function_base.dat

#CHECK
function check {
 outfile=$2
 if [ ! -e $1 ]; then 
  echo -e "\n"$(date +%H:%M:%S)" \n ERROR: I could not find $1 in "$(pwd)". Exiting... \n" | tee -a $outfile
  #clear; 
  echo "Exiting -- please read the $outfile" 
  exit
 fi
}

function check2 {
 outfile=$2
 if [ ! -e $1 ]; then 
  echo -e "\n"$(date +%H:%M:%S)" \n ERROR: I could not find $1 in "$(pwd)". Exiting... \n" | tee -a  $outfile
  #clear; 
  echo "Exiting -- please read the $outfile and $(pwd)/STD_ERR0" 
  exit
 fi
}

function check_minN {
 outfile=$2
 local _coul=$3
 local _use=$4
 if [ ! -e $1 ]; then 
  echo -e "\n"$(date +%H:%M:%S)" \nERROR: I could not find $1 in "$(pwd)".\nSetting the option \"coulomb\" to \"gmx\". If you want to use \"coulomb=coul\" please provide the right files to GMXPBSA.\n" | tee -a  $outfile
 eval $_coul="gmx";
 eval $_use="n";
 fi
}

function check_minY {
 outfile=$2
 local _coul=$3
 local _use=$4
 local _min=$5
 if [ ! -e $1 ]; then 
  echo -e "\n"$(date +%H:%M:%S)" \nERROR: I could not find $1 in "$(pwd)".\nSetting the option \"min\" to \"n\" and the option \"coulomb\" to \"gmx\". If you want to use \"min=y\" please provide the right files to GMXPBSA.\n" | tee -a  $outfile
 eval $_coul="gmx";
 eval $_use="n";
 eval $_min="n";
 fi
}


function check_run {
	if [ -d  $1 ]; then
		echo  -e "\n"$(date +%H:%M:%S)"\n The directory $1 is already present in "$(pwd)". Please remove it or choose an appropriate value for the variable \"run\" in the INPUT.dat file.\n" | tee -a REPORTFILE0;
		echo "Exiting -- please read the REPORTFILE0"
 		exit
	fi	
}

function check_DIR {
	if ! [ -d  $1 ]; then
		echo -e "The Folder $1 that you indicated in the INPUT.dat file does not exist.\nExiting...."| tee -a REPORTFILE0;
	exit
	fi
}

function check_NOdir {
	if [ -d  $1 ]; then
		echo  -e "\n"$(date +%H:%M:%S)"\nYou choose \"ff_modified=n\", then please remove or displace (in each MD* directoy) the directory \"*.ff\" \n" | tee -a REPORTFILE0;
		echo "Exiting -- please read the REPORTFILE0"
 		exit
	fi	
}


#SET VARIABLE
function set_variable {
	local _Var=$1
	local myVar=$(awk -v Var=$_Var '{ if($1==Var) print $2}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then echo -e "$1 variable is unset!!! "; exit; fi
	control=`echo $myVar | awk '{N=split($0,v," "); print N}'`
	if [ $control -gt 1 ]; then echo -e "$1 variable was set two times!!! "; exit; fi
}

function set_variable_multiple {
	local _Var=$1
	local fields=$(awk -v Var=$_Var '{ if($1==Var) print NF}' INPUT.dat);
	local myVar=$(awk -v Var=$_Var -v Fields=$fields '{ if($1==Var) for (i=2;i<=Fields;i++) print $i}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then echo -e "$1 variable is unset!!! "; exit; fi
}
function set_variable_multiple_default {
	local _Var=$1
	local fields=$(awk -v Var=$_Var '{ if($1==Var) print NF}' INPUT.dat);
	local myVar=$(awk -v Var=$_Var -v Fields=$fields '{ if($1==Var) for (i=2;i<=Fields;i++) print $i}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then eval $_Var="'$2'"; fi
}

function set_variable_default {
	local _Var=$1
	local myVar=$(awk -v Var=$_Var '{ if($1==Var) print $2}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then eval $_Var="'$2'"; echo -e "Setting variable $1 to the default value $2" | tee -a REPORTFILE0; fi
	control=`echo $myVar | awk '{N=split($0,v," "); print N}'`
	if [ $control -gt 1 ]; then echo -e "$1 variable was set two times!!! "; exit; fi
}

