# read the secondary structure records from an edited version
# of a STRIDE output file and return the information in the form:
#    {SSType chain1 resid1 chain2 resid2} {... }
proc vmd_read_stride_ss {stride_filename} {
   set response {}
   # open the STRIDE file
   set infile [open $stride_filename r]
   # read until the end of file
   while {[gets $infile line]} {
      set str [string range $line 0 2]
      if {$str == "LOC"} {
         set str [string range $line 5 14]
	 if {$str == "AlphaHelix"} {
	    set ss helix
	 }
	 if {$str == "310Helix  "} {
	    set ss helix310
	 }
	 if {$str == "PIHelix   "} {
	    set ss pihelix
	 }
	 if {$str == "Strand    "} {
	    set ss sheet
	 }
	 if {$str == "Bridge    "} {
	    set ss bridge
	 }
	 if {$str == "Coil      "} {
	    set ss coil
	 }
	 if {$str == "TurnI     "} {
	    set ss turn
	 }
	 if {$str == "TurnII    "} {
	    set ss turn
	 }
	 if {$str == "TurnII'   "} {
	    set ss turn
	 }
	 if {$str == "TurnIII   "} {
	    set ss turn
	 }
	 if {$str == "TurnIV    "} {
	    set ss turn
	 }
	 if {$str == "TurnV     "} {
	    set ss turn
	 }
	 if {$str == "TurnVI    "} {
	    set ss turn
	 }
	 if {$str == "TurnVII   "} {
	    set ss turn
	 }
	 if {$str == "TurnVIII  "} {
	    set ss turn
	 }
	 set chain1 [string range $line 28 28]
	 set resid1 [string range $line 23 26]
	 set chain2 [string range $line 46 46]
	 set resid2 [string range $line 41 44]
	 lappend response [list $ss $chain1 $resid1 $chain2 $resid2]
	 continue
      }
      
      # also, if read blank line then there are no more def's
        if {$str == ""} {
            break
        }
   }
   # close the file and return the list of info
   close $infile
   return $response
}

#### Now a driver to get info from this routine
# Return 0 if no information available
# Return 1 otherwise
proc vmd_use_stride_ss {molid stride_filename} {
    # get the list of information
    set ssdata [vmd_read_stride_ss $stride_filename]
    # was there data?
    if {$ssdata == {}} {return 0}

#rlc's modification: first, reset everything to coil as a default
    set sel_all [atomselect $molid "all"]
    $sel_all set structure coil
    
    # Go through each of the element
    foreach ele $ssdata {
        lassign $ele ss chain1 resid1 chain2 resid2
        # if the chains are " ", don't use them
        if {$chain1 == " "} {
            set seltext "protein and (resid $resid1 to $resid2)"
        } else {
            set seltext "chain $chain1 and (resid $resid1 to $resid2)"
        }
        # get the selection/ make it the right structure/ free it
        set sel [atomselect $molid $seltext]
        $sel set structure $ss
        $sel delete
    }
    # all done, so return that I did something
    return 1
}

proc apply_stride_ss {molid stride_filename} {
	vmd_use_stride_ss $molid $stride_filename
}

puts "In order to apply the new secondary structure information, do:"
puts "apply_stride_ss <mol_id> <stride_info_filename>"
puts "       mol_id can be 'top' or the number next to the file name in"
puts "       the list of files that you have read in"