v.Add(((System.Collections.ArrayList)onew[numberOfAtoms - 1])[k]);
}
onew[numberOfAtoms - 1] = ((System.Collections.ArrayList)onew[numberOfAtoms - 1])[0];
break;
}
}
}
//Put the onew objects in the original Vector
int k2 = 0;
for (int m = 0; m < onew.Length; m++)
{
if (onew[m] != null)
{
v[positionInVector + 1 + k2] = onew[m];
k2++;
}
}
}
}
}
parent = atom;
}
else
{
//Have Vector
//System.out.println("in parseChain after else");
bool brackets = true;
System.Collections.ArrayList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
addAtoms((System.Collections.ArrayList)o, result);
if (isRingOpening(parent, result) && container.getBondCount(parent) < 4)
{
brackets = false;
}
if (brackets)
{
buffer.Append('(');
}
parseChain((System.Collections.ArrayList)o, buffer, container, parent, chiral, doubleBondConfiguration, atomsInOrderOfSmiles);
if (brackets)
{
buffer.Append(')');
}
}
positionInVector++;
//System.out.println("in parseChain after positionVector++");
}
}
/// <summary> Build edges of the RGraphs
/// This method create the edge of the RGraph and
/// calculates the incompatibility and neighbourhood
/// relationships between RGraph nodes.
///
/// </summary>
/// <param name="gr"> the rGraph
/// </param>
/// <param name="ac1"> Description of the first molecule
/// </param>
/// <param name="ac2"> Description of the second molecule
/// </param>
private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2)
{
// each node is incompatible with himself
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
SupportClass.BitArraySupport.Set(x.Forbidden, i);
}
IBond a1;
IBond a2;
IBond b1;
IBond b2;
IBond[] bondsA1 = ac1.Bonds;
IBond[] bondsA2 = ac2.Bonds;
gr.FirstGraphSize = ac1.getBondCount();
gr.SecondGraphSize = ac2.getBondCount();
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
// two nodes are neighbours if their adjacency
// relationship in are equivalent in G1 and G2
// else they are incompatible.
for (int j = i + 1; j < gr.Graph.Count; j++)
{
if (timeout > -1 && ((System.DateTime.Now.Ticks - 621355968000000000) / 10000 - start) > timeout)
{
throw new CDKException("Timeout exceeded in getOverlaps");
}
RNode y = (RNode)gr.Graph[j];
a1 = bondsA1[((RNode)gr.Graph[i]).RMap.Id1];
a2 = bondsA2[((RNode)gr.Graph[i]).RMap.Id2];
b1 = bondsA1[((RNode)gr.Graph[j]).RMap.Id1];
b2 = bondsA2[((RNode)gr.Graph[j]).RMap.Id2];
if (a2 is IQueryBond)
{
if (a1.Equals(b1) || a2.Equals(b2) || !queryAdjacency(a1, b1, a2, b2))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
else
{
if (a1.Equals(b1) || a2.Equals(b2) || (!getCommonSymbol(a1, b1).Equals(getCommonSymbol(a2, b2))))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
}
}
}
/// <summary> Build edges of the RGraphs
/// This method create the edge of the RGraph and
/// calculates the incompatibility and neighbourhood
/// relationships between RGraph nodes.
///
/// </summary>
/// <param name="gr"> the rGraph
/// </param>
/// <param name="ac1"> Description of the first molecule
/// </param>
/// <param name="ac2"> Description of the second molecule
/// </param>
private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2)
{
// each node is incompatible with himself
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
SupportClass.BitArraySupport.Set(x.Forbidden, i);
}
IBond a1;
IBond a2;
IBond b1;
IBond b2;
IBond[] bondsA1 = ac1.Bonds;
IBond[] bondsA2 = ac2.Bonds;
gr.FirstGraphSize = ac1.getBondCount();
gr.SecondGraphSize = ac2.getBondCount();
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
// two nodes are neighbours if their adjacency
// relationship in are equivalent in G1 and G2
// else they are incompatible.
