void expandNode(Node node) {
// System.out.println(node.toString(target));
QuerySequenceElement el = sequence.get(node.sequenceElNum);
if (el.center == null) // This node describers a bond that closes a ring
{
// Checking whether this bond is present in the target
IAtom tAt0 = node.atoms[query.getAtomNumber(el.atoms[0])];
IAtom tAt1 = node.atoms[query.getAtomNumber(el.atoms[1])];
IBond tBo = target.getBond(tAt0, tAt1);
if (tBo != null)
if (el.bonds[0].matches(tBo)) {
node.sequenceElNum++;
// stack.push(node);
if (node.sequenceElNum == sequence.size()) {
// The node is not added in the stack if the end of the sequence is reached
isomorphismFound = true;
if (FlagStoreIsomorphismNode) isomorphismNodes.add(node);
} else stack.push(node);
}
} else {
targetAt.clear();
IAtom tAt = node.atoms[el.centerNum];
List<IAtom> conAt = target.getConnectedAtomsList(tAt);
for (int i = 0; i < conAt.size(); i++) {
if (!containsAtom(node.atoms, conAt.get(i))) targetAt.add(conAt.get(i));
}
if (el.atoms.length <= targetAt.size()) generateNodes(node);
}
}
private boolean isTerminal(IAtom atom, IAtomContainer atomContainer) {
int numberOfHeavyAtomsConnected = 0;
for (IAtom connected : atomContainer.getConnectedAtomsList(atom)) {
if (connected.getSymbol().equals("H")) {
continue;
}
++numberOfHeavyAtomsConnected;
}
return numberOfHeavyAtomsConnected < 2;
}
/**
* Partition the bonding partners of a given atom into ring atoms and non-ring atoms
*
* @param atom The atom whose bonding partners are to be partitioned
* @param ring The ring against which the bonding partners are checked
* @param ringAtoms An AtomContainer to store the ring bonding partners
* @param nonRingAtoms An AtomContainer to store the non-ring bonding partners
*/
public void partitionNonRingPartners(
IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms) {
java.util.List atoms = molecule.getConnectedAtomsList(atom);
for (int i = 0; i < atoms.size(); i++) {
IAtom curAtom = (IAtom) atoms.get(i);
if (!ring.contains(curAtom)) {
nonRingAtoms.addAtom(curAtom);
} else {
ringAtoms.addAtom(curAtom);
}
}
}
/**
* Returns the bridge atoms, that is the outermost atoms in the chain of more than two atoms which
* are shared by two rings
*
* @param sharedAtoms The atoms (n > 2) which are shared by two rings
* @return The bridge atoms, i.e. the outermost atoms in the chain of more than two atoms which
* are shared by two rings
*/
private IAtom[] getBridgeAtoms(IAtomContainer sharedAtoms) {
IAtom[] bridgeAtoms = new IAtom[2];
IAtom atom;
int counter = 0;
for (int f = 0; f < sharedAtoms.getAtomCount(); f++) {
atom = sharedAtoms.getAtom(f);
if (sharedAtoms.getConnectedAtomsList(atom).size() == 1) {
bridgeAtoms[counter] = atom;
counter++;
}
}
return bridgeAtoms;
}
private Map<IAtom, List<String>> labelAtomsBySymbol(IAtomContainer atomCont) {
Map<IAtom, List<String>> label_list = new HashMap<>();
for (int i = 0; i < atomCont.getAtomCount(); i++) {
List<String> label = new ArrayList<>(7);
for (int a = 0; a < 7; a++) {
label.add(a, "Z9");
}
IAtom refAtom = atomCont.getAtom(i);
/*
* Important Step: Discriminate between source atom types
*/
String referenceAtom;
if (refAtom instanceof IQueryAtom) {
referenceAtom =
((IQueryAtom) refAtom).getSymbol() == null ? "*" : ((IQueryAtom) refAtom).getSymbol();
// System.out.println("referenceAtom " + referenceAtom);
} else if (!(refAtom instanceof IQueryAtom) && this.matchAtomType) {
referenceAtom =
refAtom.getAtomTypeName() == null ? refAtom.getSymbol() : refAtom.getAtomTypeName();
} else {
referenceAtom = refAtom.getSymbol();
}
label.set(0, referenceAtom);
List<IAtom> connAtoms = atomCont.getConnectedAtomsList(refAtom);
int counter = 1;
for (IAtom negAtom : connAtoms) {
String neighbouringAtom;
if (refAtom instanceof IQueryAtom) {
neighbouringAtom =
((IQueryAtom) negAtom).getSymbol() == null ? "*" : ((IQueryAtom) negAtom).getSymbol();
// System.out.println("neighbouringAtom " + neighbouringAtom);
} else if (!(negAtom instanceof IQueryAtom) && this.matchAtomType) {
neighbouringAtom =
negAtom.getAtomTypeName() == null ? negAtom.getSymbol() : negAtom.getAtomTypeName();
} else {
neighbouringAtom = negAtom.getSymbol();
}
label.set(counter, neighbouringAtom);
counter += 1;
}
// System.out.println("label " + label);
bubbleSort(label);
label_list.put(refAtom, label);
}
return label_list;
}
/**
* Obtain the ligands connected to the 'atom' excluding 'exclude'. This is mainly meant as util
* for double-bond labelling.
