Contents

• Contents
• List of Figures
• List of Tables
• Introduction
  • Guide organization
  • Document style conventions
  • For more information on BioCoRE, MDTools, NAMD, and VMD
  • Contacting the authors
  • Credits and Program Reference
  • Copyright and Disclaimer
  • Registering VMD
  • Acknowledgments
• Source Code File Structure
  • Directory tree structure
  • Using the RCS system
• Using the Configure Script and Makefile
  • The configure script
  • Setting the configuration parameters
    • Installation parameters
    • Compilation parameters
  • Configuring the Makefile
    • Optional program components
    • Supported operating systems
  • Compiling VMD
  • Makefile commands
    • src directory Makefile commands
    • doc directory Makefile commands
    • Makefile commands for either directory
  • Changing the configure script
    • Adding new configurable parameters
    • Adding new configuration options
    • Adding support for a new architecture
• Source Code Style Guide
  • Naming conventions
    • Class names
    • Class member variable names
    • Class member function names
    • Global variable names
    • Global function names
    • Source code file names
    • Documentation file names
  • Creating new files
    • File formats
• Program Structure
  • Program component descriptions
    • Utility objects
    • Display objects
    • Molecule objects
    • Remote connection objects
    • User interface objects
    • Tracker objects
  • Main VMD execution loop
  • External library descriptions
• Function and Class Descriptions
  • Utility functions
  • Utility objects
    • Inform
    • NameList
    • ResizeArray
    • Stack
  • Display objects
    • ColorList
    • ColorUser
    • DispCmd
    • DisplayDevice
    • Displayable
    • Matrix4
    • Scene
  • Molecule objects
    • Animation
    • Atom
    • BaseMolecule
    • DrawMolecule
    • Molecule
    • Timestep
  • Remote connection objects
  • User interface objects
    • Command
    • CommandQueue
    • Mouse
    • UIObject
    • UIText
  • Tracker objects
• About this document ...