# -------------------------------------------------------------------
#
# Copyright (C) 2005-2015 by Global Phasing Limited
#
# This code is distributed under the terms and conditions of the CCP4
# Program Suite Licence Agreement as a CCP4 Application.  A copy of
# the CCP4 licence can be obtained by writing to the CCP4 Secretary,
# Daresbury Laboratory, Warrington WA4 4AD, UK.
#
# Authors: (2005-2015) Clemens Vonrhein
#
# -------------------------------------------------------------------

#CCP4i_cvs_Id $Id: autoSHARP.script,v 1.22 2015/11/06 10:07:43 vonrhein Exp $

global job_params
global system
global env
global configure

set workdir [GetDefaultDirPath]
set log_file $job_params(LOG_FILE)
set job_id $job_params(JOB_ID)
set taskname $job_params(TASKNAME)
set log_dir $job_params(JOB_ID)_$job_params(TASKNAME)
set ccp4i_deffile [FileJoin [GetDefaultDirPath] CCP4_DATABASE $job_params(JOB_ID)_$job_params(TASKNAME).def ]
set tcl_version [info tclversion]

append text "\n"
# create initial directory for autoSHARP run
while { [file exists "$workdir/$log_dir/$TITLE.$autoSHARP_jobi"] } {
    incr $autoSHARP_jobi
}
set autoSHARP_dir "$workdir/$log_dir/$TITLE.$autoSHARP_jobi"
if { ![file isdirectory $autoSHARP_dir] } {
    file mkdir $autoSHARP_dir
} 
AddOutputDir $autoSHARP_dir

set dot_autoSHARP "$autoSHARP_dir/.autoSHARP"

#puts "dot_autoSHARP = $dot_autoSHARP"