*
* @param atom an atom
* @param container a structure to which 'atom' belongs
* @param exclude exclude this atom - can not be null
* @return the ligands
*/
private static ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude) {
List<IAtom> neighbors = container.getConnectedAtomsList(atom);
ILigand[] ligands = new ILigand[neighbors.size() - 1];
int i = 0;
for (IAtom neighbor : neighbors) {
if (neighbor != exclude)
ligands[i++] = new Ligand(container, new VisitedAtoms(), atom, neighbor);
}
return ligands;
}
/**
* Place hydrogens connected to the provided atom <i>atom</i> using the specified
* <i>bondLength</i>.
*
* @param container atom container
* @param bondLength bond length to user
* @throws IllegalArgumentException thrown if the <i>atom</i> or <i>container</i> was null or the
* atom has connected atoms which have not been placed.
*/
@TestMethod("testNoConnections,testNullContainer,unplacedNonHydrogen")
public void placeHydrogens2D(IAtomContainer container, IAtom atom, double bondLength) {
if (container == null)
throw new IllegalArgumentException("cannot place hydrogens, no container provided");
if (atom.getPoint2d() == null)
throw new IllegalArgumentException("cannot place hydrogens on atom without coordinates");
logger.debug(
"placing hydrogens connected to atom ", atom.getSymbol(),
": ", atom.getPoint2d());
logger.debug("bond length", bondLength);
AtomPlacer atomPlacer = new AtomPlacer();
atomPlacer.setMolecule(container);
List<IAtom> connected = container.getConnectedAtomsList(atom);
IAtomContainer placed = container.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer unplaced = container.getBuilder().newInstance(IAtomContainer.class);
// divide connected atoms into those which are have and haven't been placed
for (final IAtom conAtom : connected) {
if (conAtom.getPoint2d() == null) {
if (conAtom.getSymbol().equals("H")) {
unplaced.addAtom(conAtom);
} else {
throw new IllegalArgumentException(
"cannot place hydrogens, atom has connected" + " non-hydrogens without coordinates");
}
} else {
placed.addAtom(conAtom);
}
}
logger.debug("Atom placement before procedure:");
logger.debug("Centre atom ", atom.getSymbol(), ": ", atom.getPoint2d());
for (int i = 0; i < unplaced.getAtomCount(); i++) {
logger.debug("H-" + i, ": ", unplaced.getAtom(i).getPoint2d());
}
Point2d centerPlacedAtoms = GeometryTools.get2DCenter(placed);
atomPlacer.distributePartners(atom, placed, centerPlacedAtoms, unplaced, bondLength);
logger.debug("Atom placement after procedure:");
logger.debug("Centre atom ", atom.getSymbol(), ": ", atom.getPoint2d());
for (int i = 0; i < unplaced.getAtomCount(); i++) {
logger.debug("H-" + i, ": ", unplaced.getAtom(i).getPoint2d());
}
}
/**
* Prepare the target molecule for analysis.
*
* <p>We perform ring perception and aromaticity detection and set up the appropriate properties.
* Right now, this function is called each time we need to do a query and this is inefficient.
