parameter suffix suffix2 rseed protein 

set dir      = .
set dir2     = ./{$suffix}
set dir3     = ./{$suffix2}

# Input data
set atomlist = {$protein}
set sequence = {$protein}
set hsqcpl       = hs15n 	
set hncapl       = hnca
set hncocapl     = hncoca
set hncopl       = hnco
set cbpl         = hncacb
set cconhpl      = cconh
#set hcconhpl	 = hcconh
#set hncacopl     = hncaco
#set hcchpl       = hcch       # must be unfolded
#set n15noesypl   = n15no

set refhsqcpl       = hs15n_{$suffix2}
set refhncapl       = hnca_{$suffix2}
set refhncocapl     = hncoca_{$suffix2}
set refhncopl       = hnco_{$suffix2}
set refcconhpl      = cconh_{$suffix2}
#set refhcconhpl     = hcconh_{$suffix2}
set refcbpl         = hncacb_{$suffix2}
#set refhncacopl      = hncaco_{$suffix2}
#set refhcchpl       = hcch_{$suffix2}     
#set refn15tocsypl   = to15n_{$suffix2}

# macro to be used for writing out best assignment
set savemacro   = write 

set name     = {$suffix}  #suffix to name output files
set sizePop  = 100        # 10  ...for testing
                          # 25-100 ...for production

seed random numbers $rseed

N15H1
   set N15H1_w1         = 2       # w1 of garant -> w2 of XEASY list == N
   set N15H1_w2         = 1       # w2 of garant -> w1 of XEASY list == HN
#   set N15H1_acc_w1     = 0.02
#   set N15H1_acc_w2     = 0.2
   load peaks N15H1 $dir/$hsqcpl   

HNCA
#   set HNCA_acc_w1      = 0.04   # w1 of garant -> w1 of XEASY list == HN
#   set HNCA_acc_w2      = 0.15   # w2 of garant -> w3 of XEASY list == N
#   set HNCA_acc_w3      = 0.05   # w3 of garant -> w2 of XEASY list == CA
   set HNCA_w1          = 1
   set HNCA_w2          = 3
   set HNCA_w3          = 2
   load peaks HNCA      $dir/$hncapl

HN_CO_CA
#    set HN_CO_CA_acc_w1  = 0.02
#    set HN_CO_CA_acc_w2  = 0.2
#    set HN_CO_CA_acc_w3  = 0.2
    set HN_CO_CA_w1      = 1
    set HN_CO_CA_w2      = 3
    set HN_CO_CA_w3      = 2
    load peaks HN_CO_CA  $dir/$hncocapl

HNCO
#    set HNCO_acc_w1      = 0.04
#    set HNCO_acc_w2      = 0.15
#    set HNCO_acc_w3      = 0.05
    set HNCO_w1          = 1
    set HNCO_w2          = 3
    set HNCO_w3          = 2
    load peaks HNCO      $dir/$hncopl

CBCANH
   set CBCANH_w1     = 1	# w1 of XEASY-list -> w1 (garant) == HN
   set CBCANH_w2     = 3	# w3 of XEASY-list -> w2 (garant) == N
   set CBCANH_w3     = 2	# w2 of XEASY-list -> w3 (garant) == CA/CB
#   set CBCANH_acc_w1 = 0.04	# 
#   set CBCANH_acc_w2 = 0.12
#   set CBCANH_acc_w3 = 0.20
   load peaks CBCANH $dir/$cbpl

C_CO_NH
#    set C_CO_NH_acc_w1   = 0.04
#    set C_CO_NH_acc_w2   = 0.12
#    set C_CO_NH_acc_w3   = 0.2
    set C_CO_NH_w1       = 1
    set C_CO_NH_w2       = 3
    set C_CO_NH_w3       = 2
    load peaks C_CO_NH   $dir/$cconhpl

#HC_CO_NH
#    set HC_CO_NH_acc_w1   = 0.025
#    set HC_CO_NH_acc_w2   = 0.3
#    set HC_CO_NH_acc_w3   = 0.3
#    set HC_CO_NH_w1       = 1
#    set HC_CO_NH_w2       = 3
#    set HC_CO_NH_w3       = 2
#    load peaks HC_CO_NH   $dir/$hcconhpl

