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README
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STAAR
Version 2.0; January 2011
Copyright (C) 2011 University of Tennessee, Knoxville
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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 is 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.
Oh, and if you don't want to use this code on your own computer, we
have considered developing a web page to take user requests to run on
our own server. Stay tuned!
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