*
* @throws CDKException if there is a problem in ring perception or aromaticity detection, which
* is usually related to a timeout in the ring finding code.
*/
private void initializeMolecule() throws CDKException {
// Code copied from
// org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor;
Map<String, Integer> valencesTable = new HashMap<String, Integer>();
valencesTable.put("H", 1);
valencesTable.put("Li", 1);
valencesTable.put("Be", 2);
valencesTable.put("B", 3);
valencesTable.put("C", 4);
valencesTable.put("N", 5);
valencesTable.put("O", 6);
valencesTable.put("F", 7);
valencesTable.put("Na", 1);
valencesTable.put("Mg", 2);
valencesTable.put("Al", 3);
valencesTable.put("Si", 4);
valencesTable.put("P", 5);
valencesTable.put("S", 6);
valencesTable.put("Cl", 7);
valencesTable.put("K", 1);
valencesTable.put("Ca", 2);
valencesTable.put("Ga", 3);
valencesTable.put("Ge", 4);
valencesTable.put("As", 5);
valencesTable.put("Se", 6);
valencesTable.put("Br", 7);
valencesTable.put("Rb", 1);
valencesTable.put("Sr", 2);
valencesTable.put("In", 3);
valencesTable.put("Sn", 4);
valencesTable.put("Sb", 5);
valencesTable.put("Te", 6);
valencesTable.put("I", 7);
valencesTable.put("Cs", 1);
valencesTable.put("Ba", 2);
valencesTable.put("Tl", 3);
valencesTable.put("Pb", 4);
valencesTable.put("Bi", 5);
valencesTable.put("Po", 6);
valencesTable.put("At", 7);
valencesTable.put("Fr", 1);
valencesTable.put("Ra", 2);
valencesTable.put("Cu", 2);
valencesTable.put("Mn", 2);
valencesTable.put("Co", 2);
// do all ring perception
AllRingsFinder arf = new AllRingsFinder();
IRingSet allRings;
try {
allRings = arf.findAllRings(atomContainer);
} catch (CDKException e) {
logger.debug(e.toString());
throw new CDKException(e.toString(), e);
}
// sets SSSR information
SSSRFinder finder = new SSSRFinder(atomContainer);
IRingSet sssr = finder.findEssentialRings();
for (IAtom atom : atomContainer.atoms()) {
// add a property to each ring atom that will be an array of
// Integers, indicating what size ring the given atom belongs to
// Add SSSR ring counts
if (allRings.contains(atom)) { // it's in a ring
atom.setFlag(CDKConstants.ISINRING, true);
// lets find which ring sets it is a part of
List<Integer> ringsizes = new ArrayList<Integer>();
IRingSet currentRings = allRings.getRings(atom);
int min = 0;
for (int i = 0; i < currentRings.getAtomContainerCount(); i++) {
int size = currentRings.getAtomContainer(i).getAtomCount();
if (min > size) min = size;
ringsizes.add(size);
}
atom.setProperty(CDKConstants.RING_SIZES, ringsizes);
atom.setProperty(CDKConstants.SMALLEST_RINGS, sssr.getRings(atom));
} else {
atom.setFlag(CDKConstants.ISINRING, false);
}
// determine how many rings bonds each atom is a part of
int hCount;
if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET) hCount = 0;
else hCount = atom.getImplicitHydrogenCount();
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
int total = hCount + connectedAtoms.size();
for (IAtom connectedAtom : connectedAtoms) {
if (connectedAtom.getSymbol().equals("H")) {
hCount++;
}
}
atom.setProperty(CDKConstants.TOTAL_CONNECTIONS, total);
atom.setProperty(CDKConstants.TOTAL_H_COUNT, hCount);
if (valencesTable.get(atom.getSymbol()) != null) {
int formalCharge =
atom.getFormalCharge() == CDKConstants.UNSET ? 0 : atom.getFormalCharge();
atom.setValency(valencesTable.get(atom.getSymbol()) - formalCharge);
}
}
for (IBond bond : atomContainer.bonds()) {
if (allRings.getRings(bond).getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
for (IAtom atom : atomContainer.atoms()) {
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
int counter = 0;
IAtom any;
for (IAtom connectedAtom : connectedAtoms) {
any = connectedAtom;
if (any.getFlag(CDKConstants.ISINRING)) {
counter++;
}
}
atom.setProperty(CDKConstants.RING_CONNECTIONS, counter);
}
// check for atomaticity
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
} catch (CDKException e) {
logger.debug(e.toString());
throw new CDKException(e.toString(), e);
}
}
/**
* This routine is called 'getRing() in Figueras original article finds the smallest ring of which
* rootNode is part of.
