#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Library.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#
#CCP4i_cvs_Id $Id$
#===========================================================================
#
# superpose.script
#
#===========================================================================

  if { $RUN_PDBMERGE} {
    set XYZOUT_LOCAL [GetTmpFileName -ext pdb]
  } else {
    set XYZOUT_LOCAL $XYZOUT
  }

  if { [regexp GES $SUPERPOSE_MODE ] } {

    set cmd "[BinPath gesamt] \"$XYZIN1\" -s \"$GES_FIXED\" \"$XYZIN2\" -s \"$GES_MOVING\" -o \"$XYZOUT_LOCAL\""
    set status [Execute $cmd "" program_status report ]

  } elseif { [regexp SSM $SUPERPOSE_MODE ] } {

    set cmd "[BinPath superpose] \"$XYZIN2\" -s \"$SSM_MOVING\" \"$XYZIN1\" -s \"$SSM_FIXED\" -o \"$XYZOUT_LOCAL\""
    set status [Execute $cmd "" program_status report ]

  } elseif { [regexp TOP $SUPERPOSE_MODE ] } {

# Make a directory to work in so no chance of two top jobs fighting for
# the same fort.nn

    set topp_dir [SetOutputFileRoot -tmp]_topp_

    DeleteFile $topp_dir
    CreateDir $topp_dir
    ChangeDirectory  $topp_dir
    set newfile_root [file root [file tail $TOPOUT ] ]

    WriteToLog "Creating directory $topp_dir for output files"

    set tmp_log_file [GetTmpFileName -ext log]

    CreateComScript topp topp_script -nocontinue

    set status [Execute [BinPath topp] $topp_script \
	program_status report -copy_log $tmp_log_file ]

    set addoutfile AddOutputFile

    if { [ReadFile $tmp_log_file log_list] &&
	[ExtractTextLine $log_list guoguang 0 all outfile ] } {
      set n 0
      while { [ExtractTextLine - "Superimposed coordinates" 0 5 outfile] } {
         incr n; set newfile [subst $newfile_root]_$n.pdb
         MoveFile [FileJoin $topp_dir $outfile] \
		[FileJoin [GetDefaultDirPath $DIR_TOPOUT] $newfile] -overwrite
         append addoutfile " $newfile $DIR_TOPOUT"
      }
    }
      
    DeleteFile $tmp_log_file
    eval "$addoutfile"


  } else {

    CreateComScript lsqkab lsqkab_script

    set cmd "[BinPath lsqkab] XYZIN2 \"$XYZIN2\""
    if [regexp FIT|COMPARE  $SUPERPOSE_MODE] { append cmd " XYZIN1 \"$XYZIN1\"" }
    if $IFOUTPUTXYZ { append cmd " XYZOUT \"$XYZOUT_LOCAL\"" }
    if $IFOUTPUTDELTAS { 
      append DELTAS [SetOutputFileRoot] _deltas.log
      append cmd " DELTAS $DELTAS" 
    }
    if $IFOUTPUTRMS {
      append RMSTAB [SetOutputFileRoot] _rmstab.graph
      append cmd " RMSTAB $RMSTAB"
    }

    set status [Execute $cmd $lsqkab_script program_status report ]

    if $IFOUTPUTDELTAS { AddOutputFile $DELTAS $job_params(PROJECT) }
    if $IFOUTPUTRMS { AddOutputFile $RMSTAB $job_params(PROJECT) }
  }

  if { $RUN_PDBMERGE} {

    CreateComScript pdb_merge pdb_merge_script
    set cmd "[BinPath pdb_merge] xyzin1 \"$XYZIN1\" xyzin2 \"$XYZOUT_LOCAL\" xyzout \"$XYZOUT\""
    set status [Execute $cmd $pdb_merge_script program_status report ]
    
  }