BuildAMol leverages an atom-substitution strategy to connect molecular fragments, enabling the direct spatial positioning of one molecule relative to another. This approach involves designating a set of four atoms, two from each fragment. A rigid body transformation is then employed to precisely align the fragments by superimposing two atoms from one fragment onto their counterparts in the other fragment. This ensures proper spatial arrangement for bonding. Subsequently, a new bond is formed between a designated atom from each fragment, while the corresponding atoms used for alignment are removed. This method ensures the resulting molecule has realistic bond lengths and angles, provided both fragment molecules are chemically sound.