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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.

class diagram of the model classes

The View Classes

All of the classes that handle the display are named ____View


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


An important class that controls the simulation.