/// <summary> Checks for single atom cases before doing subgraph/isomorphism search
///
/// </summary>
/// <param name="g1"> AtomContainer to match on
/// </param>
/// <param name="g2"> AtomContainer as query
/// </param>
/// <returns> List of List of RMap objects for the Atoms (not Bonds!), null if no single atom case
/// </returns>
public static System.Collections.ArrayList checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2)
{
if (g2.AtomCount == 1)
{
System.Collections.ArrayList arrayList = new System.Collections.ArrayList();
IAtom atom = g2.getAtomAt(0);
if (atom is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom;
for (int i = 0; i < g1.AtomCount; i++)
{
if (qAtom.matches(g1.getAtomAt(i)))
{
arrayList.Add(new RMap(i, 0));
}
}
}
else
{
System.String atomSymbol = atom.Symbol;
for (int i = 0; i < g1.AtomCount; i++)
{
if (g1.getAtomAt(i).Symbol.Equals(atomSymbol))
{
arrayList.Add(new RMap(i, 0));
}
}
}
return(arrayList);
}
else if (g1.AtomCount == 1)
{
System.Collections.ArrayList arrayList = new System.Collections.ArrayList();
IAtom atom = g1.getAtomAt(0);
for (int i = 0; i < g2.AtomCount; i++)
{
IAtom atom2 = g2.getAtomAt(i);
if (atom2 is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom2;
if (qAtom.matches(atom))
{
arrayList.Add(new RMap(0, i));
}
}
else
{
if (atom2.Symbol.Equals(atom.Symbol))
{
arrayList.Add(new RMap(0, i));
}
}
}
return(arrayList);
}
else
{
return(null);
}
}
/// <summary> Check whether a set of atoms in an atomcontainer is connected
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be check for connectedness
/// </param>
/// <returns> true if the AtomContainer is connected
/// </returns>
public static bool isConnected(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IMolecule molecule = atomContainer.Builder.newMolecule();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atomContainer.getAtomAt(f).setFlag(CDKConstants.VISITED, false);
ac.addAtom(atomContainer.getAtomAt(f));
}
IBond[] bonds = atomContainer.Bonds;
for (int f = 0; f < bonds.Length; f++)
{
bonds[f].setFlag(CDKConstants.VISITED, false);
ac.addBond(bonds[f]);
}
atom = ac.getAtomAt(0);
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
if (molecule.AtomCount == atomContainer.AtomCount)
{
return(true);
}
return(false);
}
///////////////////////////////////////////////////////////////////////////
// Query Methods
//
// This methods are simple applications of the RGraph model on atom containers
// using different constrains and search options. They give an exemple of the
// most common queries but of course it is possible to define other type of
// queries exploiting the constrain and option combinations
//
////
// Isomorphism search
/// <summary> Tests if g1 and g2 are isomorph
///
/// </summary>
/// <param name="g1"> first molecule
/// </param>
/// <param name="g2"> second molecule
/// </param>
/// <returns> true if the 2 molecule are isomorph
/// </returns>
public static bool isIsomorph(IAtomContainer g1, IAtomContainer g2)
{
if (g2.AtomCount != g1.AtomCount)
{
return(false);
}
// check single atom case
if (g2.AtomCount == 1)
{
IAtom atom = g1.getAtomAt(0);
IAtom atom2 = g2.getAtomAt(0);
if (atom is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom;
return(qAtom.matches(g2.getAtomAt(0)));
}
else if (atom2 is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom2;
return(qAtom.matches(g1.getAtomAt(0)));
}
else
{
System.String atomSymbol = atom.Symbol;
return(g1.getAtomAt(0).Symbol.Equals(atomSymbol));
}
}
return(getIsomorphMap(g1, g2) != null);
}
/// <summary> Check whether a set of atoms in an atomcontainer is connected
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be check for connectedness
/// </param>
/// <returns> true if the AtomContainer is connected
/// </returns>
public static bool isConnected(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IMolecule molecule = atomContainer.Builder.newMolecule();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atomContainer.getAtomAt(f).setFlag(CDKConstants.VISITED, false);
ac.addAtom(atomContainer.getAtomAt(f));
}
IBond[] bonds = atomContainer.Bonds;
for (int f = 0; f < bonds.Length; f++)
{
bonds[f].setFlag(CDKConstants.VISITED, false);
ac.addBond(bonds[f]);
}
atom = ac.getAtomAt(0);
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
if (molecule.AtomCount == atomContainer.AtomCount)
{
return true;
}
return false;
}
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> Returna an atom in an atomcontainer identified by id
///
/// </summary>
/// <param name="ac">The AtomContainer to search in
/// </param>
/// <param name="id">The id to search for
/// </param>
/// <returns> An atom having id id
/// </returns>
/// <throws> CDKException There is no such atom </throws>
public static IAtom getAtomById(IAtomContainer ac, System.String id)
{
for (int i = 0; i < ac.AtomCount; i++)
{
if (ac.getAtomAt(i).ID != null && ac.getAtomAt(i).ID.Equals(id))
return ac.getAtomAt(i);
}
throw new CDKException("no suc atom");
}
/// <summary> Processes the content from the connections field of the INChI.
/// Typical values look like 1-2-4-6-5-3-1, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
///
/// </summary>
/// <param name="bondsEncoding">the content of the INChI connections field
/// </param>
/// <param name="container"> the atomContainer parsed from the formula field
/// </param>
/// <param name="source"> the atom to build the path upon. If -1, then start new path
///
/// </param>
/// <seealso cref="processFormula">
/// </seealso>
public virtual void processConnections(System.String bondsEncoding, IAtomContainer container, int source)
{
//logger.debug("Parsing bond data: ", bondsEncoding);
IBond bondToAdd = null;
/* Fixme: treatment of branching is too limited! */
System.String remainder = bondsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Bond part: ", remainder);
if (remainder[0] == '(')
{
System.String branch = chopBranch(remainder);
processConnections(branch, container, source);
if (branch.Length + 2 <= remainder.Length)
{
remainder = remainder.Substring(branch.Length + 2);
}
else
{
remainder = "";
}
}
else
{
Regex pattern = new Regex("^(\\d+)-?(.*)");
//Pattern pattern = Pattern.compile("^(\\d+)-?(.*)");
//Matcher matcher = pattern.matcher(remainder);
Match matcher = pattern.Match(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String targetStr = matcher.Groups[1].Value;
int target = System.Int32.Parse(targetStr);
//logger.debug("Source atom: ", source);
//logger.debug("Target atom: ", targetStr);
IAtom targetAtom = container.getAtomAt(target - 1);
if (source != -1)
{
IAtom sourceAtom = container.getAtomAt(source - 1);
bondToAdd = container.Builder.newBond(sourceAtom, targetAtom, 1.0);
container.addBond(bondToAdd);
}
remainder = matcher.Groups[2].Value;
source = target;
//logger.debug(" remainder: ", remainder);
}
else
{
//logger.error("Could not get next bond info part");
return;
}
}
}
}
/// <summary> Returna an atom in an atomcontainer identified by id
///
/// </summary>
/// <param name="ac">The AtomContainer to search in
/// </param>
/// <param name="id">The id to search for
/// </param>
/// <returns> An atom having id id
/// </returns>
/// <throws> CDKException There is no such atom </throws>
public static IAtom getAtomById(IAtomContainer ac, System.String id)
{
for (int i = 0; i < ac.AtomCount; i++)
{
if (ac.getAtomAt(i).ID != null && ac.getAtomAt(i).ID.Equals(id))
{
return(ac.getAtomAt(i));
}
}
throw new CDKException("no suc atom");
}
/// <summary> Partitions the atoms in an AtomContainer into covalently connected components.
