{+ file: fractional_transform.inp +}
{+ directory: general +}
{+ description: Apply transformations to molecules in fractional space +}
{+ comment: 
           Applies a specified symmetry operator and translation
           vector in fractional space to each selected molecule. +}
{+ 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";

{====================== crystallographic data ========================}

{* space group *}
{* use International Table conventions with subscripts substituted
   by parenthesis *}
{===>} sg="P2(1)2(1)2(1)";

{* unit cell parameters in Angstroms and degrees *}
{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
{===>} a=61.76;
{===>} b=40.73;
{===>} c=26.74;
{===>} alpha=90;
{===>} beta=90;
{===>} gamma=90;

{============================ molecule 1 =============================}

{* select atoms to be transformed *}
{===>} atom_select_1=(all);

{* symmetry operator *}
{===>} symm_op_1=(-x+1/2,-y,z+1/2);

{* translation vector *}
{===>} vector_1=( 0 1 0 );

{============================ molecule 2 =============================}

{* select atoms to be transformed *}
{===>} atom_select_2=(none);

{* symmetry operator *}
{===>} symm_op_2=(x,y,z);

{* translation vector *}
{===>} vector_2=( 0 0 0 );

{============================ molecule 3 =============================}

{* select atoms to be transformed *}
{===>} atom_select_3=(none);

{* symmetry operator *}
{===>} symm_op_3=(x,y,z);

{* translation vector *}
{===>} vector_3=( 0 0 0 );

{============================ molecule 4 =============================}

{* select atoms to be transformed *}
{===>} atom_select_4=(none);

{* symmetry operator *}
{===>} symm_op_4=(x,y,z);

{* translation vector *}
{===>} vector_4=( 0 0 0 );

{============================ molecule 5 =============================}

{* select atoms to be transformed *}
{===>} atom_select_5=(none);

{* symmetry operator *}
{===>} symm_op_5=(x,y,z);

{* translation vector *}
{===>} vector_5=( 0 0 0 );

{============================ molecule 6 =============================}

{* select atoms to be transformed *}
{===>} atom_select_6=(none);

{* symmetry operator *}
{===>} symm_op_6=(x,y,z);

{* translation vector *}
{===>} vector_6=( 0 0 0 );

{============================ molecule 7 =============================}

{* select atoms to be transformed *}
{===>} atom_select_7=(none);

{* symmetry operator *}
{===>} symm_op_7=(x,y,z);

{* translation vector *}
{===>} vector_7=( 0 0 0 );

{============================ molecule 8 =============================}

{* select atoms to be transformed *}
{===>} atom_select_8=(none);

{* symmetry operator *}
{===>} symm_op_8=(x,y,z);

{* translation vector *}
{===>} vector_8=( 0 0 0 );

{============================ molecule 9 =============================}

{* select atoms to be transformed *}
{===>} atom_select_9=(none);

{* symmetry operator *}
{===>} symm_op_9=(x,y,z);

{* translation vector *}
{===>} vector_9=( 0 0 0 );

{============================ molecule 10 ============================}

{* select atoms to be transformed *}
{===>} atom_select_10=(none);

{* symmetry operator *}
{===>} symm_op_10=(x,y,z);

{* translation vector *}
{===>} vector_10=( 0 0 0 );

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

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

{* format output coordinates for use in o *}
{* if false then the default CNS output coordinate format will be used *}
{+ choice: true false +}
{===>} pdb_o_format=true;

{===========================================================================}
{        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

 coordinates @@&coordinate_infile

 xray

   @CNS_XTALLIB:spacegroup.lib (sg=&sg;
                                sgparam=$sgparam;)

   a=&a b=&b c=&c  alpha=&alpha beta=&beta gamma=&gamma

 end

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

 while ( $done = false ) loop main

   if ( &EXIST%atom_select_$counter = true ) then

     show sum(1) ( &atom_select_$counter )

     if ( $result > 0 ) then

       coord symmetry
         &symm_op_$counter
         selection=(&atom_select_$counter)
       end

       coord fractionalize end

       coord translate
         selection=(&atom_select_$counter)
         vector=&vector_$counter
       end

       coordinate orthogonalize end
  
     end if
     evaluate ($counter=$counter+1)

   else

     evaluate ($done=true)

   end if

 end loop main

 @CNS_XTALMODULE:write_pdb (pdb_o_format=&pdb_o_format;
                            coordinate_outfile=&coordinate_outfile;
                            sgparam=$sgparam;)

 stop