Virtual screening or exploratory synthesis campaigns may not have a rich body of heuristics or benchmark studies for new applications. Then, it becomes necessary to pair a fingerprint to a similarity measure. This choice is called "a measure" here for brevity. AIMSim automates this search via the MeasureSearch Task class (Supporting Information S3.2). A bar graph enumerating the score and neighbor correlations for the top n user-specified measures can be displayed. Alternatively, the top measure can be programmatically extracted for module-level usage. This Task is automatically launched when the measure is set to 'determine' in the configuration file. The user can constrain the optimization to specific fingerprints and similarity measures or to only metric distances which can be used for clustering. We illustrate a use case in for this on the QM9 dataset in section S4 of the Supporting Information.