{+ file: manipulate.inp +}
{+ directory: xtal_util +}
{+ description: Performs operations and analysis on 
                reciprocal space arrays and can create new arrays. +}
{+ authors: Axel T. Brunger +}
{+ 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(

{====================== 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=65.508;
{===>} b=72.216;
{===>} c=45.035;
{===>} alpha=90;
{===>} beta=90;
{===>} gamma=90;

{* input reflection file(s) *}
{* specify non-anomalous reflection file(s) (if any)
   before anomalous reflection file(s) *}
{===>} reflection_infile_1="mbp_refine.hkl";
{===>} reflection_infile_2="";
{===>} reflection_infile_3="";
{===>} reflection_infile_4="";
{===>} reflection_infile_5="";

{=========================== output file =============================}

{* output reflection file *}
{===>} reflection_outfile="manipulate.hkl";

{======================== global operations ==========================}

{* flip Friedel mates of all reciprocal space arrays *}
{* this will operate on all array types, including complex and 
   Hendrickson-Lattman groups *}
{+ choice: true false +}
{===>} flip=false;

{===================== declaration of new arrays =====================}

{* declare new arrays reciprocal space arrays, give name (must not exist)
   and type *}
{* note: for Hendrickson-Lattman type arrays, the name refers to the
   base name.  Four arrays will be created with name "base-name"a, 
   "base-name"b, "base-name"c, and "base-name"d. *}
{+ table: rows=9 cols=2 "name" "type" +}   

{===>} new.1.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.1.type="";

{===>} new.2.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.2.type="";

{===>} new.3.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.3.type="complex";

{===>} new.4.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.4.type="complex";

{===>} new.5.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.5.type="complex";

{===>} new.6.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.6.type="complex";

{===>} new.7.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.7.type="complex";

{===>} new.8.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.8.type="complex";

{===>} new.9.name=""; 
{+ choice: "integer" "complex" "real" "hendrickson-lattman" +}
{===>} new.9.type="complex";

{===================== operations on arrays ==========================}

{* remarks *}
{+ list: please note:
         1. operations on grouped structure factor arrays (e.g., 
            Hendrickson-Lattman coefficients) must be performed on 
            the individual arrays.
         2. specify () for all operations not in use 
         3. specify (none) for all reflection selections not in use +}
   
{* operation 1 *}
{===>} op.1.expression=();
{* reflection selection for operation 1 *}
{===>} op.1.selection=(none);

{* operation 2 *}
{===>} op.2.expression=();
{* reflection selection for operation 2 *}
{===>} op.2.selection=(none);

{* operation 3 *}
{===>} op.3.expression=();
{* reflection selection for operation 3 *}
{===>} op.3.selection=(none);

{* operation 4 *}
{===>} op.4.expression=();
{* reflection selection for operation 4 *}
{===>} op.4.selection=(none);

{* operation 5 *}
{===>} op.5.expression=();
{* reflection selection for operation 5 *}
{===>} op.5.selection=(none);

{* operation 6 *}
{===>} op.6.expression=();
{* reflection selection for operation 6 *}
{===>} op.6.selection=(none);

{* operation 7 *}
{===>} op.7.expression=();
{* reflection selection for operation 7 *}
{===>} op.7.selection=(none);

{* operation 8 *}
{===>} op.8.expression=();
{* reflection selection for operation 8 *}
{===>} op.8.selection=(none);

{* operation 9 *}
{===>} op.9.expression=();
{* reflection selection for operation 9 *}
{===>} op.9.selection=(none);

{============================ analysis ===============================}

{* remarks *}
{+ list: please note:
         1. specify () for all expressions not in use 
         2. specify (none) for all reflection selections not in use +}

{* output analysis file *}
{===>} analyse_outfile="manipulate.list";

{* analysis expression 1 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.1.property="average";
{===>} analysis.1.expression=();
{* reflection selection for analysis 1 *}
{===>} analysis.1.selection=(none);

{* analysis expression 2 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.2.property="average";
{===>} analysis.2.expression=();
{* reflection selection for analysis 2 *}
{===>} analysis.2.selection=(none);

{* analysis expression 3 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.3.property="average";
{===>} analysis.3.expression=();
{* reflection selection for analysis 3 *}
{===>} analysis.3.selection=(none);

{* analysis expression 4 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.4.property="average";
{===>} analysis.4.expression=();
{* reflection selection for analysis 4 *}
{===>} analysis.4.selection=(none);

{* analysis expression 5 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.5.property="average";
{===>} analysis.5.expression=();
{* reflection selection for analysis 5 *}
{===>} analysis.5.selection=(none);

{* analysis expression 6 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.6.property="average";
{===>} analysis.6.expression=();
{* reflection selection for analysis 6 *}
{===>} analysis.6.selection=(none);

