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| This page provides download links to the simulator and other relevant materials. |
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Java and Java3d
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| In order to run the simulator you must have Java and Java3d installed on your computer. These can be obtained from Sun Microsystems' website. |
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The Simulator
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| There are two versions of the simulator available. The first is the current version and is the recommended one for download.
The second is the simulator as it was when I finished my fourth year project. The files are in .zip format. |
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| To use the current version: |
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Once downloaded, unzip the file into a new directory.
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Enter the main directory and change the Makefile to point to the directory containing Java.
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Compile the class files with the command make.
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Run the simulation with the command make sim.
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Once downloaded, unzip the file into a new directory.
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enter the main directory with the command cd current (from with in the new directory).
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Compile the class files with the command javac *.java */*.java.
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Run the simulation with the command java Simulator.
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Dissertation
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| You can download a copy of my fourth year dissertation which explains in detail the workings of the old version of the simulator from the link below.
The dissertation is in .doc (Word) format. |
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PDB Reader
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| PDB reader was created as a tool for automating the process of creating abstract protein models. PDB reads in protein description files from the Protein Data Bank. Although it is not compatible with current versions of the simulator due to development of the latter, it could be adapted to do so relatively easily.
The reader works by parsing the PDB files, which document the positions of the individual atoms in a protein. It then turns this information
into XML file compatible with older versions of the simulator. In the process it can cluster the atoms to either amino acid level, or to a user
defined level of clustering. This clustering approximates the shape of the protein, while reducing the amount of components used to
represent it. The PDB reader is available for download here: |
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Once downloaded, unzip the file into a new directory.
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Enter the main directory and change the Makefile to point to the directory containing Java.
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Compile the class files with the command make.
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Run the reader with the command make reader.
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