/**
* 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()]);
}
