{+ file: rename_segid.inp +}
{+ directory: general +}
{+ description: Rename segid(s) +}
{+ comment: 
           Reads in a coordinate and structure file, renames the
           selected segid information and writes out a new 
           coordinate and structure file +}
{+ authors: Axel T. Brunger, and Paul D. Adams +}
{+ copyright: Yale University +}

{- Guidelines for using this file:
   - all strings must be quoted by double-quotes
   - logical variables (true/false) are not quoted
   - do not remove any evaluate statements from the file -}

{- begin block parameter definition -} define(

{======================= molecular structure ==========================}

{* input molecular structure file *}
{===>} structure_infile="fab2hfl.mtf";

{* input coordinate file *}
{===>} coordinate_infile="fab2hfl.pdb";

{========================== renaming segids ==========================}

{+ table: rows=10 numbered
          cols=2 "old segid" "new segid" +}

{===>} segid_old_1="L";
{===>} segid_new_1="A";

{===>} segid_old_2="H";
{===>} segid_new_2="B";

{===>} segid_old_3="";
{===>} segid_new_3="";

{===>} segid_old_4="";
{===>} segid_new_4="";

{===>} segid_old_5="";
{===>} segid_new_5="";

{===>} segid_old_6="";
{===>} segid_new_6="";

{===>} segid_old_7="";
{===>} segid_new_7="";

{===>} segid_old_8="";
{===>} segid_new_8="";

{===>} segid_old_9="";
{===>} segid_new_9="";

{===>} segid_old_10="";
{===>} segid_new_10="";

{=========================== output files ============================}

{* output molecular structure file *}
{===>} structure_outfile="rename_segid.mtf";

{* output coordinate file *}
{===>} coordinate_outfile="rename_segid.pdb";

{===========================================================================}
{        things below this line do not normally need to be changed          }
{===========================================================================}

 ) {- end block parameter definition -}

 checkversion 1.2

 evaluate ($log_level=quiet)

 structure @@&structure_infile end

 coordinate @@&coordinate_infile

 evaluate ($segnum=1)
 evaluate ($done=false)

 while ( $done = false ) loop safe

   if ( &exist_segid_old_$segnum = true ) then
     if ( &segid_old_$segnum # &segid_new_$segnum ) then
       evaluate ($segtmp="T^" + encode($segnum))
       do (segid=$segtmp) (segid=&segid_old_$segnum)
     end if
   else
     evaluate ($done=true)
   end if

   evaluate ($segnum=$segnum+1)

 end loop safe

 evaluate ($segnum=1)
 evaluate ($done=false)

 while ( $done = false ) loop rename

   if ( &exist_segid_old_$segnum = true ) then
     if ( &segid_old_$segnum # &segid_new_$segnum ) then
       evaluate ($segold="T^" + encode($segnum))
       evaluate ($segid=capitalize(&segid_new_$segnum))
       do (segid=$segid) (segid=$segold)
     end if
   else
     evaluate ($done=true)
   end if

   evaluate ($segnum=$segnum+1)

 end loop rename

 write structure output=&structure_outfile end

 write coordinate output=&coordinate_outfile end

 stop