# Script reading structure files (in any VMD-readable format), adding them as frames in trajectory and saving the trajectory in peaces (to avoid extremely big DCD files)
# Inspired John Stone's animatepdbs
# Parameters:
#  fileNameFormat - a Tcl format string which describes the fileName/numbering
#           used.
#  start  - "frame number" of first PDB file in sequence
#  end    - "frame number" of last PDB file in sqeuence
#
#Examples:
#  To load a sequence of PDB files named 0.pdb 1.pdb 2.pdb 3.pdb 
#  one would call this proc with:  animatepdbs "%d.pdb" 0 3
#
#  To load a sequence of PDB files named foo0000.pdb foo0001.pdb foo0002.pdb
#  one would call this proc with:  animatepdbs "foo%04d.pdb" 0 2


# ______________________ User parameters section ==>
set outFrames 500;	# ==>	 Maximal number of frames in the output file
set configFileName {/simulations/test_steered_simulation/update_parameters_conf.txt};	# ==>	Symmetrization Configuration file name


# ______________________ Procedures declaration
proc filterFileList {fileList mask} {
	set newFileList {}
	foreach fileName $fileList {
		if {[string match -nocase $mask $fileName]==1} {
			lappend newFileList $fileName
		}
	}
	return $newFileList
}


proc filterFileListRegexp {fileList mask} {
	set newFileList {}
	set mask "\^$mask\$"
	foreach fileName $fileList {
		if {[regexp $mask $fileName]==1} {
			lappend newFileList $fileName
		}
	}
	return $newFileList
}

proc execBash {bashCommand {simulationDescription "Simulation"}} {
	# Procedure writes received bash shell command into the bash_command file, and executes it
	set bashCommandFile [open ./bash_command w]
	puts $bashCommandFile $bashCommand
	close $bashCommandFile
	
	puts "$simulationDescription started"
	exec {./bash_command}
	puts "$simulationDescription finished"
}




proc coordinates2dcd {filesPath fileNameFormat {fileType ""} {outFrames ""} {start ""} {end ""}} {
	if {[llength $filesPath] > 0} {;	# Go to the working folder
		cd $filesPath
	}
	
	# ____ Autodetect the first and last files numbers
	if {([llength $start] == 0)|([llength $end] == 0)} {;	#start or end numbers were not specified
		set fileNameMask [regsub {%[0-9]*[dui]{1}} $fileNameFormat "\[0-9\]*"]
		set fileList [lsort [filterFileListRegexp [exec ls]  $fileNameMask]]
		set start [scan [lindex $fileList 0] $fileNameFormat]
		set end [scan [lindex $fileList end] $fileNameFormat]
		puts "[llength $fileList] file(s) found: from [lindex $fileList 0]   to   [lindex $fileList end]"
	}
	
	# ____ Load the first file
	set fileName [format $fileNameFormat [expr {$start}]]
	puts "Reading initial file $fileName in the sequence"
	if {[llength $fileType]>0} {
		mol new $fileName type $fileType waitfor all
	} else {
		if {[catch {mol new $fileName waitfor all}]!=0} {mol new $fileName type pdb waitfor all}
	}
	
	# ____ Load the rest of files
	set firstDcdFrame 0
	set filesRead 1
	puts "Reading coordinates files and writing sets of frames into DCD..."
	incr start
	for {set i $start} {$i <= $end} {incr i 1} {
		set fileName [format $fileNameFormat [expr {$i}]]
		
		if {[llength $fileType]>0} {
			mol addfile $fileName type $fileType waitfor all
		} else {
			if {[catch {mol addfile $fileName waitfor all}]!=0} {mol addfile $fileName type pdb waitfor all}
		}
		
		incr filesRead
		 
		set framesRead [molinfo top get numframes]
		if {[llength $outFrames]>0} {
			if {$framesRead>=$outFrames} {;	# Maximal number of frames in the output file reached
				set lastDcdFrame [expr {$firstDcdFrame+$framesRead-1}]
				set firstDcdFrameString [format "%0[string length $end]d" $firstDcdFrame]
				set lastDcdFrameString [format "%0[string length $end]d" $lastDcdFrame]
				animate write dcd [join "[molinfo top get name] _frames $firstDcdFrameString to $lastDcdFrameString .dcd" {}] beg 0 end [expr {$outFrames-1}] waitfor all 
				set firstDcdFrame [expr {$lastDcdFrame+1}]
				animate delete beg 0 end [expr {$outFrames-1}]
				
			}
		}
	}
	
	
	if {[molinfo top get numframes]>0} {
		set lastDcdFrame [expr {$firstDcdFrame+[molinfo top get numframes]-1}]
		set firstDcdFrameString [format "%0[string length $end]d" $firstDcdFrame]
		set lastDcdFrameString [format "%0[string length $end]d" $lastDcdFrame]
		animate write dcd [join "[molinfo top get name] _frames $firstDcdFrameString to $lastDcdFrameString .dcd" {}] waitfor all 
		animate delete all
	}
	
	puts "[expr {$lastDcdFrame+1}] frames from $filesRead files read"
	
	puts "Writing DCD trajectory finished!"
}

# ______________________________________ autodetect fileNames and pathways
# find out what is the name of simmetrization status file and total number of steps
set fileLook [open $configFileName r];	# Open configuration file
while {[gets $fileLook line] >= 0} {
	set lineRecognize [lindex $line 0]
	switch -regexp $lineRecognize {
		"^workingFolder$" {;	# Simulation files path
			set workingFolder [lindex $line 1]
			cd $workingFolder
		}
		default {}
	}
}
close $fileLook

# __________________________ Executable part

# Read from temporary file with list of filemasks for consolidation and make consolidation
set fileLook [open "$workingFolder/consolidation_temp.txt" r]
while {[gets $fileLook line] >= 0} {
	# coordinates2dcd "$workingFolder" "$line" {} $outFrames
	if {[regexp {.namd$} $line]} {
		# NAMD output log file
		if {[catch {
			set fileNameMask [regsub {%[0-9]*[dui]{1}} $line "\[0-9\]*"]
			set fileList [lsort [filterFileListRegexp [exec ls]  $fileNameMask]]
			execBash "cat $fileList > [lindex $fileList 0]_all-namd-logs.txt" "$line Logs consolidation"
		}]!=0} {
			puts "Consolidation of '$line' unsuccessful"
		} else {
			puts "Consolidation of '$line' finished"
		}
	} elseif {[regexp {.xsc$} $line]} {
		# XSC cell file
		if {[catch {
			set fileNameMask [regsub {%[0-9]*[dui]{1}} $line "\[0-9\]*"]
			set fileList [lsort [filterFileListRegexp [exec ls]  $fileNameMask]]
			execBash "cat $fileList > [lindex $fileList 0]_all-xsc.txt" "$line Logs consolidation"
		}]!=0} {
			puts "Consolidation of '$line' unsuccessful"
		} else {
			puts "Consolidation of '$line' finished"
		}
	} else {
		# Coordinate files
		if {[catch {coordinates2dcd "$workingFolder" "$line" {} $outFrames}]!=0} {
			puts "Consolidation of '$fileMask' unsuccessful"
		} else {
			puts "Consolidation of '$fileMask' finished"
		}
	}
}
close $fileLook


exit