for (int j = i + 1; j < gr.Graph.Count; j++)
{
if (timeout > -1 && ((System.DateTime.Now.Ticks - 621355968000000000) / 10000 - start) > timeout)
throw new CDKException("Timeout exceeded in getOverlaps");
RNode y = (RNode)gr.Graph[j];
a1 = bondsA1[((RNode)gr.Graph[i]).RMap.Id1];
a2 = bondsA2[((RNode)gr.Graph[i]).RMap.Id2];
b1 = bondsA1[((RNode)gr.Graph[j]).RMap.Id1];
b2 = bondsA2[((RNode)gr.Graph[j]).RMap.Id2];
if (a2 is IQueryBond)
{
if (a1.Equals(b1) || a2.Equals(b2) || !queryAdjacency(a1, b1, a2, b2))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
else
{
if (a1.Equals(b1) || a2.Equals(b2) || (!getCommonSymbol(a1, b1).Equals(getCommonSymbol(a2, b2))))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
}
}
}
/// <summary> Transforms an AtomContainer into a BitSet (which's size = number of bond
/// in the atomContainer, all the bit are set to true)
///
/// </summary>
/// <param name="ac"> AtomContainer to transform
/// </param>
/// <returns> The bitSet
/// </returns>
public static System.Collections.BitArray getBitSet(IAtomContainer ac)
{
System.Collections.BitArray bs;
int n = ac.getBondCount();
if (n != 0)
{
bs = new System.Collections.BitArray((n % 64 == 0 ? n / 64 : n / 64 + 1) * 64);
for (int i = 0; i < n; i++)
{
SupportClass.BitArraySupport.Set(bs, i);
}
}
else
{
bs = new System.Collections.BitArray(64);
}
return bs;
}
/// <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);
}
/**
* Very quick and easy isomorphism check.
*
* @param molecule1 the molecule1
* @param fragsToCompare the frags to compare
*
* @return true, if successful
*/
private bool identicalAtoms(IAtomContainer molecule1, List<IAtomContainer> fragsToCompare)
{
var molFormula = MolecularFormulaTools.GetMolecularFormula(molecule1);
var molFormulaString = MolecularFormulaTools.GetString(molFormula);
for (var i = 0; i < fragsToCompare.Count; i++)
{
//no match
if (molecule1.getBondCount() != fragsToCompare[i].getBondCount() && molecule1.getAtomCount() != fragsToCompare[i].getAtomCount())
{
continue;
}
//Molecular Formula redundancy check
var molFormulaFrag = MolecularFormulaTools.GetMolecularFormula(fragsToCompare[i]);
var molFormulaFragString = MolecularFormulaTools.GetString(molFormulaFrag);
if (molFormulaString.Equals(molFormulaFragString))
{
return true;
}
}
//no match found
return false;
}
/// <summary>
/// Convert isotope labels to hilighting.
