#
#     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 $Id$
#===========================================================================
#
# mr_solution.script
#
#===========================================================================

# Source the file with utility procedures for running amore
  source [SearchPath TOP utils amore_utils.tcl ]
  source [SearchPath TOP utils pdb_utils.tcl ]
  set alphabet [list " " A B C D E F G H I J K L M N O P Q R S T U V W X Y Z]
  set tmp_log [GetTmpFileName -ext log ]

# Get the file root and extension for the output file
# For >1 solution output files will have a "_n" inserted in file name
  set xyzout_ext  [file extension $XYZOUT]
  if { $xyzout_ext == "" } { set xyzout_ext ".pdb" }
  set xyzout_root [file rootname $XYZOUT]
  set fileout_list ""
  set output_list "AddOutputFile "

#-------------------------------------------------------------------
# Open the solution file and read in solutions
#-------------------------------------------------------------------
  if { ![ReadFile $SOLFIL text -split] } {
    TerminateScript 0 -report "Can not read solution file $SOLFIL"
  }
  set ns 1; set nm 0
  foreach line $text {
    if { ![regexp {^#} $line ] && [llength $line] > 6 } {
      if { $nm <  $N_MODELS } { incr nm } else { incr ns; set nm 1 }
      set EULER_1($ns,$nm) [lindex $line 2]
      set EULER_2($ns,$nm) [lindex $line 3]
      set EULER_3($ns,$nm) [lindex $line 4]
      set COM_1($ns,$nm) [lindex $line 5]
      set COM_2($ns,$nm) [lindex $line 6]
      set COM_3($ns,$nm) [lindex $line 7]
    }
  }
  set N_SOLUTIONS $ns
#----------------------------------------------------------------------------
# Run pdbset to translate and rotate molecule 
#----------------------------------------------------------------------------
  for { set ns 1 } { $ns <= $N_SOLUTIONS } { incr ns } {
    set tmp_pdb_list ""

    set nch 0
    for { set nm 1 } { $nm <= $N_MODELS } { incr nm } {
      set tmpxyz($nm) [GetTmpFileName -ext pdb]
      set comline "[BinPath pdbset] XYZIN \"$XYZSHFT($nm)\" XYZOUT \"$tmpxyz($nm)\""
      set pdbset_comfile ""
      lappend tmp_pdb_list $tmpxyz($nm)

# Get chain list from input file
      if { ![PdbGetChains $XYZSHFT($nm) chn_list chn_ranges] } {
         # No chain ids found
         set chn_list [list " "]
      }
# Make CHAIN keywords for PDBSET script
      set chn_lines ""
      foreach chnid $chn_list {
	incr nch
	if { $nch > 26 } { set nch 1 }
	append chn_lines "CHAIN $chnid [lindex $alphabet $nch]\n"
      }
      set chn_lines [string trim $chn_lines "\n"]

# Write a com file to do the translate
      WriteComFile pdbset_comfile \
"CELL $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6
SPACEGROUP $SPACE_GROUP
$chn_lines
ROTATE EULER $EULER_1($ns,$nm) $EULER_2($ns,$nm) $EULER_3($ns,$nm)
SHIFT FRACTIONAL $COM_1($ns,$nm) $COM_2($ns,$nm) $COM_3($ns,$nm)"

      set status [Execute $comline  $pdbset_comfile program_status report ]

    }

#----------------------------------------------------------------------------
# Merge the temporary transformed pdb files into one file
# using utility from $CCP4I_TOP/utils/amore_utils.tcl
#----------------------------------------------------------------------------
    if { $N_SOLUTIONS <= 1 } {
      set fileout $XYZOUT
    } else {
      set fileout $xyzout_root; append fileout _$ns $xyzout_ext
    }
    DeleteFile $fileout
    if { $N_MODELS <= 1 } {
      MoveFile $tmpxyz(1) $fileout
    } else {
      set status [MergePdbFiles $fileout $tmp_pdb_list]
    }
    lappend fileout_list $fileout
    append output_list "$fileout PROJECT "
  }

#-------------------------------------------------------------------------
# Look for bad contacts in the newly created pdb file
#-------------------------------------------------------------------------
  if { $IFBADCONTACTS } {


#    set LPOUT ""; append LPOUT [file rootname $file] "_contacts.dat"

    set INTRA_RES 0
    set INTRA_MOL 1
    if { [regexp CA $CONTACT_MODE] } {
      set N_ATOM_RADII 1
      set ATOMTYPE(1) CA
      set ATOMRADIUS(1) 1.5
    } else {
      set N_ATOM_RADII 0
    }

    CreateComScript distang distang_comfile

  set ns 0; foreach file $fileout_list { incr ns;

    set comline "[BinPath distang] XYZIN \"$file\""

    set status [Execute $comline $distang_comfile \
        program_status report -copy_log $tmp_log ]

# Find total number of close contacts for this model
    set nbumps($ns) 0; set log_text ""
    ReadFile $tmp_log log_text
    set line [ExtractFromText $log_text "Number of Close Contacts to Symmetry" \
		3 all]
    while { ![regexp DISTANG $line] } {
      if { [llength $line] == 5 } { \
	set nbumps($ns) [expr $nbumps($ns) + [lindex $line 4] ] }
      set line [ExtractFromText - {} 1 all]
    }
    DeleteFile $tmp_log
  }

  }
#--------------------------------------------------------------------
# Output summary of close contacts to log file
#--------------------------------------------------------------------

  if { $IFBADCONTACTS } { 
  
set log_text "SUMMARY OF CLOSE-CONTACTS FOR ALL SOLUTION(S)

Number of instances of Calpha-Calpha distances less than 6 Angstrom
between adjacent symmetry elements

"
  for { set ns 1 } { $ns <= $N_SOLUTIONS } { incr ns } {
    append log_text "\nSolution $ns   $nbumps($ns) close contacts"
  }

  WriteToLog $log_text

  }

  eval $output_list