Abstracted Protein Simulator
This page documents the format of the XML files used by the simulator. The XML processing is handled by the NeuroML development kit for java. The XML files take the form of a list of lists, where each of the inner lists is one of the ones described below. The outer list has the following form:
<neuroml class="reader.XMLList">

<!-- begin inner list definitions -->

<!-- end inner list definitions -->

The Landscape component specifies a particle's interaction with the simulation space, that is, how does it move in the presence of Brownian Motion.
Rule Template
The RuleTemplate component defines a single rule governing the behaviour of bonds.
Bond Template
The component defining the a particle bond. It lists the rules which govern the behaviour of the bond.
Particle Template
The component defining a single particle in the simulation.
SimObject Template
The component defining an object class in the simulation.
The component defining a single object in the simulation.