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be partitioned into connected components, i.e. molecules
/// </param>
/// <returns> A SetOfMolecules.
///
/// </returns>
/// <cdk.dictref> blue-obelisk:graphPartitioning </cdk.dictref>
public static ISetOfMolecules partitionIntoMolecules(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IElectronContainer eContainer = null;
IMolecule molecule = null;
ISetOfMolecules molecules = atomContainer.Builder.newSetOfMolecules();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atom.setFlag(CDKConstants.VISITED, false);
ac.addAtom(atom);
}
IElectronContainer[] eContainers = atomContainer.ElectronContainers;
for (int f = 0; f < eContainers.Length; f++)
{
eContainer = eContainers[f];
eContainer.setFlag(CDKConstants.VISITED, false);
ac.addElectronContainer(eContainer);
}
while (ac.AtomCount > 0)
{
atom = ac.getAtomAt(0);
molecule = atomContainer.Builder.newMolecule();
sphere.Clear();
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
molecules.addMolecule(molecule);
ac.remove(molecule);
}
return(molecules);
}
/// <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;
}
/// <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);
}
/// <summary> Configures atoms in an AtomContainer to
/// carry all the correct data according to their element type.
///
/// </summary>
/// <param name="container"> The AtomContainer to be configured
/// </param>
public virtual void configureAtoms(IAtomContainer container)
{
for (int f = 0; f < container.AtomCount; f++)
{
configure(container.getAtomAt(f));
}
}
/// <summary> A method to remove AtomListeners.
/// AtomListeners are used to detect changes
/// in Atom objects within this AtomContainer and to notifiy
/// registered Listeners in the event of a change.
/// If an object looses interest in such changes, it should
/// unregister with this AtomContainer in order to improve
/// performance of this class.
/// </summary>
public static void unregisterAtomListeners(IAtomContainer container)
{
for (int f = 0; f < container.AtomCount; f++)
{
container.getAtomAt(f).removeListener(container);
}
}
/// <summary> Uses precomputed set of ALL rings and performs an aromaticity detection
/// based on Hueckels 4n + 2 rule.
///
/// </summary>
/// <param name="ringSet"> set of ALL rings
/// </param>
/// <param name="removeAromaticityFlags"> Leaves ChemObjects that are already marked as
/// aromatic as they are
/// </param>
/// <param name="atomContainer"> AtomContainer to be searched for rings
/// </param>
/// <returns> True, if molecules contains an
/// aromatic feature
/// </returns>
public static bool detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet, bool removeAromaticityFlags)
{
bool foundSomething = false;
if (removeAromaticityFlags)
{
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atomContainer.getAtomAt(f).setFlag(CDKConstants.ISAROMATIC, false);
}
for (int f = 0; f < atomContainer.ElectronContainerCount; f++)
{
IElectronContainer electronContainer = atomContainer.getElectronContainerAt(f);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
((IRing)ringSet.getAtomContainer(f)).setFlag(CDKConstants.ISAROMATIC, false);
}
}
IRing ring = null;
RingSetManipulator.sort(ringSet);
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
ring = (IRing)ringSet.getAtomContainer(f);
//logger.debug("Testing for aromaticity in ring no ", f);
if (AromaticityCalculator.isAromatic(ring, atomContainer))
{
ring.setFlag(CDKConstants.ISAROMATIC, true);
for (int g = 0; g < ring.AtomCount; g++)
{
ring.getAtomAt(g).setFlag(CDKConstants.ISAROMATIC, true);
}
for (int g = 0; g < ring.ElectronContainerCount; g++)
{
IElectronContainer electronContainer = ring.getElectronContainerAt(g);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, true);
}
}
foundSomething = true;
//logger.debug("This ring is aromatic: ", f);
}
else
{
//logger.debug("This ring is *not* aromatic: ", f);
}
}
return(foundSomething);
}
public virtual void printAtoms(IAtomContainer ac)
{
for (int i = 0; i < ac.AtomCount; i++)
{
//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'"
System.Console.Out.Write(ac.getAtomAt(i).getProperty("ST_ATOMNO").ToString() + ",");
}
}
/// <returns> The summed charges of all atoms in this AtomContainer.
/// </returns>
public static double getTotalCharge(IAtomContainer atomContainer)
{
double charge = 0.0;
for (int i = 0; i < atomContainer.AtomCount; i++)
{
charge += atomContainer.getAtomAt(i).getCharge();
}
return(charge);
}
/// <returns> The summed implicit hydrogens of all atoms in this AtomContainer.
/// </returns>
public static int getTotalHydrogenCount(IAtomContainer atomContainer)
{
int hCount = 0;
for (int i = 0; i < atomContainer.AtomCount; i++)
{
hCount += atomContainer.getAtomAt(i).getHydrogenCount();
}
return(hCount);
}
/// <summary> Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer. This method
/// puts the element symbol before the morgan number, usefull for finding out how many different rests are connected to an atom.
///
/// </summary>
/// <param name="atomContainer"> The atomContainer to analyse.
/// </param>
/// <returns> The morgan numbers value.
/// </returns>
public static System.String[] getMorganNumbersWithElementSymbol(IAtomContainer atomContainer)
{
int[] morgannumbers = getMorganNumbers(atomContainer);
System.String[] morgannumberswithelement = new System.String[morgannumbers.Length];
for (int i = 0; i < morgannumbers.Length; i++)
{
morgannumberswithelement[i] = atomContainer.getAtomAt(i).Symbol + "-" + morgannumbers[i];
}
return(morgannumberswithelement);
}
public static void resetFlags(IAtomContainer ac)
{
for (int f = 0; f < ac.AtomCount; f++)
{
ac.getAtomAt(f).setFlag(CDKConstants.VISITED, false);
}
for (int f = 0; f < ac.ElectronContainerCount; f++)
{
ac.getElectronContainerAt(f).setFlag(CDKConstants.VISITED, false);
}
}
public virtual bool allSaturated(IAtomContainer ac)
{
//logger.debug("Are all atoms saturated?");
for (int f = 0; f < ac.AtomCount; f++)
{
if (!isSaturated(ac.getAtomAt(f), ac))
{
return(false);
}
}
return(true);
}
/// <returns> The summed positive formal charges of all atoms in this AtomContainer.