{* analysis expression 7 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.7.property="average";
{===>} analysis.7.expression=();
{* reflection selection for analysis 7 *}
{===>} analysis.7.selection=(none);

{* analysis expression 8 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.8.property="average";
{===>} analysis.8.expression=();
{* reflection selection for analysis 8 *}
{===>} analysis.8.selection=(none);

{* analysis expression 9 *}
{+ choice: "average" "sum" "element" "min" "max" "rms" "norm" +}
{===>} analysis.9.property="average";
{===>} analysis.9.expression=();
{* reflection selection for analysis 9 *}
{===>} analysis.9.selection=(none);

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

 ) {- end block parameter definition -}

checkversion 1.3

evaluate ($log_level=quiet)

xray                                   

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

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

   evaluate ($counter=1)
   evaluate ($done=false)
   while ( $done = false ) loop read
    if ( &exist_reflection_infile_$counter = true ) then
      if ( &BLANK%reflection_infile_$counter = false ) then
       reflection
         @@&reflection_infile_$counter
       end
      end if
    else
     evaluate ($done=true)
    end if
    evaluate ($counter=$counter+1)
   end loop read

   if (&flip=true) then
      flip
   end if
  
   if ( $log_level = verbose ) then
     set message=normal echo=on end
   else
     set message=off echo=off end
   end if
 
   evaluate ($jj=1)
   while ($jj<10) loop cpp
      if ( &BLANK%new.$jj.name = false ) then
         if ( &BLANK%new.$jj.type = true ) then
             display 
             display ***************************************
             display Error, new array $jj: no type specified
             display ***************************************
             abort
         end if
         if (&new.$jj.type="hendrickson-lattman") then
            evaluate ($namehl.a=&new.$jj.name+"a") 
            evaluate ($namehl.b=&new.$jj.name+"b") 
            evaluate ($namehl.c=&new.$jj.name+"c") 
            evaluate ($namehl.d=&new.$jj.name+"d") 
            declare name=$STRIP%namehl.a type=real domain=reciprocal end
            declare name=$STRIP%namehl.b type=real domain=reciprocal end
            declare name=$STRIP%namehl.c type=real domain=reciprocal end
            declare name=$STRIP%namehl.d type=real domain=reciprocal end
            group 
                  type=hl 
                  object=$STRIP%namehl.a object=$STRIP%namehl.b object=$STRIP%namehl.c object=$STRIP%namehl.d 
            end
            do ( $STRIP%namehl.a= 0 ) ( all ) 
            do ( $STRIP%namehl.b= 0 ) ( all ) 
            do ( $STRIP%namehl.c= 0 ) ( all ) 
            do ( $STRIP%namehl.d= 0 ) ( all ) 
         else
            declare name=&STRIP%new.$jj.name type=&STRIP%new.$jj.type domain=reciprocal end
            do ( &STRIP%new.$jj.name = 0 ) ( all ) 
         end if
      end if
      evaluate ($jj=$jj+1)
   end loop cpp

   evaluate ($jj=1)
   while ($jj<10) loop opp
      if ( &QUOTE%op.$jj.selection # "( none )") then
         do &STRIP%op.$jj.expression  &STRIP%op.$jj.selection 
      end if
      evaluate ($jj=$jj+1)
   end loop opp

   evaluate ($jj=1)
   while ($jj<10) loop ana
      if ( &QUOTE%analysis.$jj.selection # "( none )") then
      
         
         if ( &BLANK%analyse_outfile = false ) then
            if (&analysis.$jj.property="element") then
               set display=&analyse_outfile end
               set print=&analyse_outfile end
               display
               display  Components of  &STRIP%analysis.$jj.expression  for \
selected reflections with  &STRIP%analysis.$jj.selection 
            end if
         end if
         
         show &STRIP%analysis.$jj.property  &STRIP%analysis.$jj.expression 
                                       &STRIP%analysis.$jj.selection 
          
         if ( &BLANK%analyse_outfile = false ) then
            set display=&analyse_outfile end
            if (&analysis.$jj.property # "element") then
               display
               display  &STRIP%analysis.$jj.property of  &STRIP%analysis.$jj.expression  for \
selected reflections with  &STRIP%analysis.$jj.selection  : $result
            end if
         end if

         set display=OUTPUT end
                  
      end if
      evaluate ($jj=$jj+1)
   end loop ana
 
   set message=on end
   set echo=on end
end

if ( &BLANK%reflection_outfile = false ) then 
   
   set display=&reflection_outfile end

   @CNS_XTALMODULE:write_hkl_header (sg=&STRIP%sg;
                                     sgparam=$sgparam;)

   xray
 
     write reflection
        output=&reflection_outfile  
        sele=( all ) 
     end
       
   end

   set display=OUTPUT end     

end if

stop