An Overview of the Protein Simulator Code Structure
Java Doc
The source code is documented in more detail in the Java Documentation.Code overview
The code is strucured around the Model-View-Controller design pattern.
The Model Classes
The model contains all of the representations of real world objects - SimObject, SimParticle, SimBond and their templates - SimObjectTemplate, SimParticleTemplate, etc. These classes are all in the directory called 'model'.
The templates (e.g. SimParticleTemplate) contain information such as shape and bonding rules. The instances (e.g. SimParticle) contain informations specific to each instance such as position.
The View Classes
All of the classes that handle the display are named ____View
Java3DHandler
A separate module that handles the 3d display.The Controller Classes
All of the classes that take user input and update the model are named ____Controller