#
#     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 $Id$
#===========================================================================
#
# check.script
#
#===========================================================================
  global system

# Source file with utility procedures
  source [SearchPath TOP src CCP4_utils.tcl]

# Go to scratch directory cos these programs dump files in current directory

  ChangeDirectory [GetEnvPath CCP4_SCR]

  if $RUN_RAMPAGE {

    # Generate command line
    set cmd "[BinPath rapper]"

    set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
    set paramsfile [FileJoin $rapperdatadir params.xml]

    append cmd " $paramsfile rampage --pdb "
    append cmd "  \"$XYZIN\""
    append cmd " --rampage-postscript \"$PSOUT\""
    if {[string first "No title given" $TITLE] == -1} {
	append cmd " --rampage-title \"$TITLE\""
    }
    append cmd " --rapper-dir \"$rapperdatadir\""

    # Run Rampage
    set status [Execute $cmd {} program_status report]
     
  }

  if $RUN_SFCHECK {

    # Set the output file basename
    set basename [SetOutputFileRoot -tmp]

    CreateComScript sfcheck sfcheck_script -nocontinue

    DeleteFile sfcheck.log

    # Generate command line
    set cmd "[BinPath sfcheck]"
    if { $SFCHECK_MODE != "STRUCTURE" } {
      append cmd " HKLIN \"$HKLIN\""
    }
    if { $SFCHECK_MODE != "EXPERIMENT" } {
      append cmd " XYZIN \"$XYZIN\""
    }
    append cmd " PATH_SCR \"$basename\" PATH_OUT \"$basename\""

    # Run Sfcheck
    set status [Execute $cmd $sfcheck_script program_status report]

    if [ReadFile $LOG_FILE text ] {
      set status [expr 1 - [ExtractTextLine $text ERROR: 0 all err_line] ]
      ExtractTextLine $text Plotfile: 0 2 psfile
      if { $psfile != "" && [file exists $psfile] } { 
        MoveFile $psfile $ANALYSIS_FILE
      }
    }

    # Locate verbose Sfcheck logfile and add this to the main log file
    append sfcheck_verbose_log "$basename" "sfcheck.log"
    if { [file exists $sfcheck_verbose_log] } {
      WriteToLog "Transcribing verbose Sfcheck log file $sfcheck_verbose_log"
      TranscribeFile $sfcheck_verbose_log $LOG_FILE
      DeleteFile $sfcheck_verbose_log
    } else {
      WriteToLog "Unable to find verbose Sfcheck log file $sfcheck_verbose_log"
    }

    # Deal with anisothermal corrected data
    if { $SFCHECK_MODE != "STRUCTURE" && $SFCHECK_ANISOTHERMAL_CORR } {
      append sfcheck_cif "$basename" "sfcheck.hkl"
      if { [file exists $sfcheck_cif] } {

	# Convert to MTZ
	set tmp_hklout [GetTmpFileName -ext mtz]
        set cmd "[BinPath cif2mtz] HKLIN $sfcheck_cif HKLOUT $tmp_hklout"
	set script "END\n"
        WriteFile [set cif2mtz_script [GetTmpFileName -ext com]] $script
        set status [Execute $cmd $cif2mtz_script program_status report]

	# Acquire crystal and dataset of source columns
	switch $SFCHECK_DATA {
      SF { set label $F1 }
	  I  { set label $I1 }
      SF_ANOM { set label $F2 }
	  I_ANOM  { set label $I2 }
        }
	GetMtzDatasetFromLabel $HKLIN $label xtal dataset

	# Append to input file using CAD
	set cmd "[BinPath cad] HKLIN1 $HKLIN HKLIN2 $tmp_hklout HKLOUT $HKLOUT"
	set script "LABIN FILE 1 ALL\nLABIN FILE 2 E1=FP E2=SIGFP\nLABOUT FILE 2 E1=$F_ISO E2=$SIGF_ISO\nXNAME FILE 2 E1 TO E2=$xtal\nDNAME FILE 2 E1 TO E2=$dataset\nEND\n"
        WriteFile [set cad_script [GetTmpFileName -ext com]] $script
	set status [Execute $cmd $cad_script program_status report]

