#/bin/bash
#########################script 2 is used for submit the jobs into clusters
#########################CC(C(=O)O)Oc1c(cc(cc1Cl)C=C2C(=O)OC(=N2)c3cccc4c3cc[nH]4)OC	s10__13609480__13428708	440.839	38589	7.20	-1.00	4
if [ 1 = $# ]
then
name=$1
mountdir=`pwd`
workdir=${mountdir}/${name}
cd $workdir
if test -e Cov$name-pattern.sh; then rm -rf Cov$name-pattern.sh; fi
if test -e Cov$name-pattern.out; then rm -rf Cov$name-pattern.out;fi
if test -e Cov$name-pattern.err; then rm -rf Cov$name-pattern.err;fi
echo "prepare submit jobs"
echo "#!/bin/csh
#\$ -S /bin/csh
#\$ -cwd
#\$ -o $workdir/Cov$name-pattern.out
#\$ -e $workdir/Cov$name-pattern.err 
#\$ -t 1-1
#\$ -q matt.q
hostname
date
#cd /scratch
#mkdir -p $USER/Cov$name-pattern
#cd $USER/Cov$name-pattern
#cp $workdir/${name}.smi .
set name=${name}
set num1=\`cat ${name}.smi | wc -l\`
cp /nfs/exa/work/stefan/Anions/MWT-300-400/xiaobo-scripts/2019-11-9-xiaobo_combine_version.txt . 
source /nfs/soft/www/apps/zinc15/envs/production/env.csh
setenv molgrep /nfs/soft/tools/apps/molgrep/molgrep.py
\$molgrep smarts -f 2019-11-9-xiaobo_combine_version.txt ${name}.smi filter-${name}.smi
rm 2019-11-9-xiaobo_combine_version.txt
set num2=\`cat filter-${name}.smi | wc -l\`
echo \"\${name}	\$num1	\$num2 in 50000\"
date
#cp -r filter-${name}.smi $workdir/.
#cd ../
#rm -rf Cov$name-pattern">Cov$name-pattern.csh
#sleep 5
qsub Cov$name-pattern.csh
cd ${mountdir}
else
	echo "bash method1-step1-2019-11-16-updated-john-csh.sh Enamine-500-smiles-xaa-xaa-xaa"
	exit
fi