#STAAR: __ST__atistical __A__nalysis of __A__romatic __R__ings Version 2.0; October 2012

Copyright (C) 2012 University of Tennessee, Knoxville

STAAR searches a set of PDB files for possible anion-quadrupole interactions.

Other files to read in the top-level source directory:

 INSTALL           Installation instructions.
 LICENSE           The GNU General Public License (GPLv3).

STAAR uses the gzstream library for the decompression of PDB files that are compressed. The library source code can be found in its entirety in the gzstream folder. I did have to make a change to the code because the istream '!' operator was not working correctly to check for a valid open. What I did was to add a failure flag to one of the classes and a get function named fail(). It returns true if the file could not be opened. The gzstream library is freely available under the LGPLv2.1 library that can be seen in gzstream/COPYING.lib. For more information on the gzstream library, please visit their page at: http://www.cs.unc.edu/Research/compgeom/gzstream/

The STAAR code was not intended to be library of code that you could plug into to develop more code. This is evident by the amount of hoops you would have to jump through just to compile it. This is mainly due to the OpenBabel dependency. However, if you wish to use it as a library, you should be able to as we have done it a couple of times. The only thing that is truly specifc to STAAR are the Options.{cpp,hpp} files, but from my recollection nothing else depends on those files. There are limited options in the PDB reader as we were only concerned with the ATOM lines (well, for one of our side projects, HETATM lines). If you need support for other PDB features, you will need to edit PDB.{cpp,hpp}. Anyway, good luck.

The scripts folder contains some scripts and codes for parsing the GAMESS output, added the results to the STAAR output, dealing with some of the database stuff, etc. Speaking on this folder, here are some explanations of the codes in there [Disclaimer: they weren't created with general applicability in mind. They were simply created for our own specific needs, but we are including them in case you might need them for reference]:

 downloadPDB - This will download a supplied list of PDBs from 
                the RCSB website
 getNewPDBFiles - Similar to downloadPDB, but it will only 
                  download whatever hasn't already been 
                  downloaded before
 make_scripts - Makes the submission scripts and submits the jobs
                to the Newton cluster.  This is specific to our 
                needs, so it may not help others much. Check the
                comments inside the script for more explanations
 parseGamess.pl - Perl script to parse out the information from 
                  the GAMESS runs.  Again, this is somewhat 
                  specific to our needs, but you can use it as a 
                  guideline, if you wish
 splitInput - Splits a large list of PDBs into multiple smaller 
              ones.  Again, specific to our needs
 stats - Gets stats about our runs.  This one is actually one you
         can use on your own, assuming you don't have results 
         split up. 

If you would rather not download and compile this code on your own system, please visit staar.bio.utk.edu where you can upload your zipped PDB file and run through the analysis on our servers. This website already includes the results for all PDB files from 9 May 2012.

If you choose to use this code, website, or results produced from this work, please cite the following paper:

Jenkins, D. D., Harris, J. B., Howell, E. E., Hinde, R. J. and Baudry, J. (2012), STAAR: Statistical analysis of aromatic rings. J. Comput. Chem.. doi: 10.1002/jcc.23164