# vmd tcl script to create a series of files with
# the time series of the backbone dihedral angles (including 
# the improper ones) from the different temperature simulations.
#
# (c) 2003 by axel.kohlmeyer@ruhr-uni-bochum.de

for {set t 280} {$t < 405} {set t [expr $t + 10]} {
    puts "loading data for $t kelvin."
    set mol [mol new "monom-$t.psf" waitfor all]
    mol addfile "monom-$t.dcd" molid $mol  waitfor all
    animate goto 0
    set n  [ molinfo $mol get numframes ]
    puts "processing $n frames"

    # create an array of selections for the sequence of atoms
    # the first and the last residue have to be treated differently
    set ia 0
    for {set ir 1} {$ir < 9} { incr ir } {
        set a($ia) [ atomselect $mol "resid $ir and name N" ]
        incr ia
        set a($ia) [ atomselect $mol "resid $ir and name CA" ]
        incr ia
        set a($ia) [ atomselect $mol "resid $ir and name C" ]
        incr ia    
    }

    set ie [expr $ia - 3]
    puts "ia: $ia  / ie: $ie"
    set f 0
    for {set i 0} {$i < $ie} {incr i} {
        set j $i
        # grab 4 atom indices
        $a($j) frame $f
        $a($j) update
        set v1 [lindex [$a($j) get index] 0]
        incr j
        $a($j) frame $f
        $a($j) update
        set v2 [lindex [$a($j) get index] 0]
        incr j
        $a($j) frame $f
        $a($j) update
        set v3 [lindex [$a($j) get index] 0]
        incr j
        $a($j) frame $f
        $a($j) update
        set v4 [lindex [$a($j) get index] 0]
        # ...and create a dihedral label from it
        label add Dihedrals $mol/$v1 $mol/$v2 $mol/$v3 $mol/$v4
    }


    for {set i 0} {$i < $ie} {incr i} {
        label graph Dihedrals $i "bb-dihed-$t-$i.dat"
    }

    puts "cleaning up..."
    label delete Dihedrals all
    #close $fp
    mol delete $mol
}

quit