job_dir=$1
ip_dir=$2

cp -r $ip_dir/ipatch_base/* $job_dir
#chmod a+rxw -R $job_dir
cd $job_dir

PY3_ENV=/home/sanjuan/miniconda3/envs/sabbox_env/bin/python

#python RunABIpatch.py --abf AB.pdb --agf AG.pdb $3  --jobid $job_dir # ORIGINAL
#python $(dirname $ip_dir)/bin/annotate_ss $job_dir/output_folder/solution.pdb $job_dir/output_folder/solution.pdb # ORIGINAL

# MODIFIED - Broncio 16 May 2022
PYTHONPATH=/home/sanjuan/miniconda3/envs/sabbox_env/lib/python3.8/ $PY3_ENV RunABIpatch.py --abf AB.pdb --agf AG.pdb $3  --jobid $job_dir
PYTHONPATH=/home/sanjuan/miniconda3/envs/sabbox_env/lib/python3.8/ $PY3_ENV $(dirname $ip_dir)/bin/annotate_ss $job_dir/output_folder/solution.pdb $job_dir/output_folder/solution.pdb