{+ file: merge_structures.inp +}
{+ directory: general +}
{+ description: Merge coordinate and molecular structure information +}
{+ comment: 
           Reads in two or more coordinate and structure files,
           checks for overlapping atom definitions, and writes out
           a merged 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 structures =========================}

{* Structure file, coordinate file, new segid and residue number increment *}
{* if the new segid is blank the old segid will not be renamed *}
{* if the residue increment is non-zero all residue numbers will be
   incremented by this number *}
{+ table: rows=10 numbered 
          cols=4 "structure file" "coordinate file" "new segid" 
                 "residue increment" +}

{===>} structure_infile_1="mbp_sites.mtf";
{===>} coordinate_infile_1="mbp_sites.pdb";
{===>} segid_file_1="mol1";
{===>} resid_inc_1=10;

{===>} structure_infile_2="amy.mtf";
{===>} coordinate_infile_2="amy.pdb";
{===>} segid_file_2="mol2";
{===>} resid_inc_2=0;

{===>} structure_infile_3="";
{===>} coordinate_infile_3="";
{===>} segid_file_3="";
{===>} resid_inc_3=0;

{===>} structure_infile_4="";
{===>} coordinate_infile_4="";
{===>} segid_file_4="";
{===>} resid_inc_4=0;

{===>} structure_infile_5="";
{===>} coordinate_infile_5="";
{===>} segid_file_5="";
{===>} resid_inc_5=0;

{===>} structure_infile_6="";
{===>} coordinate_infile_6="";
{===>} segid_file_6="";
{===>} resid_inc_6=0;

{===>} structure_infile_7="";
{===>} coordinate_infile_7="";
{===>} segid_file_7="";
{===>} resid_inc_7=0;

{===>} structure_infile_8="";
{===>} coordinate_infile_8="";
{===>} segid_file_8="";
{===>} resid_inc_8=0;

{===>} structure_infile_9="";
{===>} coordinate_infile_9="";
{===>} segid_file_9="";
{===>} resid_inc_9=0;

{===>} structure_infile_10="";
{===>} coordinate_infile_10="";
{===>} segid_file_10="";
{===>} resid_inc_10=0;

{* check for overlapping atom definitions after merging *}
{+ choice: true false +}
{===>} check_overlap=true;

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

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

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

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

 ) {- end block parameter definition -}

 checkversion 1.2

 evaluate ($log_level=quiet)

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

 while ( $done = false ) loop struct

   do (refx=0) (all)

   if ( &BLANK%structure_infile_$struct = false ) then
     structure @@&structure_infile_$struct end
   end if

   if ( &BLANK%coordinate_infile_$struct = false ) then
     coordinate @@&coordinate_infile_$struct
   end if

   if ( &resid_inc_$struct # 0 ) then
     do (resid=encode(decode(resid)+&resid_inc_$struct)) (attr refx=9999)
   end if

   if ( &BLANK%segid_file_$struct = false ) then
     evaluate ($segid="T^" + encode($struct))
     do (segid=$segid) (attr refx=9999)
   end if

   evaluate ($struct=$struct+1)

   if ( &BLANK%structure_infile_$struct = true ) then
     evaluate ($done=true)
   end if

 end loop struct

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

 while ( $done = false ) loop rename

   if ( &BLANK%segid_file_$struct = false ) then
     evaluate ($segold="T^" + encode($struct))
     evaluate ($segid=capitalize(&segid_file_$struct))
     do (segid=$segid) (segid=$segold)
   end if

   evaluate ($struct=$struct+1)

   if ( &BLANK%structure_infile_$struct = true ) then
     evaluate ($done=true)
   end if

 end loop rename

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

 while ( $done = false ) loop check

   if ( $log_level = verbose ) then
     set message=normal echo=on end
   else
     set message=off echo=off end
   end if

   if ( &check_overlap = true ) then

     if ( $struct > 1 ) then

       for $id in id (all) loop overlap

         show (segid) (id $id)
         evaluate ($segid=$result)
         show (resid) (id $id)
         evaluate ($resid=$result)
         show (name) (id $id)
         evaluate ($name=$result)

         show sum(1) (segid $QUOTE%segid and resid $resid and name $name)
  
         if ( $result > 1 ) then
           evaluate ($segid="""+$segid+""")
           display >>>> Overlapping molecular structure information for
           display >>>> atom: segid $segid and resid $resid and name $name
           display >>>> there are $result atoms selected
           abort
         end if

       end loop overlap

     end if

   end if

   set message=normal end
   set echo=on end

   evaluate ($struct=$struct+1)

   if ( &BLANK%structure_infile_$struct = true ) then
     evaluate ($done=true)
   end if

 end loop check

 show sum(1) (not(known))

 if ( $result > 0 ) then
   display >>>> Warning: there are still missing coordinates for $result atoms
   show (name) (not(known))
 end if

 write structure output=&structure_outfile end

 write coordinate output=&coordinate_outfile end

 stop