# % $Id: residue_rmsd.tcl,v 1.4 2006/03/06 23:56:46 timisgro Exp $

proc rmsd_residue_over_time {{mol top} res debut refer} {
    
    # use frame 0 for the reference
# utilisé pour aligner les résidus avant rmsd
    set reference [atomselect $mol "protein and resname FMN" frame $refer]
    # the frame being compared
# utilisé pour aligner les résidus avant rmsd
    set compare [atomselect $mol "protein and resname FMN"]
    #make a selection with all atoms
    set all [atomselect top all]
    #get the number of frames
    set num_steps [molinfo $mol get numframes]
puts "Number of steps $num_steps ..."
    #open file for writing
    set fil [open data_rmsd.dat w]
    
    #init tableau rmsd
    for {set ff $debut} {$ff < $num_steps} {incr ff} {
         set rmsd($ff) 0
         }
    
    #loop over all frames in the trajectory
    for {set frame $debut} {$frame < $num_steps} {incr frame} {
	puts "Calculating rmsd for frame $frame ..."
	# get the correct frame
	$compare frame $frame
        $all frame $frame
	# compute the transformation
	set trans_mat [measure fit $compare $reference]
	# do the alignment
	$all move $trans_mat
	
	# compute the RMSD
	#loop through all residues
	foreach r $res {
	    set ref [atomselect $mol "protein and resid $r and noh and not mass 1.008000" frame 0$refer]
	    set comp [atomselect $mol "protein and resid $r and noh and not mass 1.008000" frame $frame]
	    set rmsd($frame) [expr $rmsd($frame) + [measure rmsd $comp $ref]]
	    $comp delete
	    $ref delete
	}
	
    }

for {set frame $debut} {$frame < $num_steps} {incr frame} {
puts $fil " $frame \t $rmsd($frame)"
}
    close $fil
}