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OK, this further takes down the computation time:
CDKBenchmark.testPerceiveAtomType avgt 10 124423.327 ± 22679.255 ns/op
CDKBenchmark.testPerceiveOneByOne avgt 10 182389.348 ± 40002.280 ns/op
I also tried passing around the full map, all the way down to the methods that determine if an nitrogen is part of an amide or thioamide, but that undid basically all of the above speed up... must have done something wrong.
For now, please have a look at this. I'm looking forward to hear the advantage on parsing the 100k random ChEMBL compounds...