#HN_CA_CO
#    set HN_CA_CO_acc_w1   = 0.025
#    set HN_CA_CO_acc_w2   = 0.3
 #   set HN_CA_CO_acc_w3   = 0.3
 #   set HN_CA_CO_w1       = 1
 #   set HN_CA_CO_w2       = 3
 #   set HN_CA_CO_w3       = 2
 #   load peaks HN_CA_CO   $dir/$hncacopl

#N15TOCSY
#  set N15TOCSY_w1     = 2    # H axis
#  set N15TOCSY_w2     = 3    # 15N axis
#  set N15TOCSY_w3     = 1    # HN axis	
#  set N15TOCSY_acc_w1 = 0.05
#  set N15TOCSY_acc_w2 = 0.3
#  set N15TOCSY_acc_w3 = 0.05
#  load peaks N15TOCSY $dir/$n15tocsypl

#HCCH24
#   set HCCH24_w1     = 3
#   set HCCH24_w2     = 2
#   set HCCH24_w3     = 1
#   load peaks HCCH24 $dir/$hcchpl

set pick_acc      = 1.0   #e.g. HNCA_acc_w1 * pick_acc
                          #defines maximal difference between 
                          #chemical shifts in different spectra 

load sequence  $sequence
load comparison sequence $sequence

#pseudocorrection #corrections applied when generating expected NOEs from homologous protein

define atom probability "HE(GLN)" 1.0   # exclude NH2 side chains
define atom probability "HD(ASN)" 1.0   # exclude NH2 side chains
define atom probability "HE(ARG)" 1.0   # exclude NH side chains
define atom probability "NZ(LYS)" 1.0   # exclude NH side chains
define atom probability "CD(GLN)" 1.0   # exclude NH2 side chains
define atom probability "CG(ASN)" 1.0   # exclude NH2 side chains
define atom probability "CD(GLU)" 1.0   # exclude NH2 side chains
define atom probability "CG(ASP)" 1.0   # exclude NH2 side chains

make coherences			# generate all possible coherences
make couplings			# generate couplings
#make noe			# generate noe's if no homologous structure
make peaks			# generate expected peaks

# define shifts according to secondary structure
#define secondary shifts CalcSecondarytrunc.txt

load comparison assignments N15H1 $dir3/$refhsqcpl $atomlist 0.0
load comparison assignments HNCA $dir3/$refhncapl $atomlist 0.0
load comparison assignments HNCO $dir3/$refhncopl $atomlist 0.0
load comparison assignments HN_CO_CA $dir3/$refhncocapl $atomlist 0.0
load comparison assignments CBCANH $dir3/$refcbpl $atomlist 0.0
load comparison assignments C_CO_NH $dir3/$refcconhpl $atomlist 0.0
#load comparison assignments HC_CO_NH $dir3/$refhcconhpl $atomlist 0.0
#load comparison assignments HN_CA_CO $dir3/$refhncacopl $atomlist 0.0
#load comparison assignments N15TOCSY $dir3/$reftocsypl $atomlist 0.0
#load comparison assignments HCCH24 $dir3/$refhcchpl $atomlist 0.0

check inconsistencies

# insert fixed assignments here
#do i 26 40
#	fix assignments "HN($i)"
#	fix assignments "N($i)"
#	fix assignments "C($i)"
#	fix assignments "CA($i)"
#end do

#reset user assignments HNCA
#reset user assignments HNCO
#reset user assignments HN_CO_CA
#reset user assignments CBCANH
#reset user assignments C_CO_NH

# this section defins the columns listed in thre report (.log)
criteria fragment intrainter intra 0 0
criteria fragment intrainter seq 1 1
criteria fragment correct ok
criteria comment on ok
criteria fragment correct okN N
criteria comment on okN
criteria fragment correct okHN HN
criteria comment on okHN
criteria fragment correct okCA CA
criteria comment on okCA
#criteria fragment SScorrect SSok
#criteria comment on SSok
criteria fragment mapping map
criteria comment on map
criteria comment on intra
criteria threshold intra 0.6 0.8
#criteria coherence mapping mapco
#criteria comment on mapco

opt $sizePop $savemacro

quit