All molecular modeling programs generally need to know what are the atoms in all residue types, what are the atom pairs that are covalently bonded to each other (i.e., molecular topology), and what are the ideal bond lengths, angles, dihedral angles, and improper dihedral angles (i.e., internal coordinates and stereochemical restraints). This information is stored in the residue topology and parameter libraries, which are manipulated by MODELLER scripts using the Libraries class (see Section 6.5.
For commands dealing with generating, patching, and mutating molecular topology, see the model class reference, in section 6.6.