{+ file: alternate.inp +}
{+ directory: general +}
{+ description: Generate alternate conformations or multiple conformers +}
{+ 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 =========================}

{* structure file *}
{===>} structure_infile="amy.mtf";

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

{========================== atom selection ===========================}

{* select atoms to have multiple conformations *}
{===>} atom_select=(resid 10 or resid 20);

{* number of multiple conformations to make for selected atoms - upto 9 *}
{* Different conformers will be given the segids AC1, AC2 .... ACn. 
   Note that the original segid of the selected atoms will be overwritten
   by these segids, unless single character chain ids are used.  You must
   specify the new segids in the alternate conformation section in all 
   subsequent files.  *}
{===>} num_conf=2;

{* preprend chain identifier (which must be a single character) *}
{+ choice: true false +}
{===>} chain_prepend=true;

{* scale occupancy *}
{+ choice: true false +}
{===>} scale_occupancy=true;

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

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

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

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

 ) {- end block parameter definition -}

 checkversion 1.3

 evaluate ($log_level=quiet)

 structure @&structure_infile end

 coordinates @&coordinate_infile

 if ( &chain_prepend = true ) then
   do (segid=segid + "AC1") (&atom_select)
   if ( &scale_occupancy = true ) then
     do (q=q/&num_conf) (segid %AC1)
   end if
 else
   do (segid="AC1") (&atom_select)
   if ( &scale_occupancy = true ) then
     do (q=q/&num_conf) (segid AC1)
   end if
 end if

 evaluate ($conf=2)
 while ( $conf <= &num_conf ) loop conf
   if ( &chain_prepend = true ) then
     evaluate ($segid_old="")
     evaluate ($counter=0)
     for $id in id ( segid %AC1 ) loop segids
       show (segid - "AC1") (id $id)
       evaluate ($segid_new=$result)
       if ( $segid_new # $segid_old ) then
         evaluate ($counter=$counter+1)
         evaluate ($segid_$counter=$segid_new)
         evaluate ($segid_old=$segid_new)
       end if
     end loop segids
     evaluate ($segcounter=$counter)
     evaluate ($counter=1)
     while ( $counter <= $segcounter) loop change
       evaluate ($segid_base=$segid_$counter + "AC1")
       evaluate ($segid=$segid_$counter + "AC" + encode($conf))
       duplicate sele=(segid $segid_base) segid=$segid end
       evaluate ($counter=$counter+1)
     end loop change    
   else
     evaluate ($segid="AC" + encode($conf))
     duplicate sele=(segid AC1) segid=$segid end
   end if
   evaluate ($conf=$conf+1)
 end loop conf

 write structure output=&structure_outfile end
 write coord output=&coordinate_outfile format=PDBO end

 stop