#!/bin/bash
# script for starting xleap.sh
# Stefan Henrich 29.03.2005
#
# version: 
# combine2go 23.05.05
# 19.09.2005 better handling of multiple conformations
#
# give pdb as argument
###########################################
COMBINEHOME="/home/henricsn/combine2go/"
#sdf=$COMBINEHOME"sdf/final-residue.sdf"                    #directory for SDF file
sdf=$COMBINEHOME"sdf/all_300805_3D.sdf"                    #directory for SDF file
template=$COMBINEHOME"parameter/protmin.dielc4.template"   #directory for minimize template
prgdir=$COMBINEHOME"programs/"                             #directory for programs
ligdir=$COMBINEHOME"data/urokinase/pdb/ligand/rename/"            #directory with ligand pdb files
protdir=$COMBINEHOME"data/urokinase/pdb/prepared/"                     #source directory for input pdb
targetdir="./"

getmodifpdb=$(find $protdir -maxdepth 1 -name "*.pdb")
#getmodifpdb=$protdir"1c5y.0.pdb"
##################################################################
##################################################################
# DO NOT CHANGE ANYTHING BELOW THIS LINE
# UNLESS YOU KNOW WHAT YOU ARE DOING
##################################################################
##################################################################
FILES="$getmodifpdb"
#FILES="./1o5b.192B.deprH57.modif.align.pdb"
echo 
for file in $FILES
do
	echo
	echo ---------------------------------------------------------------------------
	echo $file
##################################################################
##################################################################
	### (./A14.0.cor)
	path=$(dirname $file)/ #folder of file
	base=`basename $file `   #file without path (A14.0.cor)
	name=`expr "$base" : '\([0-9a-zA-Z][0-9a-zA-Z]*\)' ` #base name (A14)
	suffix="${base#*.}" #suffix (0.cor)
	counter=`expr "$suffix" : '\([0-9a-zA-Z][0-9a-zA-Z]*\)' ` #counter (0)
	pdb=$name; alt=$counter
	###grep residue name and sequence number of ligand pdb file
	if [ -e "$ligdir$name.0.pdb" ]; then  line=$(grep "C1" $ligdir$name".0.pdb"|uniq -w6)
	else  
		line=$(grep "C1" $ligdir$name".1.pdb"|uniq -w6)
	fi
	residue=${line:17:3}
	lig_number=${line:20:6}
	echo base $base name $name suffix $suffix counter $counter
##################################################################
	localsdf=$targetdir$residue.sdf
#	echo $prgdir"grepsdtag.linux" -t residue $residue \< $sdf \>  $localsdf
	$prgdir"grepsdtag.linux" -t residue $residue < $sdf >  $localsdf
##################################################################
	### calculate netcharge
	charge_numb=0;netcharge=0;charge=0
	chargeline=$(grep "M  CHG" $localsdf)
	charged_atoms=`echo $chargeline| awk '{ print $3 } '`
	until [ "$charged_atoms" -le "$charge_numb" ]; do
		column=$( echo "5 + $charge_numb * 2" |bc -l)
		#variable column of bash will be used in awk
		charge=`echo $chargeline| awk -v column="$column" '{ total = $column } END {print $column}'`
		netcharge=$( echo "$netcharge + $charge" |bc -l)
		let charge_numb+=1
	done
	echo residue $residue netcharge $netcharge
##################################################################
### Ligand
	if [ -e "$ligdir$name.0.pdb" ]; then  
		ligcounter=0;
		echo ligand $ligcounter
		echo 
		echo $prgdir"xleap.sh" -d $targetdir -pdb $pdb -alt $counter -n $residue -prot $file -lig $ligdir$pdb.$ligcounter.pdb -nc $netcharge -sdf $localsdf -m $template -w -notemp -bres -noedit
		$prgdir"xleap.sh" -d $targetdir -pdb $pdb -alt $counter -n $residue -prot $file -lig $ligdir$pdb.$ligcounter.pdb -nc $netcharge -sdf $localsdf -m $template -w -notemp -bres -noedit
	else
		ligcounter=1
		echo ligcounter $ligcounter
		until [ ! -e "$ligdir$name.$ligcounter.pdb" ]; do
			echo ligand $ligcounter
			echo 
			echo $prgdir"xleap.sh" -d $targetdir -pdb $pdb -alt $counter$ligcounter -n $residue -prot $file -lig $ligdir$pdb.$ligcounter.pdb -nc $netcharge -sdf $localsdf -m $template -w -notemp -bres -noedit
			$prgdir"xleap.sh" -d $targetdir -pdb $pdb -alt $counter$ligcounter -n $residue -prot $file -lig $ligdir$pdb.$ligcounter.pdb -nc $netcharge -sdf $localsdf -m $template -w -notemp -bres -noedit
			let ligcounter+=1
		done
	fi
##################################################################
	echo
	echo $(date)
	echo -----------------
	echo 
done

exit

grep -A6 "loading mimimized molecule in pymol:" sxleap010805.log > rmsd.log
grep "RMSD" local.log