We need an exception check here to fail gracefully

[tylerperyea]

This can throw an exception if a molfile fails to parse, it shouldn't fail catastrophically when that happens:

structure-indexer/src/main/java/tripod/chem/indexer/StructureIndexer.java

Line 659 in d84cb99

out.put(new Result (p, similarity,null));

Also, this can only happen because we parse the molfile as part of the payload loading:

structure-indexer/src/main/java/tripod/chem/indexer/StructureIndexer.java

Line 440 in d84cb99

mol = payload.getMol();

The thing is, we only NEED to parse the molfile if we're going to do a substructure search. For similarity searches this is an unnecessary step anyway and should probably be avoided. Perhaps it can be deferred?

The worse part about this is that throwing an exception ultimately makes the queue wait forever:

structure-indexer/src/main/java/tripod/chem/indexer/StructureIndexer.java

Lines 1608 to 1623 in d84cb99

	for (int i = 0; i < nthreads; ++i)
	in.put(POISON_PAYLOAD);
	threadPool.submit(new Runnable () {
	public void run () {
	try {
	int total = 0;
	for (Future<Integer> f : threads) {
	total += f.get();
	}
	out.put(POISON_RESULT);
	}
	catch (Exception ex) {
	ex.printStackTrace();
	}
	}
	});

Typically we shouldn't see an unparsable molfile in the index, but it does happen from time to time.