/// </returns>
public static int getTotalPositiveFormalCharge(IAtomContainer atomContainer)
{
int charge = 0;
for (int i = 0; i < atomContainer.AtomCount; i++)
{
double chargeI = atomContainer.getAtomAt(i).getFormalCharge();
if (chargeI > 0)
{
charge = (int)(charge + chargeI);
}
}
return(charge);
}
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> Tests if g2 a subgraph of g1
///
/// </summary>
/// <param name="g1"> first molecule
/// </param>
/// <param name="g2"> second molecule
/// </param>
/// <returns> true if g2 a subgraph on g1
/// </returns>
public static bool isSubgraph(IAtomContainer g1, IAtomContainer g2)
{
if (g2.AtomCount > g1.AtomCount)
{
return(false);
}
// test for single atom case
if (g2.AtomCount == 1)
{
IAtom atom = g2.getAtomAt(0);
for (int i = 0; i < g1.AtomCount; i++)
{
IAtom atom2 = g1.getAtomAt(i);
if (atom is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom;
if (qAtom.matches(atom2))
{
return(true);
}
}
else if (atom2 is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom2;
if (qAtom.matches(atom))
{
return(true);
}
}
else
{
if (atom2.Symbol.Equals(atom.Symbol))
{
return(true);
}
}
}
return(false);
}
if (!testSubgraphHeuristics(g1, g2))
{
return(false);
}
return(getSubgraphMap(g1, g2) != null);
}
/// <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);
}
public static void makeUpDownBonds(IAtomContainer container)
{
for (int i = 0; i < container.AtomCount; i++)
{
IAtom a = container.getAtomAt(i);
if (container.getConnectedAtoms(a).Length == 4)
{
int up = 0;
int down = 0;
int hs = 0;
IAtom h = null;
for (int k = 0; k < 4; k++)
{
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_UP)
{
up++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_DOWN)
{
down++;
}
if (container.getBond(a, container.getConnectedAtoms(a)[k]).Stereo == CDKConstants.STEREO_BOND_NONE && container.getConnectedAtoms(a)[k].Symbol.Equals("H"))
{
h = container.getConnectedAtoms(a)[k];
hs++;
}
}
if (up == 0 && down == 1 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_UP;
}
if (up == 1 && down == 0 && h != null && hs == 1)
{
container.getBond(a, h).Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
}
}
public virtual void printAtoms(IAtomContainer ac)
{
for (int i = 0; i < ac.AtomCount; i++)
{
//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'"
System.Console.Out.Write(ac.getAtomAt(i).getProperty("ST_ATOMNO").ToString() + ",");
}
}
public static void resetFlags(IAtomContainer ac)
{
for (int f = 0; f < ac.AtomCount; f++)
{
ac.getAtomAt(f).setFlag(CDKConstants.VISITED, false);
}
for (int f = 0; f < ac.ElectronContainerCount; f++)
{
ac.getElectronContainerAt(f).setFlag(CDKConstants.VISITED, false);
}
}
/// <summary> Reads labels.</summary>
public virtual void readSGroup(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END SGROUP".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing Sgroup line: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
// parse the index
System.String indexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + indexString);
// parse command type
System.String type = tokenizer.NextToken();
// parse the external index
System.String externalIndexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + externalIndexString);
// the rest are key=value fields
System.Collections.Hashtable options = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
if (command.IndexOf("=") != -1)
{
options = parseOptions(exhaustStringTokenizer(tokenizer));
}
// now interpret line
if (type.StartsWith("SUP"))
{
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
int atomID = -1;
System.String label = "";
//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'"
while (keys.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'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("ATOMS"))
{
SupportClass.Tokenizer atomsTokenizer = new SupportClass.Tokenizer(value_Renamed);
System.Int32.Parse(atomsTokenizer.NextToken()); // should be 1, int atomCount =
atomID = System.Int32.Parse(atomsTokenizer.NextToken());
}
else if (key.Equals("LABEL"))
{
label = value_Renamed;
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
if (atomID != -1 && label.Length > 0)
{
IAtom atom = readData.getAtomAt(atomID - 1);
if (!(atom is IPseudoAtom))
{
atom = readData.Builder.newPseudoAtom(atom);
}
((IPseudoAtom)atom).Label = label;
readData.setAtomAt(atomID - 1, atom);
}
}
}
else
{
//logger.warn("Skipping unrecognized SGROUP type: " + type);
}
}
}
}
/// <summary> Return the RMSD of the heavy atoms between the 2 aligned molecules.
///
/// </summary>
/// <param name="firstAtomContainer"> the (largest) first aligned AtomContainer which is the reference
/// </param>
/// <param name="secondAtomContainer"> the second aligned AtomContainer
/// </param>
/// <param name="mappedAtoms"> Map: a Map of the mapped atoms
/// </param>
/// <param name="Coords3d"> boolean: true if moecules has 3D coords, false if molecules has 2D coords
/// </param>
/// <returns> double: the value of the RMSD
/// </returns>
/// <exception cref="CDK">*
///
/// </exception>
public static double getHeavyAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, System.Collections.IDictionary mappedAtoms, bool Coords3d)
{
//System.out.println("**** GT getAllAtomRMSD ****");
double sum = 0;
double RMSD = 0;
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
System.Collections.IEnumerator firstAtoms = new CSGraphT.SupportClass.HashSetSupport(mappedAtoms.Keys).GetEnumerator();
int firstAtomNumber = 0;
int secondAtomNumber = 0;
int n = 0;
//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'"
while (firstAtoms.MoveNext())
{
//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'"
firstAtomNumber = ((System.Int32)firstAtoms.Current);
try
{
secondAtomNumber = ((System.Int32)mappedAtoms[(System.Int32)firstAtomNumber]);
IAtom firstAtom = firstAtomContainer.getAtomAt(firstAtomNumber);
if (!firstAtom.Symbol.Equals("H"))
{
if (Coords3d)
{
sum = sum + System.Math.Pow(((Point3d)firstAtom.getPoint3d()).distance(secondAtomContainer.getAtomAt(secondAtomNumber).getPoint3d()), 2);
n++;
}
else
{
sum = sum + System.Math.Pow(((Point2d)firstAtom.getPoint2d()).distance(secondAtomContainer.getAtomAt(secondAtomNumber).getPoint2d()), 2);
n++;
}
}
}
catch (System.Exception ex)
{
}
}
RMSD = System.Math.Sqrt(sum / n);
return RMSD;
}
/// <summary> Return the RMSD of bonds length between the 2 aligned molecules.
///
/// </summary>
/// <param name="firstAtomContainer"> the (largest) first aligned AtomContainer which is the reference
/// </param>
/// <param name="secondAtomContainer"> the second aligned AtomContainer
/// </param>
/// <param name="mappedAtoms"> Map: a Map of the mapped atoms
/// </param>
/// <param name="Coords3d"> boolean: true if moecules has 3D coords, false if molecules has 2D coords
/// </param>
/// <returns> double: all the RMSD of bonds length
/// </returns>
/// <exception cref="CDK">*
///
/// </exception>
public static double getBondLengthRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, System.Collections.IDictionary mappedAtoms, bool Coords3d)
{
//System.out.println("**** GT getBondLengthRMSD ****");
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
System.Collections.IEnumerator firstAtoms = new CSGraphT.SupportClass.HashSetSupport(mappedAtoms.Keys).GetEnumerator();
IAtom centerAtomFirstMolecule = null;
IAtom centerAtomSecondMolecule = null;
IAtom[] connectedAtoms = null;
double sum = 0;
double n = 0;
double distance1 = 0;
double distance2 = 0;
setVisitedFlagsToFalse(firstAtomContainer);
setVisitedFlagsToFalse(secondAtomContainer);
//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'"
while (firstAtoms.MoveNext())
{
//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'"
centerAtomFirstMolecule = firstAtomContainer.getAtomAt(((System.Int32)firstAtoms.Current));
centerAtomFirstMolecule.setFlag(CDKConstants.VISITED, true);
centerAtomSecondMolecule = secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(centerAtomFirstMolecule)]));
connectedAtoms = firstAtomContainer.getConnectedAtoms(centerAtomFirstMolecule);
for (int i = 0; i < connectedAtoms.Length; i++)
{
//this step is built to know if the program has already calculate a bond length (so as not to have duplicate values)
if (!connectedAtoms[i].getFlag(CDKConstants.VISITED))
{
if (Coords3d)
{
distance1 = ((Point3d)centerAtomFirstMolecule.getPoint3d()).distance(connectedAtoms[i].getPoint3d());
distance2 = ((Point3d)centerAtomSecondMolecule.getPoint3d()).distance(secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(connectedAtoms[i])])).getPoint3d());
sum = sum + System.Math.Pow((distance1 - distance2), 2);
n++;
}
else
{
distance1 = ((Point2d)centerAtomFirstMolecule.getPoint2d()).distance(connectedAtoms[i].getPoint2d());
distance2 = ((Point2d)centerAtomSecondMolecule.getPoint2d()).distance(secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(connectedAtoms[i])])).getPoint2d());
sum = sum + System.Math.Pow((distance1 - distance2), 2);
n++;
}
}
}
}
setVisitedFlagsToFalse(firstAtomContainer);
setVisitedFlagsToFalse(secondAtomContainer);
return System.Math.Sqrt(sum / n);
}
/// <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> Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer. This method
/// puts the element symbol before the morgan number, usefull for finding out how many different rests are connected to an atom.
