=======================
 predict.awk 
=======================
#!/usr/bin/gawk -f
#  name	    : predict.awk 
#  author    : Eiso AB ; eisoab@gmail.com
#@ purpose   : make list of predicted peaks from shift-lists
#  input     : assignments ( shift.list )
#	           correlations :  [x]cor-file: spec.cor spec.xcor
#
#  example:
#           predict.awk out=sparky /software/src/PREDICT/COR/hnca.cor prot.shifts
#           predict.awk out=xeasy spec=XH.cor $name.shifts
#
#
#              for examples of corerlation files see: 
#                    /software/src/PREDICT/COR/*.cor
#               or: ./scripts/predict/COR/*.cor (from scripts.tgz)
#          
#
# disregard comments
#
# recognized input:
# 
#
# correlate nucl1 nucl2 nucl3 ref1 ref2 ref3 [ filter1 [filter2 [..]]]
#       correlation type
# correlate exit
#       skip rest of file
# dom 1 3 2 
#        after this line, 
#        switch spectral domains ; also with cmdline option: -v dom=1,3,2
#        order: 1st column,3rd column, 2nd column
#        
# # ...    comments 
#       all chars after # are skipped
#
# nodiag 1,2
#       sets var nodiag=1
#       remove diagonal peaks from plain 1,2 [ default]
#       also achieved with option:  -v nodiag=1 
#
# keepdiag
#       keep diagonal peaks
#       sets var nodiag=0
#
# CORRELATION FORMAT:
#
# correlate nucl1  nucl2 nucl3 ref1 ref2 ref3 [ filter1 [filter2 [..]]]
#   
#   the nucl. and filter keywords should match atom-names 
#   and are interpreted as:
#   1. regular expresions if given as /string/
#   2. exact matches if given as string
#      NB strings should not contain spaces
#
# examples
# expression           matches
#   ha            -> ha
#   /ha/          ->  ha1, ha2
#   /as./         -> asp, asn ; 
#   /gl[un]/      -> glu, gln
#   /[qh]b[123]?/ -> hb, hb1 hb2 hb3 qb3
#   /[qh]b/       -> hb, hb1 hb2 hb3 qb3
#   /^hn?$/       -> h , hn
#
# the ref values are relative sequence numbers
# the filters refer to relative sequence number 0
#
# that means that for this correlation the h and n atoms should 
# be from an asn or gln:
#   
#  correlate  h    c   n     0  -1  0  /asn|gln/
# 
# and in the next the c comes from and asn or gln.
#
#  correlate  h    c   n     1   0  1  /asn|gln/
#
#
# SHIFT LIST FORMAT: [free-format, input is converted to lower-case]
#   resnum resnam atnam shift shift-error
#   
#   example: 
#     20 ala ha 4.696 0.014
#
#   xeasy .prot files are also accepted
#
#   hn is converted to h unless the commandline option 
#   -v keephn=1 is used [???check]
#
#
# DEBUGGING INFO
# cmdline options
#   -v debug=1
#
#   -v out=""       show peak types  [ pktyp specname peaknr nucl1 nucl2  ....  int ]
#
#   -v out=ppm      give peak positions in ppm format [will print errors too]
#
#   -v out=asg      give peak positions + assignments 
#
#   -v out=noe      give peak positions + assignments 
#
#   -v out=nv       equal to out=xpk 
#   -v out=xpk      give nmrview (xpk) file with predicted peaks 
#                   if this option is given a *.xpk file is expected as additional input file
#                   for the header
#
#                   will be set automatically if the file 
#                   of the last argument is '.xpk'
#
#   -v out=xeasy    equal to out=peaks 
#   -v out=peaks    give xeasy (.peaks) file with predicted peaks 
#                   if this option is given a *.peaks file belonging to the spectrum 
#                   is expected as additional input file for the header
#                   
#                   will be set automatically if the file 
#                   of the last argument is '.peaks'
#
#
#   -v cyaf         cyanaformat, e.g.
#                   #CYANAFORMAT HNh
#
#   [-v] errout=1   print ppm errors as in 45.343~1.230
#
#   [-v] dom=1,2,3    set domains
#   
#   [-v] spec=name  default:XH    
#                   read from cor-file /software/src/PREDICT/COR/name.cor 
#                      [ spectrum name to insert in peaklist ]
#                   XH gives 2d hsqc (C and/or N)
#
#   -v nodiag=1    [ no diagonals ]
#   -v keepdiag=1  [ keep diagonals ]
#   -v nocharge=1  [ remove charge of residues ]
#
#   -v keepunassigned=0  [ if 1, keep unassigned shifts (ppm>900) ]
#
# or one of the following strings in the input:
# DEBUG
#    sets debug=1
# NODEBUG 
#    sets debug=0
#
#
# a .peaks  can be given as input file in order to get the peaks headers
# a .xpk    can be given as input file in order to get the peaks headers
# 
# gawk '$4>0.1 && $11>0.1 && $18 > 1{next}1' hbhacbcaconh_pred_stat.xpk > qq.xpk