Contents

• List of Figures
• List of Tables
• Introduction
  • Guide organization
  • Document style conventions
  • For more information on VMD and MDScope
  • Contacting the authors
  • Credits and program reference
  • Registering VMD
  • Acknowledgements
  • Disclaimer
• 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
    • Note for RCS users:
  • 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
      • Device-Specific Rendering.
      • Drawing Tokens.
      • #Displayable#1799> objects.
      • The #Scene#1844> .
      • Colors.
      • Picking Items.
    • 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
    • DLinkList
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • Inform
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • NameList
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • ResizeArray
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • Stack
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • Timer
      • Description
      • Constructors
      • Nonvirtual member functions
      • Method of use
  • Display objects
    • ColorList
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Method of use
    • ColorUser
      • Description
      • Constructors
      • Internal data structures
      • Virtual member functions
      • Method of use
    • DispCmd
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • DisplayDevice
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Virtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • Displayable
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Virtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • Matrix4
      • Description
      • Constructors
      • Internal data structures
      • Method of use
    • Scene
      • Description
      • Constructors
      • Internal data structures
      • Virtual member functions
      • Method of use
      • Suggestions for future changes/additions
  • Molecule objects
    • Animation
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
        • Adding new frames:
        • Updating the current position:
      • Suggestions for future changes/additions
    • Atom
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • BaseMolecule
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
    • DrawMolecule
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
    • Molecule
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
    • Timestep
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
  • Remote connection objects
  • User interface objects
    • Command
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
        • Using a Command object:
        • Developing a new class derived from Command:
      • Suggestions for future changes/additions
    • CommandQueue
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • Mouse
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • PopupMenu
      • Description
      • Constructors
      • Enumerations, lists or character name arrays
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • PopupMenuItem
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
      • Suggestions for future changes/additions
    • UIList
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Method of use
    • UIObject
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
    • UIText
      • Description
      • Constructors
      • Internal data structures
      • Nonvirtual member functions
      • Virtual member functions
      • Method of use
      • Suggestions for future changes/additions
  • Tracker objects
• About this document ...