append dot_autoSHARP_text "# ----------------------------------------\n"
append dot_autoSHARP_text "# General information about project\n"
append dot_autoSHARP_text "# ----------------------------------------\n"
append dot_autoSHARP_text "  autoSHARP_proj=\"$TITLE\"\n"
append dot_autoSHARP_text "  autoSHARP_jobi=\"$autoSHARP_jobi\"\n"
append dot_autoSHARP_text "  autoSHARP_titl=\"$autoSHARP_titl\"\n"
append dot_autoSHARP_text "  autoSHARP_type=\"$autoSHARP_type\"\n"
append dot_autoSHARP_text "  autoSHARP_rate=\"$autoSHARP_rate\"\n"
append dot_autoSHARP_text "  autoSHARP_molw=\"$autoSHARP_molw\"\n"
append dot_autoSHARP_text "  autoSHARP_nres=\"$autoSHARP_nres\"\n"
if { [IfSet $autoSHARP_pirf] }  {
    set autoSHARP_pirf [GetFullFileName1 $autoSHARP_pirf $DIR_autoSHARP_pirf]
    set autoSHARP_pirf_tail [file tail $autoSHARP_pirf]
    set autoSHARP_pirf_root [file rootname $autoSHARP_pirf_tail]
    if { ! [file exists "$autoSHARP_dir/${autoSHARP_pirf_root}.pir"] } {
	if { $tcl_version > 8.3 } {
	    file link -symbolic "$autoSHARP_dir/${autoSHARP_pirf_root}.pir" $autoSHARP_pirf
	} else {
	    file copy $autoSHARP_pirf "$autoSHARP_dir/${autoSHARP_pirf_root}.pir"
	}
    }
    set autoSHARP_pirf $autoSHARP_pirf_root
}
append dot_autoSHARP_text "  autoSHARP_pirf=\"$autoSHARP_pirf\"\n"
if { [IfSet $autoSHARP_pdbf] }  {
    set autoSHARP_pdbf [GetFullFileName1 $autoSHARP_pdbf $DIR_autoSHARP_pdbf]
    set autoSHARP_pdbf_tail [file tail $autoSHARP_pdbf]
    set autoSHARP_pdbf_root [file rootname $autoSHARP_pdbf_tail]
    if { ! [file exists "$autoSHARP_dir/${autoSHARP_pdbf_root}.pdb"] } {
	if { $tcl_version > 8.3 } {
	    file link -symbolic "$autoSHARP_dir/${autoSHARP_pdbf_root}.pdb" $autoSHARP_pdbf
	} else {
	    file copy $autoSHARP_pdbf "$autoSHARP_dir/${autoSHARP_pdbf_root}.pdb"
	}
    }
    set autoSHARP_pdbf "${autoSHARP_pdbf_root}.pdb"
}
append dot_autoSHARP_text "  autoSHARP_pdbf=\"$autoSHARP_pdbf\"\n"
append dot_autoSHARP_text "  autoSHARP_spgr=\"$autoSHARP_spgr\"\n"
append dot_autoSHARP_text "  autoSHARP_resl=\"$autoSHARP_resl\"\n"
append dot_autoSHARP_text "  autoSHARP_resh=\"$autoSHARP_resh\"\n"
append dot_autoSHARP_text "  autoSHARP_nset=\"$autoSHARP_nset\"\n"
append dot_autoSHARP_text "  autoSHARP_user=\"[GetUserId]\"\n"
append dot_autoSHARP_text "  autoSHARP_ulvl=\"$autoSHARP_ulvl\"\n"
append dot_autoSHARP_text "  autoSHARP_chtm=\"$autoSHARP_chtm\"\n"
append dot_autoSHARP_text "  autoSHARP_csum=\"$autoSHARP_csum\"\n"
append dot_autoSHARP_text "# ----------------------------------------\n"
append dot_autoSHARP_text "# autoSHARP protocol information\n"
append dot_autoSHARP_text "# ----------------------------------------\n"
if { [IfSet $autoSHARP_data_format] && $autoSHARP_data_format == "MTZS" } {
    set autoSHARP_EntryPoint 3
}
append dot_autoSHARP_text "  autoSHARP_EntryPoint=\"$autoSHARP_EntryPoint\"\n"
set autoSHARP_EntryPoint3_Path3_Opt [string index $autoSHARP_EntryPoint3_Path 0]
set autoSHARP_EntryPoint3_Path [string index $autoSHARP_EntryPoint3_Path 1]
append dot_autoSHARP_text "  autoSHARP_EntryPoint3_Path=\"$autoSHARP_EntryPoint3_Path\"\n"
append dot_autoSHARP_text "  autoSHARP_EntryPoint3_Path3_Opt=\"$autoSHARP_EntryPoint3_Path3_Opt\"\n"
if { [IfSet $autoSHARP_DetectPgm] } {
  append dot_autoSHARP_text "  autoSHARP_DetectPgm=\"$autoSHARP_DetectPgm\"\n"
} else {
  append dot_autoSHARP_text "  autoSHARP_DetectPgm=\"shelx\"\n"
}
append dot_autoSHARP_text "# ----------------------------------------\n"
append dot_autoSHARP_text "# CCP4i specific\n"
append dot_autoSHARP_text "# ----------------------------------------\n"
append dot_autoSHARP_text "  autoSHARP_RunningType=\"ccp4i\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_workdir=\"$workdir\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_fileroot=\"[SetOutputFileRoot]\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_log_file=\"$log_file\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_log_dir=\"$log_dir\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_job_id=\"$job_id\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_taskname=\"$taskname\"\n"
append dot_autoSHARP_text "  autoSHARP_ccp4i_autoSHARP_dir=\"$autoSHARP_dir\"\n"
append dot_autoSHARP_text "  autoSHARP_viewer=\"$autoSHARP_viewer\"\n"
append dot_autoSHARP_text "  CCP4I_DEFFILE=\"$ccp4i_deffile\"\n"

