README_pdbparse

#!/usr/gnu/bin/perl -w 
# Ivana, Dec 2001
# PURPOSE:  select only the lines  starting with "ATOM" from a pdb file;
# INPUT:    the pdb files should be provided as a list from stdin (piping it from ls will do):
#           the list is supposed to  contain the names of the pdb  files - the pdb files themselves 
#           should be in the directory specified as $PDBFILES below; 
#           for example: "ls pdbfiles | pdbparse.pl" ; 
#
# OUTPUT:   the "stripped" files  are saved into a
#           subdirectory  according to their "type":
#            
#           single_chain:    pdbfiles containing single chain of amino acids (AA)
#           multiple_chains: if the orginal PDB file has repeating chains of the
#                            same sequence, one  representative chain gets written here
#           unique_chains:   if the orginal PDB file has several different chains (sequqnces)
#                            one representative sequence for each is output
#           nmr:             NMR dtermined strucutres - get only the first model (what if there
#                            are several chains? )
#           thry:            theoretical model -- the current lore is that we do not use
#                            these so I ust make a soft link to the original file - just
#                            for bookkeeping purposes
#           unknwn:          files whose format is not recognized, for any reason
#
#DEPENDENCIES:  none
#
#ASSUMPTIONS:  1) To connect smoothly the output of this program to pipeline.pl
#               the pdb files should be named according to the following convention:
#                <pdb_name>.pdb [note that the older pdb files sometimes have the
#               names formatted according to pdv<pdb_name>.ent]
#              2) A sequence is termed "short" if it contains less than $CUTOFF_LENGTH
#                 amino acids. The idea is that these probably won't be interesting
#                 for pipelining.