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public string ConvertIsotopeValuesToHilighting(
IAtomContainer mol)
{
bool hilight;
string molfile2 = "";
bool clearAttachmentPointLabels = true;
bool hilightAttachmentBond = true;
List <int> atomSet = new List <int>();
List <int> bondSet = new List <int>();
for (int bi = 0; bi < mol.getBondCount(); bi++)
{
IBond b = mol.getBond(bi);
if (b.getAtomCount() != 2)
{
continue;
}
IAtom a1 = b.getAtom(0);
IAtom a2 = b.getAtom(1);
if (hilightAttachmentBond)
{
hilight = (GetMassNumber(a1) != 0 && GetMassNumber(a2) != 0);
}
else
{
hilight = (GetMassNumber(a1) < 0 && GetMassNumber(a2) < 0);
}
if (hilight)
{
bondSet.Add(bi);
}
}
//String posMap = ""; // debug (note that hydrogens can get repositioned)
for (int ai = 0; ai < mol.getAtomCount(); ai++) // scan atoms for hilighting and reset isotope values
{
IAtom a = mol.getAtom(ai);
hilight = GetMassNumber(a) < 0;
if (hilight)
{
atomSet.Add(ai);
}
//posMap += ai.ToString() + ", " + a.getSymbol() + ", " + hilight + "\r\n"; // debug
int massNo = GetMassNumber(a);
if (massNo == hilightIsotopeValue)
{
a.setMassNumber(null); // set back to original value
}
else if (massNo < 0)
{
if (clearAttachmentPointLabels)
{
a.setMassNumber(null);
}
else
{
SetMassNumber(a, -massNo); // set back to positive
}
}
}
//mol = GenerateCoordinates(mol); // (should already be done)
try { molfile2 = AtomContainerToMolFileV3000(mol); }
catch (Exception ex) { ex = ex; }
if (Lex.IsUndefined(molfile2)) // couldn't convert to v3000, just return unhilighted v2000 file
{
molfile2 = AtomContainerToMolfile(mol);
return(molfile2);
}
string txt = "MDLV30/HILITE";
if (atomSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("ATOMS", atomSet);
}
if (bondSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("BONDS", bondSet);
}
txt = BuildV3000Lines(txt);
bool hasCollection = Lex.Contains(molfile2, "M V30 END COLLECTION");
if (hasCollection) // already have collection begin and end
{
txt = txt +
"M V30 END COLLECTION";
molfile2 = Lex.Replace(molfile2, "M V30 END COLLECTION", txt);
}
else // add collection begin & end
{
txt =
"M V30 BEGIN COLLECTION\n" +
txt +
"M V30 END COLLECTION\n" +
"M V30 END CTAB";
molfile2 = Lex.Replace(molfile2, "M V30 END CTAB", txt);
}
return(molfile2);
}
/// <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>
/// (Converted from Java to C# for possible later modification)
/// Suppress any explicit hydrogens in the provided container. Only hydrogens
/// that can be represented as a hydrogen count value on the atom are
/// suppressed. The container is updated and no elements are copied, please
/// use either <seealso cref="#copyAndSuppressedHydrogens"/> if you would to preserve
/// the old instance.
/// </summary>
/// <param name="org"> the container from which to remove hydrogens </param>
/// <returns> the input for convenience </returns>
/// <seealso cref= #copyAndSuppressedHydrogens </seealso>
public IAtomContainer suppressHydrogens(IAtomContainer org)
{
bool anyHydrogenPresent = false;
for (int ai = 0; ai < org.getAtomCount(); ai++)
{
IAtom atom = org.getAtom(ai);
if ("H".Equals(atom.getSymbol()))
{
anyHydrogenPresent = true;
break;
}
}
if (!anyHydrogenPresent)
{
return(org);
}
// we need fast adjacency checks (to check for suppression and
// update hydrogen counts)
int[][] graph = GraphUtil.toAdjList(org);
int nOrgAtoms = org.getAtomCount();
int nOrgBonds = org.getBondCount();
int nCpyAtoms = 0;
int nCpyBonds = 0;
ISet <IAtom> hydrogens = new HashSet <IAtom>();
IAtom[] cpyAtoms = new IAtom[nOrgAtoms];
// filter the original container atoms for those that can/can't
// be suppressed
for (int v = 0; v < nOrgAtoms; v++)
{
IAtom atom = org.getAtom(v);
if (suppressibleHydrogen(org, graph, v))
{
hydrogens.Add(atom);
incrementImplHydrogenCount(org.getAtom(graph[v][0]));
}
else
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
// none of the hydrogens could be suppressed - no changes need to be made
if (hydrogens.Count == 0)
{
return(org);
}
org.setAtoms(cpyAtoms);
// we now update the bonds - we have auxiliary variable remaining that
// bypasses the set membership checks if all suppressed bonds are found
IBond[] cpyBonds = new IBond[nOrgBonds - hydrogens.Count];
int remaining = hydrogens.Count;
for (int bi = 0; bi < org.getBondCount(); bi++)