///
/// </summary>
/// <param name="atomContainer"> The atomContainer to analyse.
/// </param>
/// <returns> The morgan numbers value.
/// </returns>
public static System.String[] getMorganNumbersWithElementSymbol(IAtomContainer atomContainer)
{
int[] morgannumbers = getMorganNumbers(atomContainer);
System.String[] morgannumberswithelement = new System.String[morgannumbers.Length];
for (int i = 0; i < morgannumbers.Length; i++)
{
morgannumberswithelement[i] = atomContainer.getAtomAt(i).Symbol + "-" + morgannumbers[i];
}
return (morgannumberswithelement);
}
/// <summary> Returns the atom of the given molecule that is closest to the given
/// coordinates.
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="xPosition"> The x coordinate
/// </param>
/// <param name="yPosition"> The y coordinate
/// </param>
/// <param name="atomCon"> The molecule that is searched for the closest atom
/// </param>
/// <returns> The atom that is closest to the given coordinates
/// </returns>
public static IAtom getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)
{
IAtom closestAtom = null;
IAtom currentAtom;
double smallestMouseDistance = -1;
double mouseDistance;
double atomX;
double atomY;
for (int i = 0; i < atomCon.AtomCount; i++)
{
currentAtom = atomCon.getAtomAt(i);
atomX = currentAtom.X2d;
atomY = currentAtom.Y2d;
mouseDistance = System.Math.Sqrt(System.Math.Pow(atomX - xPosition, 2) + System.Math.Pow(atomY - yPosition, 2));
if (mouseDistance < smallestMouseDistance || smallestMouseDistance == -1)
{
smallestMouseDistance = mouseDistance;
closestAtom = currentAtom;
}
}
return closestAtom;
}
/// <summary> Returns the minimum and maximum X and Y coordinates of the atoms in the
/// AtomContainer. The output is returned as: <pre>
/// minmax[0] = minX;
/// minmax[1] = minY;
/// minmax[2] = maxX;
/// minmax[3] = maxY;
/// </pre>
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="container"> Description of the Parameter
/// </param>
/// <returns> An four int array as defined above.
/// </returns>
//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'"
public static double[] getMinMax(IAtomContainer container, System.Collections.Hashtable renderingCoordinates)
{
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxX = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxY = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minX = System.Double.MaxValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minY = System.Double.MaxValue;
for (int i = 0; i < container.AtomCount; i++)
{
IAtom atom = container.getAtomAt(i);
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (renderingCoordinates[atom] != null)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).x > maxX)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
maxX = ((Point2d)renderingCoordinates[atom]).x;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).x < minX)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
minX = ((Point2d)renderingCoordinates[atom]).x;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).y > maxY)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
maxY = ((Point2d)renderingCoordinates[atom]).y;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atom]).y < minY)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
minY = ((Point2d)renderingCoordinates[atom]).y;
}
}
}
double[] minmax = new double[4];
minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
return minmax;
}
/// <summary> Tests if g2 a subgraph of g1
///
/// </summary>
/// <param name="g1"> first molecule
/// </param>
/// <param name="g2"> second molecule
/// </param>
/// <returns> true if g2 a subgraph on g1
/// </returns>
public static bool isSubgraph(IAtomContainer g1, IAtomContainer g2)
{
if (g2.AtomCount > g1.AtomCount)
return false;
// test for single atom case
if (g2.AtomCount == 1)
{
IAtom atom = g2.getAtomAt(0);
for (int i = 0; i < g1.AtomCount; i++)
{
IAtom atom2 = g1.getAtomAt(i);
if (atom is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom;
if (qAtom.matches(atom2))
return true;
}
else if (atom2 is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom2;
if (qAtom.matches(atom))
return true;
}
else
{
if (atom2.Symbol.Equals(atom.Symbol))
return true;
}
}
return false;
}
if (!testSubgraphHeuristics(g1, g2))
return false;
return (getSubgraphMap(g1, g2) != null);
}
/// <summary> Rotates a molecule around a given center by a given angle
///
/// </summary>
/// <param name="atomCon"> The molecule to be rotated
/// </param>
/// <param name="center"> A point giving the rotation center
/// </param>
/// <param name="angle"> The angle by which to rotate the molecule
/// </param>
public static void rotate(IAtomContainer atomCon, Point2d center, double angle)
{
Point2d p = null;
double distance;
double offsetAngle;
IAtom atom = null;
for (int i = 0; i < atomCon.AtomCount; i++)
{
atom = atomCon.getAtomAt(i);
p = atom.getPoint2d();
offsetAngle = GeometryTools.getAngle(p.x - center.x, p.y - center.y);
distance = p.distance(center);
p.x = center.x + (System.Math.Sin(angle + offsetAngle) * distance);
p.y = center.y - (System.Math.Cos(angle + offsetAngle) * distance);
}
}
/// <summary> Checks for single atom cases before doing subgraph/isomorphism search
///
/// </summary>
/// <param name="g1"> AtomContainer to match on
/// </param>
/// <param name="g2"> AtomContainer as query
/// </param>
/// <returns> List of List of RMap objects for the Atoms (not Bonds!), null if no single atom case
/// </returns>
public static System.Collections.ArrayList checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2)
{
if (g2.AtomCount == 1)
{
System.Collections.ArrayList arrayList = new System.Collections.ArrayList();
IAtom atom = g2.getAtomAt(0);
if (atom is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom;
for (int i = 0; i < g1.AtomCount; i++)
{
if (qAtom.matches(g1.getAtomAt(i)))
arrayList.Add(new RMap(i, 0));
}
}
else
{
System.String atomSymbol = atom.Symbol;
for (int i = 0; i < g1.AtomCount; i++)
{
if (g1.getAtomAt(i).Symbol.Equals(atomSymbol))
arrayList.Add(new RMap(i, 0));
}
}
return arrayList;
}
else if (g1.AtomCount == 1)
{
System.Collections.ArrayList arrayList = new System.Collections.ArrayList();
IAtom atom = g1.getAtomAt(0);
for (int i = 0; i < g2.AtomCount; i++)
{
IAtom atom2 = g2.getAtomAt(i);
if (atom2 is IQueryAtom)
{
IQueryAtom qAtom = (IQueryAtom)atom2;
if (qAtom.matches(atom))
arrayList.Add(new RMap(0, i));
}
else
{
if (atom2.Symbol.Equals(atom.Symbol))
arrayList.Add(new RMap(0, i));
}
}
return arrayList;
}
else
{
return null;
}
}
/// <summary> Reads the bond atoms, order and stereo configuration.</summary>
public virtual void readBondBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END BOND".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing bond from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IBond bond = readData.Builder.newBond();