function set_variable_default2 {
	local _Var=$1
	local myVar=$(awk -v Var=$_Var '{ if($1==Var) print $2}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then eval $_Var="'$2'"; fi
	control=`echo $myVar | awk '{N=split($0,v," "); print N}'`
	if [ $control -gt 1 ]; then echo -e "$1 variable was set two times!!! "; exit; fi
}

function set_variable_default1 {
	local _Var=$1
        outfile=$3
	local myVar=$(awk -v Var=$_Var '{ if($1==Var) print $2}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then eval $_Var="'$2'"; echo -e "Setting variable $1 to the default value $2" | tee -a $outfile; fi
	control=`echo $myVar | awk '{N=split($0,v," "); print N}'`
	if [ $control -gt 1 ]; then echo -e "$1 variable was set two times!!! "; exit; fi
}
function set_variable_default_run {
	local _Var=$1
	local myVar=$(awk -v Var=$_Var '{ if($1==Var) print $2}' INPUT.dat);
	eval $_Var="'$myVar'"
	if [ -z "$myVar" ]; then eval $_Var="'$2'"; echo -e "Setting variable $1 to the default value $2\n"; fi
	control=`echo $myVar | awk '{N=split($0,v," "); print N}'`
	if [ $control -gt 1 ]; then echo -e "$1 variable was set two times!!! "; exit; fi
}

#UPDATE
function Update {
	local _counter=$1
	#let "picO=($_counter%23)";
	#if [ $picO -eq 0 ]; then
		 sleep 1
		echo -ne  $(date +%H:%M:%S)" Done the "$_counter"-th structure in "$(pwd)"..."\\r 
	#fi
}


#AVERAGE
function Average {
	file_input=$1
	col=$2
	name=$3
	local _av=$4

	awk 'BEGIN{
		tot=0; dev=0; count=0; av=0; 	
	}
	{
		tot=tot+$col;
		v[count]=$col;
		count=count+1;
	}
	END{
		av=tot/count;
		for(i=0;i<count;i++) dev=dev+(v[i]-av)*(v[i]-av);
		dev=sqrt(dev/count);
		err=dev/sqrt(count);	
		printf "%-23s \t=\t %-6.3f    +/-    %-4.3f   kJ/mol \n", name, av, err >> "Complete.val"
		for(i=0;i<count;i++) var[i]=sqrt((v[i]-av)*(v[i]-av));
		for(i=0;i<count;i++) { if(var[i]>2*dev)	printf "\nFRAME "i" WARNING!! The difference between the value \""name"\" of frame "i" and the relative average is greater then 2-sigma (2 times the std deviation). Consider the hypothesis to exclude this frame from the calculations!\n\n" >> "WARNINGS.dat"}
	}' col=$col name="${name}" $file_input
 	av=` awk '{tot=tot+$col;count=count+1;};END{av=tot/count; printf av}' col=$col name="${name}" $file_input`
	eval $_av="'$av'"

	}

function Average_No_Outliers {
	file_input=$1
	col=$2
	name=$3
	local _av=$4

	AV=`awk -v OUT="$5" 'BEGIN{
		tot=0; dev=0; count=1; av=0; count_out=1;frame=0; 
		N_out=split(OUT,out," ")	
	}
	{
		if(count==out[count_out]){
			count_out=count_out+1;
		}
		else{
			tot=tot+$col;
			v[frame]=$col;
			frame=frame+1;
		}
		count=count+1;
	}
	END{
		av=tot/frame;
		for(i=0;i<frame;i++) dev=dev+(v[i]-av)*(v[i]-av);
		dev=sqrt(dev/frame);
		err=dev/sqrt(frame);
		printf "%-23s \t=\t %-6.3f    +/-    %-4.3f   kJ/mol \n", name, av, err >> "Complete_No_Outliers.val";
		printf av;
	}' col=$col name="${name}" $file_input`

	eval $_av="'$AV'"

	}

# CONTROL
function Control_REPfile {
	find=$1
	i=$2
	local exclude=$3

	if [ "$(grep "$find" stru"$i".rep |  wc | awk '{print $1}')" -gt "1" ]; then
		echo -e "\nERROR!\nTher is more then one value for "$find" in "$i"-th frame\nEXITING...."| tee -a ../../REPORTFILE2;
		exit 
	fi
	if [ "$(grep "$find" stru"$i".rep |  wc | awk '{print $1}')" -lt "1" ]; then
		echo -e "Structures "$i" will be excluded since "$find" value is not available"| tee -a ../../REPORTFILE2;
		eval $exclude="'1'"
	fi


}