for {set i 1} {$i<=$autoSHARP_nset} {incr i} {
    append dot_autoSHARP_text "# ----------------------------------------\n"
    append dot_autoSHARP_text "# Dataset $i\n"
    append dot_autoSHARP_text "# ----------------------------------------\n"
    append dot_autoSHARP_text "  autoSHARP_iden_$i=\"$autoSHARP_iden($i)\"\n"
    append dot_autoSHARP_text "  autoSHARP_wave_$i=\"$autoSHARP_wave($i)\"\n"
    if { $autoSHARP_type == "MAD" } {
	append dot_autoSHARP_text "  autoSHARP_hatm_$i=\"$autoSHARP_hatm(0)\"\n"
	append dot_autoSHARP_text "  autoSHARP_nsit_$i=\"$autoSHARP_nsit(0)\"\n"
    } else {
	if { $i == 1 } {
	    append dot_autoSHARP_text "  autoSHARP_hatm_$i=\"\"\n"
	    append dot_autoSHARP_text "  autoSHARP_nsit_$i=\"0\"\n"
	} else {
	    append dot_autoSHARP_text "  autoSHARP_hatm_$i=\"$autoSHARP_hatm($i)\"\n"
	    append dot_autoSHARP_text "  autoSHARP_nsit_$i=\"$autoSHARP_nsit($i)\"\n"
	}
    }
    if { $autoSHARP_type == "MAD" && [IfSet $autoSHARP_sitf_mad] && [IfSet $DIR_autoSHARP_sitf_mad] } {
	set autoSHARP_sitf($i) $autoSHARP_sitf_mad
	set DIR_autoSHARP_sitf($i) $DIR_autoSHARP_sitf_mad
    }
    if { $autoSHARP_type == "MAD" && [IfSet $autoSHARP_sitf_mad] && [IfSet $DIR_autoSHARP_sitf_mad] } {
	set autoSHARP_sitf($i) $autoSHARP_sitf_mad
	set DIR_autoSHARP_sitf($i) $DIR_autoSHARP_sitf_mad
    }
    if { [IfSet $autoSHARP_sitf($i)] }  {
	set autoSHARP_sitf($i) [GetFullFileName1 $autoSHARP_sitf($i) $DIR_autoSHARP_sitf($i)]
	set autoSHARP_sitf_tail [file tail $autoSHARP_sitf($i)]
	set autoSHARP_sitf_root [file rootname $autoSHARP_sitf_tail]
	if { ! [file exists "$autoSHARP_dir/${autoSHARP_sitf_root}.hatom"] } {
	    if { $tcl_version > 8.3 } {
		file link -symbolic "$autoSHARP_dir/${autoSHARP_sitf_root}.hatom" $autoSHARP_sitf($i)
	    } else {
		file copy $autoSHARP_sitf($i) "$autoSHARP_dir/${autoSHARP_sitf_root}.hatom"
	    }
	}
	set autoSHARP_sitf($i) $autoSHARP_sitf_root
    }
    if { $autoSHARP_type == "MAD" || $i > 1 } {
	append dot_autoSHARP_text "  autoSHARP_sitf_$i=\"$autoSHARP_sitf($i)\"\n"
	append dot_autoSHARP_text "  autoSHARP_fone_$i=\"$autoSHARP_fone($i)\"\n"
	append dot_autoSHARP_text "  autoSHARP_ftwo_$i=\"$autoSHARP_ftwo($i)\"\n"
    } else {
	append dot_autoSHARP_text "  autoSHARP_sitf_$i=\"\"\n"
	append dot_autoSHARP_text "  autoSHARP_fone_$i=\"0.0\"\n"
	append dot_autoSHARP_text "  autoSHARP_ftwo_$i=\"0.0\"\n"
    }
    set fmid $autoSHARP_fmid($i)
    if { $fmid == "Unassigned" } { set fmid "" }
    set smid $autoSHARP_smid($i)
    if { $smid == "Unassigned" } { set smid "" }
    if { $autoSHARP_type == "MAD" || $i > 1 } {
	set dano $autoSHARP_dano($i)
	if { $dano == "Unassigned" } { set dano "" }
	set sano $autoSHARP_sano($i)
	if { $sano == "Unassigned" } { set sano "" }
	set isym $autoSHARP_isym($i)
	if { $isym == "Unassigned" } { set isym "" }
    } else {
	set dano ""
	set sano ""
	set isym ""
    }
    append dot_autoSHARP_text "  autoSHARP_fmid_$i=\"$fmid\"\n"
    append dot_autoSHARP_text "  autoSHARP_smid_$i=\"$smid\"\n"
    append dot_autoSHARP_text "  autoSHARP_dano_$i=\"$dano\"\n"
    append dot_autoSHARP_text "  autoSHARP_sano_$i=\"$sano\"\n"
    append dot_autoSHARP_text "  autoSHARP_isym_$i=\"$isym\"\n"
    set data $autoSHARP_data_mtz($i)
    set DIR_data $DIR_autoSHARP_data_mtz($i)
    set dtyp MTZ
    if { ![IfSet $data] }  {
	set data $autoSHARP_data_sca($i)
	set DIR_data $DIR_autoSHARP_data_sca($i)
        set dtyp SCA
    }
    append dot_autoSHARP_text "  autoSHARP_dtyp_$i=\"$dtyp\"\n"
    if { [IfSet $data] }  {
	set data [GetFullFileName1 $data $DIR_data]
	set data_tail [file tail $data]
	if { ! [file exists "$autoSHARP_dir/$data_tail"] } {
	    if { $tcl_version > 8.3 } {
		file link -symbolic "$autoSHARP_dir/$data_tail" $data
	    } else {
		file copy $data "$autoSHARP_dir/$data_tail"
	    }
	}
	set data $data_tail
    }
    append dot_autoSHARP_text "  autoSHARP_data_$i=\"$data\"\n"
#    set sitf $autoSHARP_sitf($i)
#    set DIR_sitf $DIR_autoSHARP_sitf($i)
#    if { [IfSet $sitf] }  {
#	set sitf [GetFullFileName1 $sitf $DIR_sitf]
#	set sitf_tail [file tail $sitf]
#	if { ! [file exists "$autoSHARP_dir/$sitf_tail"] } {
#	    if { $tcl_version > 8.3 } {
#		file link -symbolic "$autoSHARP_dir/$sitf_tail" $sitf
#	    } else {
#		file copy $sitf "$autoSHARP_dir/$sitf_tail"
#	    }
#	}
#	set sitf $sitf_tail
#    }
#    append dot_autoSHARP_text "  autoSHARP_sitf_$i=\"$sitf\"\n"
}