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
bond.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the order
try
{
System.String orderString = tokenizer.NextToken();
int order = System.Int32.Parse(orderString);
if (order >= 4)
{
//logger.warn("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = (double)order;
}
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
System.String indexAtom1String = tokenizer.NextToken();
int indexAtom1 = System.Int32.Parse(indexAtom1String);
IAtom atom1 = readData.getAtomAt(indexAtom1 - 1);
bond.setAtomAt(atom1, 0);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 1 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
System.String indexAtom2String = tokenizer.NextToken();
int indexAtom2 = System.Int32.Parse(indexAtom2String);
IAtom atom2 = readData.getAtomAt(indexAtom2 - 1);
bond.setAtomAt(atom2, 1);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 2 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// the rest are key=value fields
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//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'"
while (keys.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'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CFG"))
{
int configuration = System.Int32.Parse(value_Renamed);
if (configuration == 0)
{
bond.Stereo = CDKConstants.STEREO_BOND_NONE;
}
else if (configuration == 1)
{
bond.Stereo = CDKConstants.STEREO_BOND_UP;
}
else if (configuration == 2)
{
bond.Stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
else if (configuration == 3)
{
bond.Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// storing bond
readData.addBond(bond);
//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'"
//logger.debug("Added bond: " + bond);
}
}
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void endObject(System.String objectType)
{
//logger.debug("END: " + objectType);
if (objectType.Equals("Molecule"))
{
if (currentMolecule is IMolecule)
{
//logger.debug("Adding molecule to set");
currentSetOfMolecules.addMolecule((IMolecule)currentMolecule);
//logger.debug("#mols in set: " + currentSetOfMolecules.MoleculeCount);
}
else if (currentMolecule is ICrystal)
{
//logger.debug("Adding crystal to chemModel");
currentChemModel.Crystal = (ICrystal)currentMolecule;
currentChemSequence.addChemModel(currentChemModel);
}
}
else if (objectType.Equals("SetOfMolecules"))
{
currentChemModel.SetOfMolecules = currentSetOfMolecules;
currentChemSequence.addChemModel(currentChemModel);
}
else if (objectType.Equals("Frame"))
{
// endObject("Molecule");
}
else if (objectType.Equals("Animation"))
{
addChemSequence(currentChemSequence);
//logger.info("This file has " + ChemSequenceCount + " sequence(s).");
}
else if (objectType.Equals("Atom"))
{
currentMolecule.addAtom(currentAtom);
}
else if (objectType.Equals("Bond"))
{
//logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.AtomCount || bond_a2 > currentMolecule.AtomCount)
{
//logger.error("Cannot add bond between at least one non-existant atom: " + bond_a1 + " and " + bond_a2);
}
else
{
IAtom a1 = currentMolecule.getAtomAt(bond_a1);
IAtom a2 = currentMolecule.getAtomAt(bond_a2);
IBond b = currentChemFile.Builder.newBond(a1, a2, bond_order);
if (bond_id != null)
{
b.ID = bond_id;
}
if (bond_stereo != -99)
{
b.Stereo = bond_stereo;
}
if (bond_order == CDKConstants.BONDORDER_AROMATIC)
{
b.setFlag(CDKConstants.ISAROMATIC, true);
}
currentMolecule.addBond(b);
}
}
else if (objectType.Equals("a-axis"))
{
// set these variables
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.A = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("b-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.B = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("c-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.C = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("SetOfReactions"))
{
currentChemModel.SetOfReactions = currentSetOfReactions;
currentChemSequence.addChemModel(currentChemModel);
/* FIXME: this should be when document is closed! */
}
else if (objectType.Equals("Reaction"))
{
//logger.debug("Adding reaction to SOR");
currentSetOfReactions.addReaction(currentReaction);
}
else if (objectType.Equals("Reactant"))
{
currentReaction.addReactant((IMolecule)currentMolecule);
}
else if (objectType.Equals("Product"))
{
currentReaction.addProduct((IMolecule)currentMolecule);
}
else if (objectType.Equals("Crystal"))
{
//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'"
//logger.debug("Crystal: " + currentMolecule);
}
}
/// <summary> Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
/// AtomContainer) atomContainer.
///
/// Only for similar and aligned molecules with coordinates!
///
/// </summary>
/// <param name="firstAtomContainer"> the (largest) first aligned AtomContainer which is the reference
/// </param>
/// <param name="secondAtomContainer"> the second aligned AtomContainer
/// </param>
/// <returns> a Map of the mapped atoms
/// </returns>
/// <exception cref="CDKException"> Description of the Exception
/// </exception>
public static System.Collections.IDictionary mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, System.Collections.IDictionary mappedAtoms)
{
//System.out.println("**** GT MAP ATOMS ****");
//Map atoms onto each other
if (firstAtomContainer.AtomCount < 1 & secondAtomContainer.AtomCount < 1)
{
return mappedAtoms;
}
RMap map;
IAtom atom1;
IAtom atom2;
int countMappedAtoms = 0;
System.Collections.IList list;
try
{
list = UniversalIsomorphismTester.getSubgraphAtomsMap(firstAtomContainer, secondAtomContainer);
//System.out.println("ListSize:"+list.size());
for (int i = 0; i < list.Count; i++)
{
map = (RMap)list[i];
atom1 = firstAtomContainer.getAtomAt(map.Id1);
atom2 = secondAtomContainer.getAtomAt(map.Id2);
if (checkAtomMapping(firstAtomContainer, secondAtomContainer, firstAtomContainer.getAtomNumber(atom1), secondAtomContainer.getAtomNumber(atom2)))
{
mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(atom1)] = (System.Int32)secondAtomContainer.getAtomNumber(atom2);
countMappedAtoms++;
//System.out.println("#:"+countMappedAtoms+" Atom:"+firstAtomContainer.getAtomNumber(atom1)+" is mapped to Atom:"+secondAtomContainer.getAtomNumber(atom2));
}
else
{
System.Console.Out.WriteLine("Error: Atoms are not similar !!");
}
}
}
catch (CDKException e)
{
// TODO Auto-generated catch block
System.Console.Out.WriteLine("Error in UniversalIsomorphismTester due to:");
SupportClass.WriteStackTrace(e, Console.Error);
}
return mappedAtoms;
}
/// <summary> Uses precomputed set of ALL rings and performs an aromaticity detection
/// based on Hueckels 4n + 2 rule.
