=======================
 pdb2pdb.awk 
=======================
#!/usr/bin/gawk -f
#@ purpose: - reformat ATOM records for various conventions
#@          - set B-factors for residues and/or atoms
#   
# change bfactors:
#   feed it lines like these before the pdb-file: 
#   
#       bfac res 12 ala 20.00
#       bfac res 12 ala model 1 20.00   # for single model in cluster
#       bfac atom 12 ala ha 20.00
# pdb2pdb.awk bfacfile pdb-file
# gawk -f `which pdb2pdb.awk` bfacfile pdb-file
# or 
# echo bfac res 11 ser 37.50 | gawk -f pdb2pdb.awk - pdb-file
#
# options: 
# -v pedantic=1 : do not change  "2HB " to "HB2 "
# -v preloc=1 :  change  " HXn" to "nHX" for X=[A-Z][0-9]? n=[1-3]
# -v preloc=2 :  change  "HXXn " to "nHXX" for n=[0-9]
# -v keepq=1 : keep pseudo-atoms [Q*] default keepq=0
# -v defaultcharge=1 : change to ARG+ HIS LYS+ ASP- GLU- ( for molmol )
# -v use_occ=1 : print occupancy records [ default=1 if not already present ]
# -v use_bfac=1 : print Bfactor records [ default=0 if not already present ]
# -v gmx=1 : prepare for gromacs [gmx] ile cd1->cd ile hd11-> hd1 etc # 
# -v dyana=1 : prepare for dyana [non-iupac]  # 
# -v cyana=1 : prepare for cyana [iupac]  # 
# -v dres=0  : add dres=residuenumber
# -v skipsol=0  : skip residue name=SOL [remove water]
#
# -v fixnum=1   : fix numbering to ascending, every resnr has only one resname
#                     (unlike xplor output)  
# -v fixchain=1   : add chains xplor files with different segids and repair HG11->1HG1  
# -v upper=1 :  make uppercase
#