The core sub-package of BuildAMol provides the essential framework for constructing molecular structures. It provides foundational classes representing the building blocks of molecules (Atom and Residue), as well as higher-level classes (Molecule and Linkage) to handle the assembly process. BuildAMol leverages a hierarchical data structure, similar to the one used by Biopython . In this approach, complex molecules are organized as a series of nested building blocks. For instance, individual Atom objects are grouped into a Residue object representing a molecular fragment. This hierarchical organization allows for efficient access and manipulation of specific parts within complex molecules, a significant advantage for fragment-based assembly workflows.