Guide organization

As mentioned, this guide is designed to aid users who are interested in modifying or extending the current implementation of VMD. This manual is organized into the following chapters following this introduction:

• Source code file structure (section 2)
  What subdirectories exist within the VMD working directory tree, and how to use the RCS (Revision Control System) to access and modify source files.
• Using the configure script and makefile (section 3)
  The design and use of the configure script, which creates the proper Makefile needed to compile VMD for a particular architecture and set of options, and how to use the Makefile once it has been created.
• Source code style guide (section 4)
  A set of guidelines used (mostly) in the naming of C++ classes, functions and variables, and a set of steps to follow when adding new objects and source code files to VMD.
• Program structure (section 5)
  A comprehensive overview of the design of VMD, concentrating on the organization and relationship of the various C++ objects which make up the program.
• Function and class descriptions (section 6)
  With section 5, the major part of the Programmer's Guide. This section provides a standard description for each utility function and object class in C++, outlining how to use each class and, for the main base classes in VMD, how to define and create new derived classes.