mol new deh.prmtop
set stepSize 10

if { [info exists env(SASA_STEP_SIZE) ] } {
    set stepSize $env(SASA_STEP_SIZE)
}
mol addfile deh.dcd step $stepSize waitfor all

puts $argv
puts [lindex $argv 0]
set arg [lindex $argv 0]
set offsetType [lindex $argv 1]
if { $offsetType  == "wt" } { 
    set leftResids "(residue 190 to 194 229 to 233) and not dnaback"
    set rightResids "(residue 199 to 203 220 to 224) and not dnaback"
}else if { $offsetType == "insertion" } {
    set leftResids "(residue 190 to 194 231 to 235) and not dnaback"
    set rightResids "(residue 200 to 204 221 to 225) and not dnaback"
} else if { $offsetType == "deletion" } {
    set leftResids "(residue 190 to 194 227 to 231) and not dnaback"
    set rightResids "(residue 198 to 202 219 to 223) and not dnaback"
}
#I'm using the residues up to the alanine on the helix, position 160 on the second protein and 69 on the first.
if { $arg == "1" } {
    set sel [atomselect top "fragment 0 and resid < 70"]
    set sname "proteinA"
}

if { $arg == "2" } {
    set sel [atomselect top "fragment 1 and resid < 161"]
    set sname "proteinB"
}

if { $arg == "3" } {
    set sel [atomselect top "nucleic"]
    set sname "nucleic"
}

if { $arg == "4" } {
    set sel [atomselect top "(fragment 0 and resid < 70) or nucleic"]
    set sname "proteinAnucleic"
}

if { $arg == "5" } {
    set sel [atomselect top "(fragment 1 and resid < 161) or nucleic"]
    set sname "proteinBnucleic"
}
if { $arg == "6" } {
    set sel [atomselect top "(fragment 0 and resid < 70) or (fragment 1 and resid < 161)"]
    set sname "proteinprotein"
}
if { $arg == "7" } {
    #Left half site, alone
    set sel [atomselect top $leftResids]
    set sname "lefthalf"
}
if { $arg == "8" } {
    #Right half site, alone
    set sel [atomselect top $rightResids]
    set sname "righthalf"
}
if { $arg == "9" } { 
    #left site with protein
    set sel [atomselect top "(${leftResids}) or (fragment 0 and resid < 70)"]
    set sname "lefthalfprotein"
}
if { $arg == "10" } { 
    #right site with protein
    set sel [atomselect top "(${rightResids}) or (fragment 1 and resid < 161)"]
    set sname "righthalfprotein"
}


puts $sname
puts [$sel num]
source ../../../src/calcSasa.vmd
set endFrame [molinfo top get numframes]
calcSasa [list $sel] "$sname.dat" 0 $endFrame 1

exit