BuildAMol simplifies user interaction by channeling most operations through the Molecule class. This class acts as a central hub, providing methods for users to perform various actions on molecular structures. For convenience, some frequently used functions, like reading PDB files or connecting fragments, are available as both standalone functions and methods within the Molecule class. The key distinction lies in their behavior: standalone functions typically create a new copy of the molecule, whereas CHARMM BuildAMol PubChem PDBCD Amino Acid Linkages Glycosidic Linkages Lipid Linkages 50 Million Compounds Amino Acids methods directly modify the existing molecule object. However, both functionalities can be customized using optional arguments.