      } else {
        WriteToLog "Unable to find verbose Sfcheck CIF file $sfcheck_cif"
      }
    }
  }

  if $RUN_PROCHECK {

  set ext_list [list 01 02 03 04 05 06 07 08 09 10 ]
  set check_list [list ramchand allramac chi1_chi2 mainchpar sidechpar \
		residprop bondlenth bondangle planargps distortgm ]

  set outfile_root [file join [GetEnvPath CCP4_SCR] \
	[file root [ file tail $XYZIN]]  ]


# Edit the procheck.prm to switch colour on/off and get sensible output 
# file names

  if { ![file exists procheck.prm] } {
    CopyFile [FileJoin [GetEnvPath CINCL] procheck.prm] procheck.prm }
  if $PROCHECK_COLOUR  { set colour Y } else { set colour N }

  if { [ReadFile procheck.prm prm_text -split] } {
    foreach line $prm_text {
      if [regexp "plots in colour" $line] {
        set line [lreplace $line 0 0 $colour]
#      } elseif [regexp "9-character description" $line] {
#        set line [lreplace $line 0 0 Y]
      }
      append prm_text_out "$line\n"
    }
    WriteFile procheck.prm $prm_text_out -overwrite
  }

# Copy the procheck data files 
  if { ![file exists resdefs.dat ] } {
    CopyFile [FileJoin [GetEnvPath CINCL] resdefs.data] resdefs.dat }

 if { ![file exists prodata ] } {
    CopyFile [FileJoin [GetEnvPath CINCL] procheck.dat ] prodata }


# Create a command script contain just the name of the input file
  WriteFile [set procheck_script [GetTmpFileName -ext _com]] "$XYZIN"

# cleanup
  WriteToLog "Running cleanup program\nOutput coordinates in file: $outfile_root.new" 
  set status [Execute "[BinPath proclean]" $procheck_script program_status report -nocomments]

# secstr

  WriteToLog "Running secstr program\n Output data in file: $outfile_root.rin"
  set status [Execute "[BinPath secstr]" $procheck_script program_status report -nocomments]

# nb

  WriteToLog "Running nb program\nNon-Bonded Interactionsn Output data in file: $outfile_root.nb" 
  set status [Execute "[BinPath nb]" $procheck_script program_status report -nocomments]

# anglen

  WriteToLog "Running anglen program\nCalculation of Bond Lengths and Angles
Output data in file: $outfile_root.lan" 
  set status [Execute "[BinPath anglen]" $procheck_script program_status report -nocomments]

# Create a command script contain the name of the input file, chain and resolution
# and a N
  WriteFile $procheck_script "$XYZIN\n$CHAIN_ID\n$RESOLUTION\nN" -overwrite

#tplot
# We still run tplot for the chi1-chi2 distributions, but we hide the Ramachandran plots

  WriteToLog "Running tplot program\nchi1-ch2 Distributions" 
  set status [Execute "[BinPath tplot]" $procheck_script program_status report -nocomments]

# Create a command script contain the name of the input file, chain and resolution
  WriteFile $procheck_script "$XYZIN\n$CHAIN_ID\n$RESOLUTION" -overwrite

#pplot

  WriteToLog "Running pplot program\nStereochemical Quality Plots" 
  set status [Execute "[BinPath pplot]" $procheck_script program_status report -nocomments]

# bplot
  WriteToLog "Running probplot program\nMain Chain Bond Lengths & Angles"
  set status [Execute "[BinPath probplot]" $procheck_script program_status report -nocomments]

# Add summary files to end of log file

  TranscribeFile $outfile_root.out $LOG_FILE
  TranscribeFile $outfile_root.sum $LOG_FILE

# Cleanup some of these data files

  DeleteFiles prodata resdef.dat ps.number 

# Change name of postscript files to something more workable
  
  set outfiles AddOutputFile
  set file_root [file rootname [file tail $XYZIN] ]
  for { set n 2 } { $n <= 9 } { incr n } {
    set file0 [subst $file_root]_[lindex $ext_list $n].ps
    if [file exists $file0] {
      set file1 [SetOutputFileRoot]_[lindex $check_list $n].ps
      MoveFile $file0 $file1 -overwrite
      append outfiles " $file1 PROJECT"
      if $PROCHECK_PRINT  { catch "exec $PRINT_CMD $file1" }
    }
  }
  eval  "$outfiles"

  }