/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers of another
* AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* Removes all atoms and electronContainers of a given atomcontainer from this container.
*
* @param atomContainer The atomcontainer to be removed
*/
public void remove(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
removeAtom(atomContainer.getAtom(f));
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
removeBond(atomContainer.getBond(f));
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
removeLonePair(atomContainer.getLonePair(f));
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
removeSingleElectron(atomContainer.getSingleElectron(f));
}
}
/**
* A unit test for JUnit with C=CCCl # C=CC[Cl+*]
*
* @cdk.inchi InChI=1/C3H7Cl/c1-2-3-4/h2-3H2,1H3
*/
@Test
public void testCompareIonized() throws Exception {
IAtomContainer molA = builder.newInstance(IAtomContainer.class);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(0, 1, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(1, 2, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
molA.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molA);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
lpcheck.saturate(molA);
double resultA =
((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
IAtomContainer molB = builder.newInstance(IAtomContainer.class);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(0, 1, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(1, 2, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
molB.getAtom(3).setFormalCharge(1);
molB.addSingleElectron(3);
molB.addLonePair(3);
molB.addLonePair(3);
molB.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molB);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
lpcheck.saturate(molB);
Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
double resultB =
((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
Assert.assertNotSame(resultA, resultB);
}
/**
* Get all paths of lengths 0 to the specified length.
*
* <p>This method will find all paths upto length N starting from each atom in the molecule and
* return the unique set of such paths.
*
* @param container The molecule to search
* @return A map of path strings, keyed on themselves
*/
private Integer[] findPaths(IAtomContainer container) {
ShortestPathWalker walker = new ShortestPathWalker(container);
// convert paths to hashes
List<Integer> paths = new ArrayList<Integer>();
int patternIndex = 0;
for (String s : walker.paths()) {
int toHashCode = s.hashCode();
paths.add(patternIndex, toHashCode);
patternIndex++;
}
/*
* Add ring information
*/
IRingSet sssr = Cycles.essential(container).toRingSet();
RingSetManipulator.sort(sssr);
for (Iterator<IAtomContainer> it = sssr.atomContainers().iterator(); it.hasNext(); ) {
IAtomContainer ring = it.next();
int toHashCode = String.valueOf(ring.getAtomCount()).hashCode();
paths.add(patternIndex, toHashCode);
patternIndex++;
}
/*
* Check for the charges
*/
List<String> l = new ArrayList<String>();
for (Iterator<IAtom> it = container.atoms().iterator(); it.hasNext(); ) {
IAtom atom = it.next();
int charge = atom.getFormalCharge() == null ? 0 : atom.getFormalCharge();
if (charge != 0) {
l.add(atom.getSymbol().concat(String.valueOf(charge)));
}
}
Collections.sort(l);
int toHashCode = l.hashCode();
paths.add(patternIndex, toHashCode);
patternIndex++;
l = new ArrayList<String>();
/*
* atom stereo parity
*/
for (Iterator<IAtom> it = container.atoms().iterator(); it.hasNext(); ) {
IAtom atom = it.next();
int st = atom.getStereoParity() == null ? 0 : atom.getStereoParity();
if (st != 0) {
l.add(atom.getSymbol().concat(String.valueOf(st)));
}
}
Collections.sort(l);
toHashCode = l.hashCode();
paths.add(patternIndex, toHashCode);
patternIndex++;
if (container.getSingleElectronCount() > 0) {
StringBuilder radicalInformation = new StringBuilder();
radicalInformation.append("RAD: ").append(String.valueOf(container.getSingleElectronCount()));
paths.add(patternIndex, radicalInformation.toString().hashCode());
patternIndex++;
}
if (container.getLonePairCount() > 0) {
StringBuilder lpInformation = new StringBuilder();
lpInformation.append("LP: ").append(String.valueOf(container.getLonePairCount()));
paths.add(patternIndex, lpInformation.toString().hashCode());
patternIndex++;
}
return paths.toArray(new Integer[paths.size()]);
}