///
/// </summary>
/// <param name="ringSet"> set of ALL rings
/// </param>
/// <param name="removeAromaticityFlags"> Leaves ChemObjects that are already marked as
/// aromatic as they are
/// </param>
/// <param name="atomContainer"> AtomContainer to be searched for rings
/// </param>
/// <returns> True, if molecules contains an
/// aromatic feature
/// </returns>
public static bool detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet, bool removeAromaticityFlags)
{
bool foundSomething = false;
if (removeAromaticityFlags)
{
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atomContainer.getAtomAt(f).setFlag(CDKConstants.ISAROMATIC, false);
}
for (int f = 0; f < atomContainer.ElectronContainerCount; f++)
{
IElectronContainer electronContainer = atomContainer.getElectronContainerAt(f);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
((IRing)ringSet.getAtomContainer(f)).setFlag(CDKConstants.ISAROMATIC, false);
}
}
IRing ring = null;
RingSetManipulator.sort(ringSet);
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
ring = (IRing)ringSet.getAtomContainer(f);
//logger.debug("Testing for aromaticity in ring no ", f);
if (AromaticityCalculator.isAromatic(ring, atomContainer))
{
ring.setFlag(CDKConstants.ISAROMATIC, true);
for (int g = 0; g < ring.AtomCount; g++)
{
ring.getAtomAt(g).setFlag(CDKConstants.ISAROMATIC, true);
}
for (int g = 0; g < ring.ElectronContainerCount; g++)
{
IElectronContainer electronContainer = ring.getElectronContainerAt(g);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, true);
}
}
foundSomething = true;
//logger.debug("This ring is aromatic: ", f);
}
else
{
//logger.debug("This ring is *not* aromatic: ", f);
}
}
return foundSomething;
}
private static bool checkAtomMapping(IAtomContainer firstAC, IAtomContainer secondAC, int posFirstAtom, int posSecondAtom)
{
IAtom firstAtom = firstAC.getAtomAt(posFirstAtom);
IAtom secondAtom = secondAC.getAtomAt(posSecondAtom);
if (firstAtom.Symbol.Equals(secondAtom.Symbol) && firstAC.getConnectedAtoms(firstAtom).Length == secondAC.getConnectedAtoms(secondAtom).Length && firstAtom.BondOrderSum == secondAtom.BondOrderSum && firstAtom.MaxBondOrder == secondAtom.MaxBondOrder)
{
return true;
}
else
{
return false;
}
}
/// <summary> Reads labels.</summary>
public virtual void readSGroup(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END SGROUP".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing Sgroup line: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
// parse the index
System.String indexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + indexString);
// parse command type
System.String type = tokenizer.NextToken();
// parse the external index
System.String externalIndexString = tokenizer.NextToken();
//logger.warn("Skipping external index: " + externalIndexString);
// the rest are key=value fields
System.Collections.Hashtable options = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
if (command.IndexOf("=") != -1)
{
options = parseOptions(exhaustStringTokenizer(tokenizer));
}
// now interpret line
if (type.StartsWith("SUP"))
{
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
int atomID = -1;
System.String label = "";
//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'"
while (keys.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'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("ATOMS"))
{
SupportClass.Tokenizer atomsTokenizer = new SupportClass.Tokenizer(value_Renamed);
System.Int32.Parse(atomsTokenizer.NextToken()); // should be 1, int atomCount =
atomID = System.Int32.Parse(atomsTokenizer.NextToken());
}
else if (key.Equals("LABEL"))
{
label = value_Renamed;
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
if (atomID != -1 && label.Length > 0)
{
IAtom atom = readData.getAtomAt(atomID - 1);
if (!(atom is IPseudoAtom))
{
atom = readData.Builder.newPseudoAtom(atom);
}
((IPseudoAtom)atom).Label = label;
readData.setAtomAt(atomID - 1, atom);
}
}
}
else
{
//logger.warn("Skipping unrecognized SGROUP type: " + type);
}
}
}
}
/// <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> 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> Configures atoms in an AtomContainer to
/// carry all the correct data according to their element type.
///
/// </summary>
/// <param name="container"> The AtomContainer to be configured
/// </param>
public virtual void configureAtoms(IAtomContainer container)
{
for (int f = 0; f < container.AtomCount; f++)
{
configure(container.getAtomAt(f));
}
}
/// <summary> Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
/// AtomContainer) atomcontainer. It is recommend to sort the atomContainer due to their number of atoms before
/// calling this function.
///
/// The molecules needs to be aligned before! (coordinates are needed)
///
/// </summary>
/// <param name="firstAtomContainer"> the (largest) first aligned AtomContainer which is the reference
/// </param>
/// <param name="secondAtomContainer"> the second aligned AtomContainer
/// </param>
/// <param name="searchRadius"> the radius of space search from each atom
/// </param>
/// <returns> a Map of the mapped atoms
/// </returns>
/// <exception cref="CDKException"> Description of the Exception
/// </exception>
public static System.Collections.IDictionary mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, double searchRadius, System.Collections.IDictionary mappedAtoms)
{
//to return the mapping setProperty("MappedAtom",AtomNumber)
//System.out.println("**** MAP ATOMS ****");
getLargestAtomContainer(firstAtomContainer, secondAtomContainer);
double[][] distanceMatrix = new double[firstAtomContainer.AtomCount][];
for (int i = 0; i < firstAtomContainer.AtomCount; i++)
{
distanceMatrix[i] = new double[secondAtomContainer.AtomCount];
}
for (int i = 0; i < firstAtomContainer.AtomCount; i++)
{
Point3d firstAtomPoint = firstAtomContainer.getAtomAt(i).getPoint3d();
//System.out.println("Closest atoms of "+firstAtomContainer.getAtoms()[i].getSymbol()+" :");
for (int j = 0; j < secondAtomContainer.AtomCount; j++)
{
distanceMatrix[i][j] = firstAtomPoint.distance(secondAtomContainer.getAtomAt(j).getPoint3d());
//System.out.println("Distance "+i+" "+j+":"+distanceMatrix[i][j]);
}
//System.out.println(" Atoms from the secondAtomContainer");
}
//System.out.println();
//System.out.print("\t");
//for (int j=0;j<secondAtomContainer.getAtomCount();j++){
//System.out.print(j+" "+secondAtomContainer.getAtomAt(j).getSymbol()+"\t");
//}
double tmp = 0;
for (int i = 0; i < firstAtomContainer.AtomCount; i++)
{
//System.out.print(i+" "+firstAtomContainer.getAtomAt(i).getSymbol()+"\t");
for (int j = 0; j < secondAtomContainer.AtomCount; j++)
{
tmp = System.Math.Floor(distanceMatrix[i][j] * 10);
//System.out.println(tmp/10+"\t");
}
}
double minimumDistance = searchRadius;
int countMappedAtoms = 0;
for (int i = 0; i < firstAtomContainer.AtomCount; i++)
{
minimumDistance = searchRadius;
for (int j = 0; j < secondAtomContainer.AtomCount; j++)
{
if (distanceMatrix[i][j] < searchRadius && distanceMatrix[i][j] < minimumDistance)
{
//System.out.println("Distance OK "+i+" "+j+":"+distanceMatrix[i][j]+" AtomCheck:"+checkAtomMapping(firstAtomContainer,secondAtomContainer, i, j));
//check atom properties
if (checkAtomMapping(firstAtomContainer, secondAtomContainer, i, j))
{