{
IBond bond = org.getBond(bi);
if (remaining > 0 && (hydrogens.Contains(bond.getAtom(0)) || hydrogens.Contains(bond.getAtom(1))))
{
remaining--;
continue;
}
cpyBonds[nCpyBonds++] = bond;
}
// we know how many hydrogens we removed and we should have removed the
// same number of bonds otherwise the container is strange
if (nCpyBonds != cpyBonds.Length)
{
throw new System.ArgumentException("number of removed bonds was less than the number of removed hydrogens");
}
org.setBonds(cpyBonds);
return(org);
}
/// <summary> Description of the Method
///
/// </summary>
/// <param name="ac"> The AtomContainer to be searched
/// </param>
/// <param name="pathes"> A vectoring storing all the pathes
/// </param>
/// <param name="ringSet"> A ringset to be extended while we search
/// </param>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
private void doSearch(IAtomContainer ac, System.Collections.ArrayList pathes, IRingSet ringSet)
{
IAtom atom = null;
/*
* First we convert the molecular graph into a a path graph by
* creating a set of two membered pathes from all the bonds in the molecule
*/
initPathGraph(ac, pathes);
if (debug)
{
System.Console.Out.WriteLine("BondCount: " + ac.getBondCount() + ", PathCount: " + pathes.Count);
}
do
{
atom = selectAtom(ac);
if (atom != null)
{
remove(atom, ac, pathes, ringSet);
}
}
while (pathes.Count > 0 && atom != null);
if (debug)
{
System.Console.Out.WriteLine("pathes.size(): " + pathes.Count);
}
if (debug)
{
System.Console.Out.WriteLine("ringSet.size(): " + ringSet.AtomContainerCount);
}
}
/// <summary> The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
///
/// </summary>
public virtual void saturate(IAtomContainer atomContainer)
{
/* newSaturate(atomContainer);
}
public void oldSaturate(AtomContainer atomContainer) throws CDKException { */
IAtom partner = null;
IAtom atom = null;
IAtom[] partners = null;
IAtomType[] atomTypes1 = null;
IAtomType[] atomTypes2 = null;
IBond bond = null;
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
//logger.debug("symbol: ", atom.Symbol);
atomTypes1 = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes1.Length > 0)
{
//logger.debug("first atom type: ", atomTypes1[0]);
if (atomContainer.getBondCount(atom) == i)
{
if (atom.getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
return ;
if (atomContainer.getBond(partner, atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
if (atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
//logger.debug("Atom has " + atomContainer.getBondOrderSum(atom) + ", may have: " + atomTypes1[0].BondOrderSum);
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
return ;
if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
}
}
}
}
}
/// <summary> Selects an optimal atom for removal
/// See {@cdk.cite HAN96} for details
///
/// </summary>
/// <param name="ac"> The AtomContainer to search
/// </param>
/// <returns> The selected Atom
/// </returns>
private IAtom selectAtom(IAtomContainer ac)
{
int minDegree = 999;
// :-)
int degree = minDegree;
IAtom minAtom = null;
IAtom atom = null;
for (int f = 0; f < ac.AtomCount; f++)
{
atom = ac.getAtomAt(f);
degree = ac.getBondCount(atom);
if (degree < minDegree)
{
minAtom = atom;
minDegree = degree;
}
}
return minAtom;
}
/// <summary> The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
///
/// </summary>
public virtual void saturate(IAtomContainer atomContainer)
{
/* newSaturate(atomContainer);
* }
* public void oldSaturate(AtomContainer atomContainer) throws CDKException { */
IAtom partner = null;
IAtom atom = null;
IAtom[] partners = null;
IAtomType[] atomTypes1 = null;
IAtomType[] atomTypes2 = null;
IBond bond = null;
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
//logger.debug("symbol: ", atom.Symbol);
atomTypes1 = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes1.Length > 0)
{
//logger.debug("first atom type: ", atomTypes1[0]);
if (atomContainer.getBondCount(atom) == i)
{
if (atom.getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBond(partner, atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
if (atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
//logger.debug("Atom has " + atomContainer.getBondOrderSum(atom) + ", may have: " + atomTypes1[0].BondOrderSum);
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
}
}
}
}
}
