ProGAL

ProGAL is a Java-library for doing computational geometry with an emphasis on characterizing and representing protein structures. The implementation is in a subversion repository at the Department of Computer Science, University of Copenhagen. If you'd like access to the code (or parts of it) please contact Pawel Winter. To download a jar with the byte-code right-click the following link:

Download ProGAL.jar
Latest update: 27. June 2014

Usage

To use ProGAL simply include the jar in the class path of your project. For example, if you use a normal editor create a file ProGALTest.java with the following contents:

import ProGAL.geom2d.viewer.J2DScene;
import ProGAL.geom2d.*;

class ProGALTest{
   public static void main(String[] args){
      Circle c = new Circle(new Point(0,0), 1);
      J2DScene scene = J2DScene.createJ2DSceneInFrame();
      scene.addShape(c, java.awt.Color.BLUE);
   }
}

Then at the command-line run:

javac -cp ProGAL.jar:. ProGALTest.java
java -cp ProGAL.jar:. ProGALTest

to run a small test. If you use eclipse, simply create a project and go to the Project-menu -> Properties -> Java Build Path -> Libraries and locate the ProGAL.jar file after pressing the 'Add external jar' button. If you wish to use the 3D visualization classes (J3DScene) you need to install Java3D first. Note: Java3D is included in Java 6 and up but currently there may be some problems with Java7 compatibility. To temporarily change the java-version, type: 

export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/ #Mac
export JAVA_HOME=/usr/lib/jvm/java-6-sun/ #Ubuntu

Documentation

The documentation of ProGAL is currently maintained partly through a JavaDoc homepage and partly through a collection of examples that demonstrate the use of the library.

Alpha shape of protein 1GZX (chain A) computed in ProGAL.

Projects that contributed to ProGAL: