ROSHAMBO uses the open-source PAPER software to perform the overlap optimization, which relies on GPU computing to accelerate the concepts of Gaussian molecular shape first developed by Grant and Pickup. As this method has been extensively described elsewhere, in this note we instead focus on its integration into the larger ROSHAMBO workflow. In short, each atom is defined by a Gaussian function, and a molecular volume (or self-overlap) is an integral over atomic Gaussians. Overlaps are also calculated as integrals over these Gaussians, with a radius that can be set as uniform (defined by a default carbon radius) or specific to each atom type. ROSHAMBO allows a user to either include or ignore hydrogens when calculating these overlaps. We estimate the overlap integrals via a second-order analytic approximation, with no knowledge of pharmacaphoric features. Refer to the Theory section in the Supplemental Information for the equations employed and a discussion on the simplifications supported in ROSHAMBO for defining which atoms are considered neighbors when calculating the overlap volumes (Gaussian and proxy cutoff distances). ROSHAMBO then converts the quaternion matrices that maximize overlap into rotation/translation matrices, uses them to align the dataset molecules, and passes the aligned molecules forward for similarity score calculation.