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… of IChemObject flag VISITED for safe parallelisation
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Looks ok but I really would not share a molecule in a parallel environment. So much of the rest of the toolkit depends on this not being the case and it's just useful to draw the line there. If you want to work on something in multiple thread makes a copy but mostly you should only really need parallelism for large sets of molecules. Any method which is too slow on a single molecule on modern hardware is likely not a useful method. |
johnmay
reviewed
Sep 1, 2025
| for (Object bond : bonds) { | ||
| nextAtom = ((IBond) bond).getOther(atom); | ||
| logger.debug("BreadthFirstSearch around atom " + (container.indexOf(atom) + 1)); | ||
| List<IBond> bonds = container.getConnectedBondsList(atom); |
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You can now safely use for (IBond bond : atom.bonds())
johnmay
reviewed
Sep 1, 2025
| || nextAtom.getAtomicNumber() == IElement.N || nextAtom.getAtomicNumber() == IElement.O) | ||
| & !nextAtom.getFlag(IChemObject.VISITED)) { | ||
| //logger.debug("BDS> AtomNr:"+container.indexOf(nextAtom)+" maxBondOrder:"+container.getMaximumBondOrder(nextAtom)+" Aromatic:"+nextAtom.getFlag(CDKConstants.ISAROMATIC)+" FormalCharge:"+nextAtom.getFormalCharge()+" Charge:"+nextAtom.getCharge()+" Flag:"+nextAtom.getFlag(CDKConstants.VISITED)); | ||
| && !visited[container.indexOf(nextAtom)]) { |
johnmay
reviewed
Sep 1, 2025
| } | ||
| } else { | ||
| nextAtom.setFlag(IChemObject.VISITED, true); | ||
| visited[container.indexOf(nextAtom)] = true; |
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Makes LargestPiSystemDescriptor use an internal "visited" array instead of the IChemObject flag VISITED of the atoms for safe parallelisation over shared molecule instances.
Also, minor code improvements in exception handling and un-commented debug messages (and added a logger to the class, first of all).