minimumDistance = distanceMatrix[i][j];
mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(firstAtomContainer.getAtomAt(i))] = (System.Int32)secondAtomContainer.getAtomNumber(secondAtomContainer.getAtomAt(j));
//firstAtomContainer.getAtomAt(i).setProperty("MappedAtom",new Integer(secondAtomContainer.getAtomNumber(secondAtomContainer.getAtomAt(j))));
countMappedAtoms++;
//System.out.println("#:"+countMappedAtoms+" Atom:"+i+" is mapped to Atom"+j);
//System.out.println(firstAtomContainer.getConnectedAtoms(firstAtomContainer.getAtomAt(i)).length);
}
}
}
}
return mappedAtoms;
}
/// <summary> Reads a set of vibrations into ChemFrame.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <exception cref="IOException"> if an I/O error occurs
/// </exception>
// private void readFrequencies(IChemModel model) throws IOException
// {
/*
* FIXME: this is yet to be ported
* String line;
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* while ((line != null) && line.startsWith(" Frequencies --")) {
* Vector currentVibs = new Vector();
* StringReader vibValRead = new StringReader(line.substring(15));
* StreamTokenizer token = new StreamTokenizer(vibValRead);
* while (token.nextToken() != StreamTokenizer.TT_EOF) {
* Vibration vib = new Vibration(Double.toString(token.nval));
* currentVibs.addElement(vib);
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* for (int i = 0; i < frame.getAtomCount(); ++i) {
* line = input.readLine();
* StringReader vectorRead = new StringReader(line);
* token = new StreamTokenizer(vectorRead);
* token.nextToken();
* / ignore first token
* token.nextToken();
* / ignore second token
* for (int j = 0; j < currentVibs.size(); ++j) {
* double[] v = new double[3];
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[0] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[1] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[2] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
* }
* }
* for (int i = 0; i < currentVibs.size(); ++i) {
* frame.addVibration((Vibration) currentVibs.elementAt(i));
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* }
*/
// }
/// <summary> Reads NMR nuclear shieldings.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <param name="labelLine">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
private void readNMRData(IChemModel model, System.String labelLine)
{
IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
// Determine label for properties
System.String label;
if (labelLine.IndexOf("Diamagnetic") >= 0)
{
label = "Diamagnetic Magnetic shielding (Isotropic)";
}
else if (labelLine.IndexOf("Paramagnetic") >= 0)
{
label = "Paramagnetic Magnetic shielding (Isotropic)";
}
else
{
label = "Magnetic shielding (Isotropic)";
}
int atomIndex = 0;
for (int i = 0; i < atomCount; ++i)
{
try
{
System.String line = input.ReadLine().Trim();
while (line.IndexOf("Isotropic") < 0)
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(line);
// Find Isotropic label
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("Isotropic"))
{
break;
}
}
// Find Isotropic value
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("="))
{
break;
}
}
double shielding = System.Double.Parse(st1.NextToken());
//logger.info("Type of shielding: " + label);
ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
++atomIndex;
}
catch (System.Exception exc)
{
//logger.debug("failed to read line from gaussian98 file where I expected one.");
}
}
}
/// <summary> Multiplies all the coordinates of the atoms of the given molecule with the
/// scalefactor.
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="atomCon"> The molecule to be scaled
/// </param>
/// <param name="scaleFactor"> Description of the Parameter
/// </param>
public static void scaleMolecule(IAtomContainer atomCon, double scaleFactor)
{
for (int i = 0; i < atomCon.AtomCount; i++)
{
if (atomCon.getAtomAt(i).getPoint2d() != null)
{
atomCon.getAtomAt(i).getPoint2d().x *= scaleFactor;
atomCon.getAtomAt(i).getPoint2d().y *= scaleFactor;
}
}
}
public virtual bool allSaturated(IAtomContainer ac)
{
//logger.debug("Are all atoms saturated?");
for (int f = 0; f < ac.AtomCount; f++)
{
if (!isSaturated(ac.getAtomAt(f), ac))
{
return false;
}
}
return true;
}
private static IAtomContainer setVisitedFlagsToFalse(IAtomContainer atomContainer)
{
for (int i = 0; i < atomContainer.AtomCount; i++)
{
atomContainer.getAtomAt(i).setFlag(CDKConstants.VISITED, false);
}
return atomContainer;
}
/// <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> Return the variation of each angle value between the 2 aligned molecules.
///
/// </summary>
/// <param name="firstAtomContainer"> the (largest) first aligned AtomContainer which is the reference
/// </param>
/// <param name="secondAtomContainer"> the second aligned AtomContainer
/// </param>
/// <param name="mappedAtoms"> Map: a Map of the mapped atoms
/// </param>
/// <returns> double: the value of the RMSD
/// </returns>
/// <exception cref="CDK">*
///
/// </exception>
public static double getAngleRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, System.Collections.IDictionary mappedAtoms)
{
//System.out.println("**** GT getAngleRMSD ****");
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
System.Collections.IEnumerator firstAtoms = new CSGraphT.SupportClass.HashSetSupport(mappedAtoms.Keys).GetEnumerator();
//System.out.println("mappedAtoms:"+mappedAtoms.toString());
IAtom firstAtomfirstAC = null;
IAtom centerAtomfirstAC = null;
IAtom firstAtomsecondAC = null;
IAtom secondAtomsecondAC = null;
IAtom centerAtomsecondAC = null;
double angleFirstMolecule = 0;
double angleSecondMolecule = 0;
double sum = 0;
double n = 0;
//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'"
while (firstAtoms.MoveNext())
{
//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'"
int firstAtomNumber = ((System.Int32)firstAtoms.Current);
centerAtomfirstAC = firstAtomContainer.getAtomAt(firstAtomNumber);
IAtom[] connectedAtoms = firstAtomContainer.getConnectedAtoms(centerAtomfirstAC);
if (connectedAtoms.Length > 1)
{
//System.out.println("If "+centerAtomfirstAC.getSymbol()+" is the center atom :");
for (int i = 0; i < connectedAtoms.Length - 1; i++)
{
firstAtomfirstAC = connectedAtoms[i];
for (int j = i + 1; j < connectedAtoms.Length; j++)
{
angleFirstMolecule = getAngle(centerAtomfirstAC, firstAtomfirstAC, connectedAtoms[j]);
centerAtomsecondAC = secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(centerAtomfirstAC)]));
firstAtomsecondAC = secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(firstAtomfirstAC)]));
secondAtomsecondAC = secondAtomContainer.getAtomAt(((System.Int32)mappedAtoms[(System.Int32)firstAtomContainer.getAtomNumber(connectedAtoms[j])]));
angleSecondMolecule = getAngle(centerAtomsecondAC, firstAtomsecondAC, secondAtomsecondAC);
sum = sum + System.Math.Pow(angleFirstMolecule - angleSecondMolecule, 2);
n++;
//System.out.println("Error for the "+firstAtomfirstAC.getSymbol().toLowerCase()+"-"+centerAtomfirstAC.getSymbol()+"-"+connectedAtoms[j].getSymbol().toLowerCase()+" Angle :"+deltaAngle+" degrees");
}
}
} //if
}
return System.Math.Sqrt(sum / n);
}
/// <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> Multiplies all the coordinates of the atoms of the given molecule with the
/// scalefactor, using an external set of coordinates..
