Modern synthetic chemistry increasingly incorporates theoretical and empirical data-oriented approaches for designing functional small molecules, understanding reaction pathways, and predicting and optimizing reaction outcomes. In recent years, medium-to high-throughput experimentation techniques have provided access to large data sets suitable for subsequent statistical analysis and predictive modeling. Critically, encoding molecules in a machinereadable format is essential before any computational analysis of the physical molecular entities can commence. Although a variety of different software tools for the enumeration and encoding of in silico libraries exists, we have found a lack of suitably general, open-source tools to support accurate generation of libraries containing complex stereochemical information directly from the two-dimensional depictions familiar to all chemists.