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\subsection*{Virtual Screening Evaluation}  In order to investigate the utility of the FOMS approach we consider both the ability of shape constraint filters to generate enriched subsets and the  quality of shape similarity rankings generated using fragment aligned molecules. We compare to VAMS, which aligns all molecules to a canonical reference system based on their moments of inertia, and rdShape, the shape alignment module of rdkit \cite{rdkit} which dynamically aligns shapes to maximize their overlap. Results are reported using receiver operating characteristic curves which plot the false positive rate (FPR) with respect to the true positive rate (TPR) as the classification sensitivity threshold is changed for a ranking. For each target, conformers of the active and decoy compounds were generated using rdkit\cite{rdkit}. A maximum of 100 conformers with a minimum RMSD difference of 0.7{\AA} and an energy window cutoff of 10 were generated for each compound. For each fragment considered, the corresponding conformers were extracted into each fragment-specific subset. The subsets were then preprocessed to create VAMS and FOMS search databases. The VAMS database stores a single pose for each conformation aligned along its moments of inertia. For FOMS, if a compound contains multiple instances of the anchor fragment or the fragment contains symmetries, multiple poses per a conformation are stored to account for the multiple fragments/symmetries.