John Campbell's Java Based Software

  John W. Campbell

This software includes both Java based libraries and programs primarily related to Protein Crystallography. The library based software has sections which are of general use for a much wider range of applications. This software is associated with the CCP4 Program Suite. The software included here is as follows:

Library Classes



The Java Development Library (JDL) is a set of Java classes written both for developing Java based software for Protein Crystallography and also for more general applications. In particular, it includes a set of high level classes for developing applications requiring a graphical user interface.

Programs



PXImage is a program for displaying and examining Protein Crystallographic X-ray diffraction images. A range of measurement options are available.

The program may be run as an Applet from this Web server.



PXSim is a program for carrying out simulations of Protein Crystallographic diffraction images and analysing the unique data coverage for one or more crystal settings and series of diffraction images.

The program may be run as an Applet from this Web server.



DocExtractor is a program used to prepare documentation files from a special pre-xhtml format or by extracting documentation sections from Java code source files. It has been used in the preparation of the documentation for the Java based programs and libraries described on this page.

Diffraction Data Module (DDM)



The Diffraction Data Module (DDM) defines a set of parameters for use in the initial stages of processing or predicting sets of protein crystallographic X-ray diffraction images. It has been devised to be used with Java code built using the Java Development Library (JDL).

Downloads

The code is released under the conditions of the GNU GPL licence. It should be appreciated that some of the crystallographic calculations are derived from programs developed by the Academic community mostly in the era where such programs were freely exchanged. Many of these programs or their successors are now distributed in CCP4 Program Suite.

List of Downloads
File Name Description Date
PXImage.jar Java Archive File (.jar) for the PXImage Program (Jdl.jar also needed) 3/3/07
PXSim.jar Java Archive File (.jar) for the PXSim Program (Jdl.jar also needed) 3/3/07
Jdl.jar Java Archive File (.jar) for Java Development Library (JDL) 3/3/07
ccp4_java.tar.gz Archive File (.tar.gz) with the source, class and documentation files
prismane.img Test data - Prismane Protein image file
pris_start.ddm Test data - Prismane Protein DDM file
lys.img Test data - Lysozyme image file
lys_start.ddm Test data - Lysozyme DDM file

The complete Java code and documentation file ccp4_java.tar.gz may be uncompressed and unpacked using the gunzip and tar commands on a Linux system or WinZip on a Windows based system. If file is downloaded into say my_dir then, if required, the documentation may be generated by changing to the directory (folder) my_dir/Java/MakeDocs (folder my_dir\Java\MakeDocs for Windows) and running the script file make_docs (make_docs_win for Windows) with the command:

make_docs all

(or make_docs_win all for a Windows system)

Contact

campbell_j_w@bcs.org.uk

March 2007