VMD Programmer's Guide

A. Dalke, J. Gullingsrud, W. Humphrey, S. Izrailev, J. Stone, J. Ulrich
Version 1.3
April 6, 1999

Theoretical Biophysics Group
University of Illinois and Beckman Institute
405 N. Mathews
Urbana, IL 61801
VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/
Description The Programmer's Guide describes the structure and organization of the program VMD , and provides complete descriptions for all important object classes. This guide is designed to aid researchers interested in learning how VMD is constructed and who are interested in making modifications or improvements to the existing code. The program is logically divided into six main categories: (1) Utility objects; (2) Rendering (display) objects; (3) Molecule objects; (4) Remote connection objects; (5) User interface objects; (6) Spatial tracking and 3D pointer object. The Programmer's Guide describes first the organization and conventions used in all source files for VMD , then discusses the program design and relationship between the five components, and concludes with individual descriptions of each object class.

 
• 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
  • 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
    • 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.
      • objects.
      • The .
      • 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
    • Inform
    • NameList
    • ResizeArray
    • Stack
    • Timer
  • Display objects
    • ColorList
    • ColorUser
    • DispCmd
    • DisplayDevice
    • Displayable
    • Matrix4
    • Scene
  • Molecule objects
    • Animation
      • Adding new frames:
      • Updating the current position:
    • Atom
    • BaseMolecule
    • DrawMolecule
    • Molecule
    • Timestep
  • Remote connection objects
  • User interface objects
    • Command
      • Using a Command object:
      • Developing a new class derived from Command:
    • CommandQueue
    • Mouse
    • PopupMenu
    • PopupMenuItem
    • UIList
    • UIObject
    • UIText
  • Tracker objects
• About this document ...