*
* @param rootNode The Atom to be searched for the smallest ring it is part of
* @param molecule The molecule that contains the rootNode
* @return The smallest Ring rootnode is part of
*/
private IRing getRing(IAtom rootNode, IAtomContainer molecule) {
IAtom node, neighbor, mAtom;
List neighbors, mAtoms;
/** OKatoms is Figueras nomenclature, giving the number of atoms in the structure */
int OKatoms = molecule.getAtomCount();
/** queue for Breadth First Search of this graph */
Queue queue = new Queue();
/* Initialize a path Vector for each node */
// Vector pfad1,pfad2;
List<List<IAtom>> path = new ArrayList<List<IAtom>>(OKatoms);
List<IAtom> intersection = new ArrayList<IAtom>();
List<IAtom> ring = new ArrayList<IAtom>();
for (int f = 0; f < OKatoms; f++) {
path.set(f, new ArrayList<IAtom>());
((List<IAtom>) molecule.getAtom(f).getProperty(PATH)).clear();
}
// Initialize the queue with nodes attached to rootNode
neighbors = molecule.getConnectedAtomsList(rootNode);
for (int f = 0; f < neighbors.size(); f++) {
// if the degree of the f-st neighbor of rootNode is greater
// than zero (i.e., it has not yet been deleted from the list)
neighbor = (IAtom) neighbors.get(f);
// push the f-st node onto our FIFO queue
// after assigning rootNode as its source
queue.push(neighbor);
((List<IAtom>) neighbor.getProperty(PATH)).add(rootNode);
((List<IAtom>) neighbor.getProperty(PATH)).add(neighbor);
}
while (queue.size() > 0) {
node = (IAtom) queue.pop();
mAtoms = molecule.getConnectedAtomsList(node);
for (int f = 0; f < mAtoms.size(); f++) {
mAtom = (IAtom) mAtoms.get(f);
if (mAtom
!= ((List) node.getProperty(PATH))
.get(((List<IAtom>) node.getProperty(PATH)).size() - 2)) {
if (((List) mAtom.getProperty(PATH)).size() > 0) {
intersection =
getIntersection((List) node.getProperty(PATH), (List) mAtom.getProperty(PATH));
if (intersection.size() == 1) {
// we have found a valid ring closure
// now let's prepare the path to
// return in tempAtomSet
logger.debug("path1 ", ((List) node.getProperty(PATH)));
logger.debug("path2 ", ((List) mAtom.getProperty(PATH)));
logger.debug("rootNode ", rootNode);
logger.debug("ring ", ring);
ring = getUnion((List) node.getProperty(PATH), (List) mAtom.getProperty(PATH));
return prepareRing(ring, molecule);
}
} else {
// if path[mNumber] is null
// update the path[mNumber]
// pfad2 = (Vector)node.getProperty(PATH);
mAtom.setProperty(PATH, new ArrayList<IAtom>((List<IAtom>) node.getProperty(PATH)));
((List<IAtom>) mAtom.getProperty(PATH)).add(mAtom);
// pfad1 = (Vector)mAtom.getProperty(PATH);
// now push the node m onto the queue
queue.push(mAtom);
}
}
}
}
return null;
}
/**
* calculates the kier shape indices for an atom container
*
* @param container AtomContainer
* @return kier1, kier2 and kier3 are returned as arrayList of doubles
* @throws CDKException Possible Exceptions
*/
@Override
public DescriptorValue calculate(IAtomContainer container) {
IAtomContainer atomContainer;
try {
atomContainer = (IAtomContainer) container.clone();
} catch (CloneNotSupportedException e) {
DoubleArrayResult kierValues = new DoubleArrayResult(3);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
kierValues,
getDescriptorNames());
}
atomContainer = AtomContainerManipulator.removeHydrogens(atomContainer);
