global job_params
global system
#
#
# Source file with utility procedures
# source [SearchPath TOP src CCP4_utils.tcl]
  source [SearchPath TOP utils map_utils.tcl]
# Read the crystal parameters files
#  ReadSymops [FileJoin [GetEnvPath CLIBD] symop.lib]
#  ReadCrystalData [SearchPath TOP etc crystal.lib]
#
# Write the arp .par file

  set logfile $job_params(LOG_FILE)
  set arpwarpdir $job_params(JOB_ID)_$job_params(TASKNAME) 
  set workdir [GetDefaultDirPath]

  set parfile "$workdir/$arpwarpdir.par"
  set testfile [GetTmpFileName] 

  append partext "set WORKDIR = [GetDefaultDirPath]\n"
  append partext "set PROJECT = $job_params(PROJECT)\n"
  append partext "set JOB_ID = $job_params(JOB_ID) \n"
  append partext "set warpbin = [GetEnvPath warpbin]\n"
  append partext "set fulllogfile = $job_params(JOB_ID)_warp_ligand_details.log \n"

  append partext "set version = 7.6 \n"

# Put the name of the CCP4i def file  into the par file
  append partext "set CCP4I_DEFFILE = " [FileJoin [GetDefaultDirPath]  \
     CCP4_DATABASE $job_params(JOB_ID)_$job_params(TASKNAME).def ] \n

    AddOutputFile $LIGANDOUT PROJECT
  
# Handle file names

  foreach par [list HKLIN PROTEININ LIGANDIN LIGANDREF LIGANDOUT EXTRA_LIBRARY ] arppar [list datafile proteinfile ligandfile search_model ligandfileout extralibrary ] {
    set file [subst $[subst $par]]
    set dir [subst DIR_$[subst $par]]
    set value [GetFullFileName1 $file $dir]
    if { $value == "" } {
      append partext "set $arppar = ''" \n
    } else {
      append partext "set $arppar = $value" \n
    }
  }

# stuff the reference ligand(s) file names into the testfile.

   if { $TOGGLE_TEST == "1" } {
	set file [subst $LIGANDTEST]
	set dir [subst $DIR_LIGANDTEST]
   	set value [GetFullFileName1 $file $dir] 
   	append testtext "$value "
   	WriteFile $testfile $testtext
   	append partext "set reflist = $testfile" \n
   } else {
	append partext "set reflist = " \n
   }

# Basic params and ligand code input

   if { ![string length $LIGANDCODE] } { 
  append partext "set ligandcode = code " \n
    } else {
  append partext "set ligandcode = $LIGANDCODE " \n
    }

    foreach \
       par [ list LIGCYCLES NPARTIAL WILSON_B FP SIGFP KEEP_WATERS ] \
    arppar [ list nligandcycles partial wilsonb fp sigfp keepwaters ] {
  set value [subst $[subst $par]]
        append partext "set $arppar = $value " \n
  }

  set space_gp_number [GetSpaceGroupNumber $SPACE_GROUP]

  append partext "set sym = $space_gp_number" \n

# These are params that have to be included in quotes !!!

  append partext "set scaleopt = 'SIMPLE LSSC ANIS '" \n

    foreach \
       par [ list XYZLIM RESOL FREELABIN SCALML LIGXYZ] \
    arppar [ list xyzlim resol freelabin scalml search_position ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = ' $value '" \n
	}

    if { $WEIGHT != "AUTO" } {
     set WEIGHT [MATRIX $WMAT]	
    }

    foreach \
       par [ list REFMAX NCYCLES WEIGHT ] \
    arppar [ list refmax rrcyc weightv] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value " \n
	}

    foreach \
       par [ list KNOWNLIGPOS  LIGRAD] \
    arppar [ list known_position search_radius ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value " \n
	}


if { [file exists $parfile] } {
	   file delete -force -- $parfile
}

   WriteFile $parfile $partext
#   WriteFile $testfile $testtext
 
   file attributes $parfile -permissions 0740

   AddOutputFile $parfile PROJECT

    catch {exec [GetEnvPath warpbin]/warp_ligand.sh  $parfile >> $logfile}