32. Design Decisions

This chapter builds upon important concepts introduced in the previous section entitled Getting Started with OEChem Molecules found in the introductory chapter as well as the chapters entitled OEMols and OEGraphMols and OEQMols and Queries in OEChem. It may be beneficial to review those sections before proceeding.

As you have seen throughout this manual, the OEMol , OEGraphMol , and OEQMol are the concrete classes which handle most molecular function in OEChem. The OEGraphMol's API is defined in the OEMolBase abstract base-class, the OEMol's API is defined by the OEMolBase and OEMCMolBaseT abstract base-classes, and the OEQMol 's API is defined by the OEMolBase and abstract base- classes. The OEMCMolBaseT class publicly inherits from the OEMolBase class, which in turn inherits from the OEBase class. Similarly, the OEQMolBase class publicly inherits from the OEMolBase class, which again inherits from the OEBase class. An OEGraphMol, can be passed to any function which takes an OEMolBase argument. An OEMol can be passed to any function which takes an OEMCMolBaseT or OEMolBase argument, and an OEQMol can be passed to any function which takes an OEQMolBase or OEMolBase argument.

Simplistic OEChem inheritance scheme:
                OEBase
                 /|\
                  |
                  |
             --> OEMolBase ---------------- OEGraphMol
             |   /|\
             |    |
             |    |
             |  OEMCMolBaseT ------------- OEMol
          OEQMolBase --------------------- OEQMol
<- indicates inheritance
-- indicates API correspondence without inheritance

This paragraph requires some previous knowledge of the C++ factory and smart-pointer idioms. It is standard practice when working with abstract base-classes, such as OEMolBase or OEMCMolBaseT, to define a function which returns a pointer one of these objects. These functions, called factories, give library users access to concrete objects even when only the abstract base-class is exposed in the public API . The problem with factory functions is that they require the user to manage the object's memory. When the factory function returns a pointer to an abstract base-class, it also passes ownership of the memory to the programmer. To alleviate the problems associated with memory management introduced by factories, the C++ smart-pointer idiom is often used. Simply put, a smart-pointer holds a real pointer to an object, and deallocates the pointer's memory when the smart-pointer goes out of scope (e.g. in it's destructor). In OEChem, OEGraphMols and OEMols fulfill the function of both factories and smart-pointers. This gives the user access to multiple OEMolBase and OEMCMolBase implementations without the need of worrying about memory management. The OEGraphMol and OEMol constructors allow the user to specify which OEMolBase or OEMCMolBaseT implementation they would like (i.e. - factory function), and the OEGraphMol and OEMol objects themselves act as smart-pointers, cleaning up the implementation pointers when the molecules go out of scope. The relationship between the OEQMolBase class and the OEQMol class is similar.

Subsections

				OEChem - C++ Theory Manual

				OEChem - C++ Theory Manual