IBM/SPSS Modeler 16 and 17 has hidden potential which is best discovered by running the associated MODELER_JYTHON.str stream. What you see here is a pictographic outline of the process and a screen shot of a result:

PROTEIN_STREAM_OVERALL
The process in this example is as follows:
1. Modeler/Jython/Java creates an interface so you can select a protein
2. Modeler/Jython/Java/Jmol goes out to the PDB Internet site and pulls that protein
3. Modeler/Jython/Java/Jmol displays the protein in multiple cartoon forms
4. Modeler reads the derived coordinates and sequence for more analytics within Modeler

The purpose of this blog then, is to illustrate how easy it is to interface to the world of Java through Jython and leverage its capabilities within IBM/SPSS Modeler. It will require a small initial effort to set this up. If your area of interest is biology, chemistry or graphics, you will want to try this out.

To illustrate, you follow seven steps to set this up. I recommend the first time through you follow the instructions exactly and then once you have it working, you can reconfigure the setup to suit your needs.
1. Create the directory C:/PROJECTS/JYTHON/ as your scripts folder
2. Download the Modeler_Jython.str stream into C:/PROJECTS/JYTHON/
3. Copy the pdb_names.txt text file into C:/PROJECTS/JYTHON
4. Go to http://sourceforge.net/projects/jmol/files/Jmol/Version%2013.2/Version%2013.2.8/
a. – download Jmol-13.2.8-binary.zip
b. – open zip file
c. – copy jmol.jar to the C:/PROJECTS/JYTHON/ folder (should be 6941KB in size)
d. – copy the Jmol GNU Lesser General Public License COPYRIGHT.txt file to the same folder
5. Execute Modeler 16 or 17
6. Load MODELER_JYTHON.str into Modeler
7. Run the stream (run should complete within 30 seconds)
x – make sure you’re connect to the Internet

CREDITS:
Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
…(download) http://sourceforge.net/projects/jmol/files/Jmol
PDB: http://www.rcsb.org/pdb/home/home.do
bioJava: http://bioinformatics.oxfordjournals.org/content/28/20/2693.full.pdf?keytype=ref&ijkey=BzJOy9GgM2XNw07
Jython: there is an enormous treasure of working Jython scripts and Java apps on the Internet which you can access through Jython

Some NOTES:
1. Yes, you can use other versions of Jmol but the first time, use version 13.2.8.. Other classes need to be accessed when using different versions of Jmol.
2. The credit for the interactive graphics is Jmol. The work is brilliant and examining the web site for other applications is worthwhile.
3. The PDB web site is beyond amazing. I supply labels to select from and the MODELER_JYTHON.str stream goes out to the web site to grab the sequences but the genius is with PDB.
4. The MODELER_JYTHON.str is a stripped down version of what is possible. You will notice there are a number of lines in the script which are commented out. These reference small parts of resources in the javaApp world which are available. It is by leveraging these capabilities and interfacing with Modeler that a whole new world of possibilities open up.
5. Once you have Jmol running, you will see the two-way communications between the applications by going into the debug window of Modeler. There you will see messages which appear in Jmol also appear in Modeler.
6. My plan is to upload streams I’ve created which illustrate the capabilities to do web scraping and matrix algebra using Jython from within IBM/SPSS Modeler.

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