{+ file: realspace_transform.inp +}
{+ directory: general +}
{+ description: Apply real-space transformations to molecules +}
{+ comment: 
           Applies a specified rotation matrix and translation
           vector to each selected molecule.
           This can be used to superpose NCS related molecules
           on a reference molecule for subsequent comparison. +}
{+ 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="eg1_dimer.mtf";

{* coordinate file *}
{===>} coordinate_infile="eg1_dimer.pdb";

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

{* select atoms to be transformed *}
{===>} atom_select_1=(segid CCCC or segid DDDD);

{* real-space rotation matrix *}
{===>} matrix_1=( -0.99993  0.01083 -0.00435 )
                ( -0.01124 -0.79318  0.60889 )
                (  0.00314  0.60889  0.79325 );

{* real-space translation vector *}
{===>} vector_1=(  174.45038    0.33061   -0.18440 );

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

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

{* real-space rotation matrix *}
{===>} matrix_2=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_3=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_4=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_5=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_6=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_7=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_8=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_9=( 1 0 0 )
                ( 0 1 0 )
                ( 0 0 1 );

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

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

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

{* real-space rotation matrix *}
{===>} matrix_10=( 1 0 0 )
                 ( 0 1 0 )
                 ( 0 0 1 );

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

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

{* output coordinate file *}
{===>} coordinate_outfile="realspace_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

 evaluate ($sg="P1")
 xray
   @CNS_XTALLIB:spacegroup.lib (sg=$sg;
                                sgparam=$sgparam;)
 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 rotate
         selection=(&atom_select_$counter)
         matrix=&matrix_$counter
       end

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