=======================
 addass2sparkysave.awk 
=======================
#!/software/bin/gawk -f
#
# put assignments from cycle*.ass in *.save file
#
# use:
#      addass2sparkysave.awk cycle6.ass \ 
#                        -v savedom=1:Hh,2:CHh" \ 
#                        -v mincontr=0.99       \ 
#                           2dnoesy.save
#
# after that:
#      ass2shift.awk sh3.seq 2dnoesy_Hh-cycle6.save > cycle6ass.shifts       
#
# and check _bad.shifts & _ass2shift.tmp for outliers
#
#
# -v seqrange=1 :   assign only pairs with residuenumber difference 
#                           within seqrange
#                                seqrange="" :  accept all
#                                seqrange=0  :  only intra
#                                seqrange=1  :  only intra & sequential 
#                           default: seqrange=""
#
# -v savedom=...      [""] : use to define the order of nuclei for the save files
#                           consists of comma-separated savefilenr:format strings
#                           
#                           the formatstrings can consist of a string of the following chars
#                                   H (protons acq dimension) 
#                                   N (hetero atom for H )    
#                                   C (hetero atom for H )    
#                                   h  (protons indirect dimension) 
#                                   h  (protons indirect dimension) 
#                                   N (hetero atom for h )   
#                                   C (hetero atom for h )   
#                           'H' and 'h' should be present , only one of 'N' and 'C' and only one 
#                           of 'n' and 'c' should be present 
#
#                           For example:
#                               savedom="1:HNh,4:HNch"
#                           
#                               means:    
#                               
#                               save-peaklist 1 has format HhN
#                                 thus is a 3D peaklist with 
#                                 -  aqc-proton(H) is in dom 1 
#                                 -  het-nucleus for acq-proton is in dom 3 ( and is Nitrogen) 
#                                 -  indirect proton is in dom 2 
#
#                               save-peaklist 4 has format HNch
#                                 thus is a 4D peaklist with 
#                                 -  aqc-proton(H) is in dom 1 
#                                 -  het-nucleus for acq-proton is in dom 2 ( and is Nitrogen) 
#                                 -  indirect proton is in dom 4 
#                                 -  het-nucleus for indirect proton is in dom 3 ( and is Carbon) 
#
# -v ov=0                : if defined and >1  overwrite assignments present in the xpk file
#                           ov=0 sets keepass=1 [don't overwrite]
#                           ov=1 sets keepass=0 [overwrite]
#
# -v unassign = all       :  if set remove all assignments present in the xpk file
# -v unassign = 1 [1-4]   :  as above but only remove assignments in dom 1 
#
#
# -v keepass = 1          :  if defined don't overwrite assignments present in the xpk file
#                           default : keepass=1 [don't overwrite]
#
# -v mincontr=0.999     :   minimum of total volume contribution 
#                           required for acceptance
#                           [ the last percentage on each assignment line 
#                             in cycle[n].ass
#                           default : keepcharge=""
#
# -v minassQ=0.8     :      acceptance threshold for assignment quality as used in 
#                           candid assign files. this parameter measures the closeness
#                           of chemical shift fit [0.0...1.0]
#                            
#                           default : keepcharge=""
#
# -v maxass=1           :   maximum nuber of different assignments 
#                           that will be put in the *.xpk file
#                           default : maxass=1
#    
# -v keepnames=1        :   if defined do not change names 
#                           from HB3 [iupac] to HB2 [pdb]
#                           default : keepnames=""
#
# -v keepcharge=1       :   if defined do keep charges
# -v keeppseudo=0       :   don't keep pseudoatoms of cyana [ convert QG2 -> HG21 ]
#                           default : keeppseudo=0
#
#
# -v dthr=4.5          :   distance threshhold for best match
# -v dsigma=1          :   accept if  <dist>+rmsdist*dsigma  <= dthr        
#
# -v dthr2=4.0         :   distance threshhold for second best match
# -v dsigma2=2         :   accept if  <dist>-rmsdist*dsigma2 >= dthr2    
#     
#
#