| Atom | Bioperl structure Object, describes an Atom |
| Chain | Bioperl structure Object, describes a chain |
| Entry | Bioperl structure Object, describes the whole entry |
| IO | Handler for Structure Formats |
| Model | Bioperl structure Object, describes a Model |
| Residue | Bioperl structure Object, describes a Residue |
| StructureI | Abstract Interface for a Structure objects |