#
#     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 $Id$
#===========================================================================
#
# dictionary.script
#
#===========================================================================

  if { $IFLIBCHECK } {

    ChangeDirectory [GetDefaultDirPath TEMPORARY]

    set FILE_OUT [file join [GetDefaultDirPath TEMPORARY] \
	[subst $job_params(PROJECT)]_$job_params(JOB_ID)]

    CreateComScript libcheck comfile -nocontinue
    set TMP_COORDS [GetTmpFileName -ext cif]

    Execute [BinPath libcheck ] $comfile status report

#    if { ![file exists $FILE_OUT.lib] } { TerminateScript 0 "ERROR: Output file $FILE_OUT.lib not found\n Libcheck program has failed" }

    MoveFile $FILE_OUT.lib $GEOM_FILE 
    MoveFile [subst $FILE_OUT]_$CHEM_COMP_ID.cif $TMP_COORDS
    if { !$IFREFMAC } {
      puts "moving   [subst $FILE_OUT]_$CHEM_COMP_ID.pdb $COORDS_FILE"
      MoveFile [subst $FILE_OUT]_$CHEM_COMP_ID.pdb $COORDS_FILE 
    }
    if { [MoveFile [subst $FILE_OUT]_$CHEM_COMP_ID.ps \
      [file join [GetDefaultDirPath] [subst $CHEM_COMP_ID]_libcheck.ps ] ] } {
    AddOutputFile [subst $CHEM_COMP_ID]_libcheck.ps PROJECT }
  }

  if { $IFREFMAC } {

    WriteComFile refmac_script "MODE NEWENTRY\nEND\n"
    set status [Execute \
     "[BinPath  refmac5 ] LIB_IN \"$GEOM_FILE\" XYZIN \"$TMP_COORDS\" XYZOUT \"$COORDS_FILE\"" \
		$refmac_script status report ]

  } 
    

# Try moving molecule to superpose the original PDB coordinates 
# input to sketcher
  set SUPERPOSE 0
  if { $SUPERPOSE && [file exists $SUPERPOSE_PDBIN ] } {
    set lsq "FIT RESIDUE ALL 1 TO 1 CHAIN A
MATCH $SUPERPOSE_RES TO $SUPERPOSE_RES"
    if { $SUPERPOSE_CHAIN != "" } { append lsq " CHAIN $SUPERPOSE_CHAIN\n" }
    append lsq "OUTPUT XYZ\nEND"
    WriteComFile lsq_script $lsq

    set TMP_COORDS [GetTmpFileName -ext pdb]

    set status [Execute \
     "[BinPath  lsqkab] XYZIN1 \"$SUPERPOSE_PDBIN\" XYZIN2 \"$COORDS_FILE\" XYZOUT \"$TMP_COORDS\"" \
	$lsq_script status report ]

    WriteToLog "Moving the temporary file $TMP_COORDS to $COORDS_FILE
This contains the coordinates from Libcheck moved to superpose the input PDB file $SUPERPOSE_PDBIN"
    MoveFile $TMP_COORDS $COORDS_FILE -overwrite
  }

  set status 1