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="atomCon"> The molecule to be scaled
/// </param>
/// <param name="scaleFactor"> Description of the Parameter
/// </param>
/// <param name="renderingCoordinates"> The set of coordinates to use coming from RendererModel2D
/// </param>
//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'"
public static void scaleMolecule(IAtomContainer atomCon, double scaleFactor, System.Collections.Hashtable renderingCoordinates)
{
for (int i = 0; i < atomCon.AtomCount; i++)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (renderingCoordinates[atomCon.getAtomAt(i)] != null)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
((Point2d)renderingCoordinates[atomCon.getAtomAt(i)]).x *= scaleFactor;
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
((Point2d)renderingCoordinates[atomCon.getAtomAt(i)]).y *= scaleFactor;
}
}
}
/// <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> Returns the minimum and maximum X and Y coordinates of the atoms in the
/// AtomContainer. The output is returned as: <pre>
/// minmax[0] = minX;
/// minmax[1] = minY;
/// minmax[2] = maxX;
/// minmax[3] = maxY;
/// </pre>
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="container"> Description of the Parameter
/// </param>
/// <returns> An four int array as defined above.
/// </returns>
public static double[] getMinMax(IAtomContainer container)
{
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxX = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MIN_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double maxY = System.Double.MinValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minX = System.Double.MaxValue;
//UPGRADE_TODO: The equivalent in .NET for field 'java.lang.Double.MAX_VALUE' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
double minY = System.Double.MaxValue;
for (int i = 0; i < container.AtomCount; i++)
{
IAtom atom = container.getAtomAt(i);
if (atom.getPoint2d() != null)
{
if (atom.X2d > maxX)
{
maxX = atom.X2d;
}
if (atom.X2d < minX)
{
minX = atom.X2d;
}
if (atom.Y2d > maxY)
{
maxY = atom.Y2d;
}
if (atom.Y2d < minY)
{
minY = atom.Y2d;
}
}
}
double[] minmax = new double[4];
minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
return minmax;
}
/// <summary> Returns a list of atoms in the shortest path between two atoms.
///
/// This method uses the Djikstra algorithm to find all the atoms in the shortest
/// path between the two specified atoms. The start and end atoms are also included
/// in the path returned
///
/// </summary>
/// <param name="atomContainer">The molecule to search in
/// </param>
/// <param name="start">The starting atom
/// </param>
/// <param name="end">The ending atom
/// </param>
/// <returns> A <code>List</code> containing the atoms in the shortest path between <code>start</code> and
/// <code>end</code> inclusive
/// </returns>
public static System.Collections.IList getShortestPath(IAtomContainer atomContainer, IAtom start, IAtom end)
{
int natom = atomContainer.AtomCount;
int endNumber = atomContainer.getAtomNumber(end);
int startNumber = atomContainer.getAtomNumber(start);
int[] d = new int[natom];
int[] previous = new int[natom];
for (int i = 0; i < natom; i++)
{
d[i] = 99999999;
previous[i] = -1;
}
d[atomContainer.getAtomNumber(start)] = 0;
System.Collections.ArrayList S = new System.Collections.ArrayList();
System.Collections.ArrayList Q = new System.Collections.ArrayList();
for (int i = 0; i < natom; i++)
{
Q.Add((System.Int32)i);
}
while (true)
{
if (Q.Count == 0)
{
break;
}
// extract min
int u = 999999;
int index = 0;
for (int i = 0; i < Q.Count; i++)
{
int tmp = ((System.Int32)Q[i]);
if (d[tmp] < u)
{
u = d[tmp];
index = i;
}
}
Q.RemoveAt(index);
S.Add(atomContainer.getAtomAt(u));
if (u == endNumber)
{
break;
}
// relaxation
IAtom[] connected = atomContainer.getConnectedAtoms(atomContainer.getAtomAt(u));
for (int i = 0; i < connected.Length; i++)
{
int anum = atomContainer.getAtomNumber(connected[i]);
if (d[anum] > d[u] + 1)
{
// all edges have equals weights
d[anum] = d[u] + 1;
previous[anum] = u;
}
}
}
System.Collections.ArrayList tmp2 = new System.Collections.ArrayList();
int u2 = endNumber;
while (true)
{
tmp2.Insert(0, atomContainer.getAtomAt(u2));
u2 = previous[u2];
if (u2 == startNumber)
{
tmp2.Insert(0, atomContainer.getAtomAt(u2));
break;
}
}
return(tmp2);
}
/// <summary> Processes the content from the connections field of the INChI.
/// Typical values look like 1-2-4-6-5-3-1, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
///
/// </summary>
/// <param name="bondsEncoding">the content of the INChI connections field
/// </param>
/// <param name="container"> the atomContainer parsed from the formula field
/// </param>
/// <param name="source"> the atom to build the path upon. If -1, then start new path
///
/// </param>
/// <seealso cref="processFormula">
/// </seealso>
public virtual void processConnections(System.String bondsEncoding, IAtomContainer container, int source)
{
//logger.debug("Parsing bond data: ", bondsEncoding);
IBond bondToAdd = null;
/* Fixme: treatment of branching is too limited! */
System.String remainder = bondsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Bond part: ", remainder);
if (remainder[0] == '(')
{
System.String branch = chopBranch(remainder);
processConnections(branch, container, source);
if (branch.Length + 2 <= remainder.Length)
{
remainder = remainder.Substring(branch.Length + 2);
}
else
{
remainder = "";
}
}
else
{
Regex pattern = new Regex("^(\\d+)-?(.*)");
//Pattern pattern = Pattern.compile("^(\\d+)-?(.*)");
//Matcher matcher = pattern.matcher(remainder);
Match matcher = pattern.Match(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String targetStr = matcher.Groups[1].Value;
int target = System.Int32.Parse(targetStr);
//logger.debug("Source atom: ", source);
//logger.debug("Target atom: ", targetStr);
IAtom targetAtom = container.getAtomAt(target - 1);
if (source != -1)
{
IAtom sourceAtom = container.getAtomAt(source - 1);
bondToAdd = container.Builder.newBond(sourceAtom, targetAtom, 1.0);
container.addBond(bondToAdd);
}
remainder = matcher.Groups[2].Value;
source = target;
//logger.debug(" remainder: ", remainder);
}
else
{
//logger.error("Could not get next bond info part");
return;
}
}
}
}
/// <summary> Reads the bond atoms, order and stereo configuration.</summary>
public virtual void readBondBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END BOND".Equals(command))
{
foundEND = true;
}
else
{
//logger.debug("Parsing bond from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IBond bond = readData.Builder.newBond();
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
bond.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the order
try
{
System.String orderString = tokenizer.NextToken();
int order = System.Int32.Parse(orderString);
if (order >= 4)
{
//logger.warn("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = (double)order;
}
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
System.String indexAtom1String = tokenizer.NextToken();
int indexAtom1 = System.Int32.Parse(indexAtom1String);
IAtom atom1 = readData.getAtomAt(indexAtom1 - 1);
bond.setAtomAt(atom1, 0);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 1 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
System.String indexAtom2String = tokenizer.NextToken();
int indexAtom2 = System.Int32.Parse(indexAtom2String);
IAtom atom2 = readData.getAtomAt(indexAtom2 - 1);
bond.setAtomAt(atom2, 1);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 2 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// the rest are key=value fields
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//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'"
while (keys.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'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CFG"))
{
int configuration = System.Int32.Parse(value_Renamed);
if (configuration == 0)
{
bond.Stereo = CDKConstants.STEREO_BOND_NONE;
}
else if (configuration == 1)
{
bond.Stereo = CDKConstants.STEREO_BOND_UP;
}
else if (configuration == 2)
{
bond.Stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
else if (configuration == 3)
{
bond.Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// storing bond
readData.addBond(bond);
//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'"
//logger.debug("Added bond: " + bond);
}
}
}