The Classes that represent the Macromolecular Structure

The Intrinsic classes combine with the Extensible classes to form the macromolecular representation. The intrinsic classes contain the essential part of the library implementation. A majority of the intrinsic classes were developed to represent and manipulate macromolecular components, for example polypeptide chains or DNA strands, secondary structures, functional sites, disulphide linkages, salt bridges, residues, and atoms. Each of these components are represented by intrinsic and extensible classes. Intrinsic classes are identified by class names starting with Intr, for example IntrAtom and IntrEntity serve as container classes for all supplied features of the macromolecule at that level.

In addition to the Intrinsic classes, there are the list classes which represent a set of macromolecular components. Such as we could have a List of SubEntities. In general we could have a list of any object. For example a chain/Entity has a list of residues/SubEntities which represents all the residues the chain carries. The Iterative classes iterate over these lists.

These classes are broadly categorized in the following way:

The Classes that represent the Primary Structure
These are the classes that represent the Chain,Residues,Atoms and Bonds of the Macromolecular structure.
The Classes that represent the Secondary Structure
These are the classes that represent the Secondary Structures of the Protein.
The List Classes
These are templatized list classes. There is the ListMgr class, which is a generalized Abstract Base Class for all the Lists. Then there are several specializations, of this ListMgr class, for representing Linear, NonLinear, MultiLinear, and Array based Lists.
The Secondary Structure List Classes
These are List classes specialized for handling various kinds of Secondary Structure Lists.
The PDBInfo, and related classes
This is the class that stores the textual information of the Protein. i.e: The COMPOUND,HEADER,SOURCE etc. records are managed in this class.
There are some other miscellaneous classes

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