Three-dimensional molecular alignment and scoring is a key part of many modern virtual screening processes, either by itself or as part of a larger workflow. Efficient and accurate alignment tools allow computational and medicinal chemists to screen available or enumerated libraries at scale, prioritizing a small list of molecules for synthesis based on similarity to a key molecule of interest. Despite the near ubiquitous use of such tools across the pharmaceutical industry, the currently available packages suffer from one or more of three key limitations: (1) they omit key features like the ability to score molecules based on both shape and color, (2) they lack documentation, maintenance, or quality-of-life features that would make them practical for widespread adoption into pharmaceutical and academic use-cases, and (3) they are proprietary (and often times financially costly) technologies that cannot be easily altered, customized, or improved.