WriteFile $dot_autoSHARP $dot_autoSHARP_text
AddOutputFile $dot_autoSHARP PROJECT

# check various environmental variables
if [info exists env(warpbin)] {
    set warpbin_tmp $env(warpbin)
    if { [IfSet $warpbin_tmp] } {
	if { [file isdirectory $warpbin_tmp] } {
	    set env(sharp_SkipReading_arpwarp) "yes"
	    set env(sushi_SkipReading_arpwarp) "yes"
	    append text  "# using ARP/wARP binaries from $warpbin_tmp\n"
	} else {
	    append text  "# unable to use ARP/wARP from $warpbin_tmp (not a directory)\n"
	}
    } else {
	append text  "# ARP/wARP not set-up (\$warpbin set to empty)?\n"
    }
} else {
    append text  "# ARP/wARP not set-up (\$warpbin not set)?\n"
}
if [info exists env(CCP4)] {
    set ccp4_tmp $env(CCP4)
    if [info exists env(CBIN)] {
	set cbin_tmp $env(CBIN)
	if [info exists env(CLIB)] {
	    set clib_tmp $env(CLIB)
	    if [info exists env(CCP4_SCR)] {
		set cscr_tmp $env(CCP4_SCR)
		if { [IfSet $ccp4_tmp] && [IfSet $cbin_tmp] && [IfSet $clib_tmp] && [IfSet $cscr_tmp] } {
		    if { [file isdirectory $ccp4_tmp] && [file isdirectory $cbin_tmp] && [file isdirectory $clib_tmp] && [file isdirectory $cscr_tmp] } {
			set env(sharp_SkipReading_ccp4) "yes"
			set env(sushi_SkipReading_ccp4) "yes"
			append text  "# using CCP4 binaries from $cbin_tmp\n"
		    }
		}
	    }
	}
    }
}
set BDG_shelxbin ""
foreach path [split $env(PATH) : ] {
    if { [file executable "$path/shelxc"] && [file executable "$path/shelxd"] } {
	set BDG_shelxbin $path
	break
    }
}
if { [IfSet $BDG_shelxbin] } {
    set env(sharp_SkipReading_shelx) "yes"
    set env(sushi_SkipReading_shelx) "yes"
    set env(BDG_shelxbin) $BDG_shelxbin
    append text  "# using $BDG_shelxbin for shelxc/shelxd binaries\n"
}
# set various environmental variables
if { [file executable "/bin/uname" ] } {
    set BDG_uname "/bin/uname"
} elseif { [file executable "/usr/bin/uname" ] } {
    set BDG_uname "/usr/bin/uname"
}
set BDG_hwsp_ini [exec $BDG_uname]
set BDG_hwsp "unknown"
#puts $BDG_hwsp
#puts $BDG_hwsp_ini
if { $BDG_hwsp_ini == "Linux" } {
    set BDG_machine [exec $BDG_uname -m]
    if { $BDG_machine == "x86_64" } {
	set BDG_hwsp "linux64"
    } else {
	set BDG_hwsp "linux"
    }
}
if { $BDG_hwsp_ini == "Darwin" } {
    set BDG_hwsp "darwin"
}
if { $BDG_hwsp != "unknown" } {
    set sharp_home [GetEnvPath SHARP_home]
    if { [IfSet $sharp_home] } {
        set env(BDG_home) $sharp_home
    }
    set cscr_tmp [GetEnvPath CCP4_SCR]
    if { [IfSet $cscr_tmp] && [file isdirectory $cscr_tmp] } {
	set BDG_scr $cscr_tmp
    } else {
	set BDG_scr "/tmp"
    }
    foreach path [split $env(PATH) : ] {
	if { [file executable "$path/perl"] } {
	    set BDG_perl "$path/perl"
	    break
	}
    }
    if { [IfSet $sharp_home] && [IfSet $BDG_scr] && [IfSet $BDG_perl] } {
	set env(BDG_scr) $BDG_scr
	set env(BDG_perl) $BDG_perl
	set env(BDG_exe) [FileJoin $sharp_home bin ${BDG_hwsp}_exe ]
	set env(BDG_com) [FileJoin $sharp_home bin sharp ]
	set env(SYMOP) [FileJoin $sharp_home database symop ]
	set env(ATOMSF) [FileJoin $sharp_home database atomsf ]
	if { [file exists [FileJoin $sharp_home database sphcluster ] ] } {
	    set env(SPHCLUSTER) [FileJoin $sharp_home database sphcluster ]
	}
	if { [file exists [FileJoin $sharp_home database syminfo.lib ] ] } {
	    set env(SYMINFO) [FileJoin $sharp_home database syminfo.lib ]
	}
	set env(sharp_SkipReading_sharp) "yes"
	set env(sushi_SkipReading_sharp) "yes"
    }