// org.openscience.cdk.interfaces.IAtom[] atoms = atomContainer.getAtoms();
java.util.List firstAtomNeighboors;
java.util.List secondAtomNeighboors;
java.util.List thirdAtomNeighboors;
DoubleArrayResult kierValues = new DoubleArrayResult(3);
double bond1;
double bond2;
double bond3;
double kier1;
double kier2;
double kier3;
double atomsCount = atomContainer.getAtomCount();
ArrayList<Double> singlePaths = new ArrayList<Double>();
ArrayList<String> doublePaths = new ArrayList<String>();
ArrayList<String> triplePaths = new ArrayList<String>();
double[] sorterFirst = new double[2];
double[] sorterSecond = new double[3];
String tmpbond2;
String tmpbond3;
for (int a1 = 0; a1 < atomsCount; a1++) {
bond1 = 0;
firstAtomNeighboors = atomContainer.getConnectedAtomsList(atomContainer.getAtom(a1));
for (int a2 = 0; a2 < firstAtomNeighboors.size(); a2++) {
bond1 =
atomContainer.getBondNumber(
atomContainer.getAtom(a1), (IAtom) firstAtomNeighboors.get(a2));
if (!singlePaths.contains(new Double(bond1))) {
singlePaths.add(bond1);
java.util.Collections.sort(singlePaths);
}
secondAtomNeighboors =
atomContainer.getConnectedAtomsList((IAtom) firstAtomNeighboors.get(a2));
for (int a3 = 0; a3 < secondAtomNeighboors.size(); a3++) {
bond2 =
atomContainer.getBondNumber(
(IAtom) firstAtomNeighboors.get(a2), (IAtom) secondAtomNeighboors.get(a3));
if (!singlePaths.contains(new Double(bond2))) {
singlePaths.add(bond2);
}
sorterFirst[0] = bond1;
sorterFirst[1] = bond2;
java.util.Arrays.sort(sorterFirst);
tmpbond2 = sorterFirst[0] + "+" + sorterFirst[1];
if (!doublePaths.contains(tmpbond2) && (bond1 != bond2)) {
doublePaths.add(tmpbond2);
}
thirdAtomNeighboors =
atomContainer.getConnectedAtomsList((IAtom) secondAtomNeighboors.get(a3));
for (int a4 = 0; a4 < thirdAtomNeighboors.size(); a4++) {
bond3 =
atomContainer.getBondNumber(
(IAtom) secondAtomNeighboors.get(a3), (IAtom) thirdAtomNeighboors.get(a4));
if (!singlePaths.contains(new Double(bond3))) {
singlePaths.add(bond3);
}
sorterSecond[0] = bond1;
sorterSecond[1] = bond2;
sorterSecond[2] = bond3;
java.util.Arrays.sort(sorterSecond);
tmpbond3 = sorterSecond[0] + "+" + sorterSecond[1] + "+" + sorterSecond[2];
if (!triplePaths.contains(tmpbond3)) {
if ((bond1 != bond2) && (bond1 != bond3) && (bond2 != bond3)) {
triplePaths.add(tmpbond3);
}
}
}
}
}
}
if (atomsCount == 1) {
kier1 = 0;
kier2 = 0;
kier3 = 0;
} else {
kier1 =
(((atomsCount) * ((atomsCount - 1) * (atomsCount - 1)))
/ (singlePaths.size() * singlePaths.size()));
if (atomsCount == 2) {
kier2 = 0;
kier3 = 0;
} else {
if (doublePaths.size() == 0) kier2 = Double.NaN;
else
kier2 =
(((atomsCount - 1) * ((atomsCount - 2) * (atomsCount - 2)))
/ (doublePaths.size() * doublePaths.size()));
if (atomsCount == 3) {
kier3 = 0;
} else {
if (atomsCount % 2 != 0) {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 =
(((atomsCount - 1) * ((atomsCount - 3) * (atomsCount - 3)))
/ (triplePaths.size() * triplePaths.size()));
} else {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 =
(((atomsCount - 3) * ((atomsCount - 2) * (atomsCount - 2)))
/ (triplePaths.size() * triplePaths.size()));
}
}
}
}
kierValues.add(kier1);
kierValues.add(kier2);
kierValues.add(kier3);
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), kierValues, getDescriptorNames());
}