/**
* Selects an optimum edge for elimination in structures without N2 nodes.
*
* <p>This might be severely broken! Would have helped if there was an explanation of how this
* algorithm worked.
*
* @param ring
* @param molecule
*/
private IBond checkEdges(IRing ring, IAtomContainer molecule) {
IRing r1, r2;
IRingSet ringSet = ring.getBuilder().newInstance(IRingSet.class);
IBond bond;
int minMaxSize = Integer.MAX_VALUE;
int minMax = 0;
logger.debug("Molecule: " + molecule);
Iterator<IBond> bonds = ring.bonds().iterator();
while (bonds.hasNext()) {
bond = (IBond) bonds.next();
molecule.removeElectronContainer(bond);
r1 = getRing(bond.getAtom(0), molecule);
r2 = getRing(bond.getAtom(1), molecule);
logger.debug("checkEdges: " + bond);
if (r1.getAtomCount() > r2.getAtomCount()) {
ringSet.addAtomContainer(r1);
} else {
ringSet.addAtomContainer(r2);
}
molecule.addBond(bond);
}
for (int i = 0; i < ringSet.getAtomContainerCount(); i++) {
if (((IRing) ringSet.getAtomContainer(i)).getBondCount() < minMaxSize) {
minMaxSize = ((IRing) ringSet.getAtomContainer(i)).getBondCount();
minMax = i;
}
}
return (IBond) ring.getElectronContainer(minMax);
}
/**
* removes all bonds connected to the given atom leaving it with degree zero.
*
* @param atom The atom to be disconnecred
* @param molecule The molecule containing the atom
*/
private void trim(IAtom atom, IAtomContainer molecule) {
List<IBond> bonds = molecule.getConnectedBondsList(atom);
for (int i = 0; i < bonds.size(); i++) {
molecule.removeElectronContainer((IBond) bonds.get(i));
}
// you are erased! Har, har, har..... >8-)
}
/**
* Eliminates one bond of this atom from the molecule
*
* @param atom The atom one bond is eliminated of
* @param molecule The molecule that contains the atom
*/
private void breakBond(IAtom atom, IAtomContainer molecule) {
Iterator<IBond> bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
if (bond.contains(atom)) {
molecule.removeElectronContainer(bond);
break;
}
}
}
/**
* Finds the Smallest Set of Smallest Rings.
*
* @param mol the molecule to be searched for rings
* @return a RingSet containing the rings in molecule
*/
public IRingSet findSSSR(IAtomContainer mol) {
IBond brokenBond = null;
IChemObjectBuilder builder = mol.getBuilder();
IRingSet sssr = builder.newInstance(IRingSet.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.add(mol);
IAtom smallest;
int smallestDegree, nodesToBreakCounter, degree;
IAtom[] rememberNodes;
IRing ring;
// Two Vectors - as defined in the article. One to hold the
// full set of atoms in the structure and on to store the numbers
// of the nodes that have been trimmed away.
// Furhter there is a Vector nodesN2 to store the number of N2 nodes
List<IAtom> fullSet = new ArrayList<IAtom>();
List<IAtom> trimSet = new ArrayList<IAtom>();
List<IAtom> nodesN2 = new ArrayList<IAtom>();
initPath(molecule);
logger.debug("molecule.getAtomCount(): " + molecule.getAtomCount());
// load fullSet with the numbers of our atoms
for (int f = 0; f < molecule.getAtomCount(); f++) {
fullSet.add(molecule.getAtom(f));
}
logger.debug("fullSet.size(): " + fullSet.size());
do {
// Add nodes of degree zero to trimset.
// Also add nodes of degree 2 to nodesN2.
// In the same run, check, which node has the lowest degree
// greater than zero.
smallestDegree = 7;
smallest = null;
nodesN2.clear();
for (int f = 0; f < molecule.getAtomCount(); f++) {
IAtom atom = molecule.getAtom(f);
degree = molecule.getConnectedBondsCount(atom);
if (degree == 0) {
if (!trimSet.contains(atom)) {
logger.debug("Atom of degree 0");
trimSet.add(atom);
}
}
if (degree == 2) {
nodesN2.add(atom);
}
if (degree < smallestDegree && degree > 0) {
smallest = atom;
smallestDegree = degree;
}
}
if (smallest == null) break;
// If there are nodes of degree 1, trim them away
if (smallestDegree == 1) {
trimCounter++;
trim(smallest, molecule);
trimSet.add(smallest);
}
// if there are nodes of degree 2, find out of which rings
// they are part of.
else if (smallestDegree == 2) {
rememberNodes = new IAtom[nodesN2.size()];
nodesToBreakCounter = 0;
for (int f = 0; f < nodesN2.size(); f++) {
ring = getRing((IAtom) nodesN2.get(f), molecule);
if (ring != null) {
// check, if this ring already is in SSSR
if (!RingSetManipulator.ringAlreadyInSet(ring, sssr)) {
sssr.addAtomContainer(ring);
rememberNodes[nodesToBreakCounter] = (IAtom) nodesN2.get(f);
nodesToBreakCounter++;
}
}
}
if (nodesToBreakCounter == 0) {
nodesToBreakCounter = 1;
rememberNodes[0] = (IAtom) nodesN2.get(0);
}
for (int f = 0; f < nodesToBreakCounter; f++) {
breakBond(rememberNodes[f], molecule);
}
if (brokenBond != null) {
molecule.addBond(brokenBond);
brokenBond = null;
}
}
// if there are nodes of degree 3
else if (smallestDegree == 3) {
ring = getRing(smallest, molecule);
if (ring != null) {
// check, if this ring already is in SSSR
if (!RingSetManipulator.ringAlreadyInSet(ring, sssr)) {
sssr.addAtomContainer(ring);
}
brokenBond = checkEdges(ring, molecule);
molecule.removeElectronContainer(brokenBond);
}
}
} while (trimSet.size() < fullSet.size());
logger.debug("fullSet.size(): " + fullSet.size());
logger.debug("trimSet.size(): " + trimSet.size());
logger.debug("trimCounter: " + trimCounter);
// molecule.setProperty(CDKConstants.SMALLEST_RINGS, sssr);
return sssr;
}