}

set browsercmd ""
set browser ""
if { [IfSet $configure(HYPERTEXT_VIEWER)] } {
    set browsercmd $configure(HYPERTEXT_VIEWER)
    if { ! [file executable $browsercmd] } {
	foreach path [split $env(PATH) : ] {
	    if { [file executable "$path/$browsercmd"] } {
		set browser "$path/$browsercmd"
		break
	    }
	}
    } else {
	set browser $browsercmd
    }
}

append text  "# ------------------------------------------------------------\n"
if { ! [IfSet $browser] } {
    append text  "# You haven't configured the browser to be used with CCP4i,\n"
    append text  "# so please open\n"
    append text  "#\n"
    append text  "#     $autoSHARP_dir/LISTautoSHARP.html\n"
    append text  "#\n"
    append text  "# in a browser (like firefox, mozilla etc). In any case:\n"
    append text  "# remember to hit the \"reload\" button of your browser\n"
    append text  "# from time to time when looking at this main log-file!\n"
    append text  "#\n"
} else {
    append text  "# If a browser didn't automatically open the following\n"
    append text  "# file, please open\n"
    append text  "#\n"
    append text  "#     $autoSHARP_dir/LISTautoSHARP.html\n"
    append text  "#\n"
    append text  "# in a browser (like firefox, mozilla etc). In any case:\n"
    append text  "# remember to hit the \"reload\" button of your browser\n"
    append text  "# from time to time when looking at this main log-file!\n"
    append text  "#\n"
}
append text  "# ------------------------------------------------------------\n"
append text  "#\n"
append text  "#  Please cite:\n"
append text  "#      Vonrhein, C, Blanc, E., Roversi, P and Bricogne,\n"
append text  "#      G. (2007). Automated structure solution with autoSHARP.\n"
append text  "#      Methods Mol Biol. 364, 215-30.\n"
append text  "#\n"
append text  "# ------------------------------------------------------------\n"
append text  "#\n"
append text  "# SHARP/autoSHARP: http://www.globalphasing.com/sharp/\n"
append text  "#\n"
append text  "# ------------------------------------------------------------\n\n"
puts -nonewline $text
WriteToLog $text

#puts "# ------------------------------------------------------------"    >> $log_file
#puts "# Please open $autoSHARP_dir/LISTautoSHARP.html in a browser"      >> $log_file
#puts "# ------------------------------------------------------------"    >> $log_file
#puts "  Please cite:"                                                    >> $log_file
#puts "      Vonrhein, C, Blanc, E., Roversi, P and Bricogne,"            >> $log_file
#puts "      G. (2007). Automated structure solution with autoSHARP."     >> $log_file
#puts "      Methods Mol. Biol. 364, 215-30."                             >> $log_file
#puts "# ------------------------------------------------------------"    >> $log_file

cd $autoSHARP_dir
set TheOS $system(OPSYS)
if { $TheOS == "WINDOWS" } {
   WriteToLog {You can not run autoSHARP on a Windows machine!} -nofoot -nohead
   WriteToLog {Please get a version for a supported platform from} -nofoot -nohead
   WriteToLog {http://www.globalphasing.com/sharp/} -nofoot -nohead
   TerminateScript 0 -report {Windows not supported for autoSHARP}
}

set env(BDG_UseOldPath) {yes}
if { [IfSet $browser] } {
    exec $browser file://$autoSHARP_dir/LISTautoSHARP.html &
}
catch {exec [GetEnvPath SHARP_home]/bin/sharp/detect.sh > LISTautoSHARP.html}