deprecated examples; keeping for reference.  Use kmeans_bs_ftmap.pl 

Objective: you've run FTMap on a bunch (>1) of configurations of a molecule 
           that had been aligned beforehand.  You wish to collect up all 
           the small molecules bound via FTMap's ugly PDBs and reduce them 
           down to unique binding sites for virtual screens.
          
1. collect all the FTMap results for blah*pdb (located in FTMaps dir, change 
   this to your taste):

perl collect_nodes.pl blah > blah_nodes.xyz

collect_nodes.pl system calls pull_bs_ftmap.pl

2. you now have an XYZ file with too many sites, let's reduce the sites further
   using a hack that leverages a connectivity (kirchoff) matrix: 
perl reduce_bs_kirchoff.pl blah_nodes.xyz  > blah_nodes_red.xyz

adjust the cutoff (currently 10 angstroms) in reduce_bs_kirchoff.pl to get more
or less sites.

steps 1 and 2 could be more elegant via a clustering scheme, but works well 
enough for now. 

RESULT:

xyz file containing mercury atoms located at the predicted binding sites. 
verify that things are how you like them by loading up the xyz file and all
the pdbs with your favorite molecular visualizer. 
