MC sampling was run at eight effective temperatures: 0, 10 -6 , 10 -5 , 0.0001, 0.001, 0.01, 0.1, and 1. Ten initial tests of 10,000 iterations were performed for each combination of molecule set, temperature, and tool. These were followed by three additional tests with first 50,000 and then 100,000 iterations for MiniDrugBank with SMIRKY, since the search space for fragment types is so large. Output for both tools was saved in two ways: a human-readable log of the run, and a comma-separated trajectory file which stores the partial score for each reference atom or fragment type and the total score at each iteration.