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fae1173 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | abs=("cr6261" "cr9114" "g6" "g6")
ab_fastas=("cr6261_3gbn_hc_lib.fasta" "cr9114_4fqi_hc_lib.fasta" "g6_2fjg_hc_lib.fasta" "g6_2fjg_lc_lib.fasta")
data_path="data/ab_mutagenesis_expts/"
out_prefix="output/ab_mutagenesis_expts/"
for ((i=0; i<${#abs[@]}; i++)); do
ab="${abs[i]}"
ab_fasta="${ab_fastas[i]}"
ab_dir_path="${data_path}${ab}/"
struc_list=("${ab_dir_path}"*.pdb)
ab_out_dir="${out_prefix}${ab}/"
# Set the default chain value
chain="H"
# Special handling for 'g6' antibody
if [[ "$ab" == "g6" ]]; then
[[ "$ab_fasta" == *"lc"* ]] && chain="L"
fi
# gather pdbs and filter the hc/lc only structure from being scored by library for the other chain
if [[ "$ab" == "g6" && "$chain" == "L" ]]; then
struc_list=($(echo "${struc_list[@]}" | tr ' ' '\n' | grep -v '_h_' | tr '\n' ' '))
elif [[ "$ab" == "g6" && "$chain" == "H" ]]; then
struc_list=($(echo "${struc_list[@]}" | tr ' ' '\n' | grep -v '_l_' | tr '\n' ' '))
fi
mkdir -p "$ab_out_dir"
for struc in "${struc_list[@]}"; do
out_file="${ab_out_dir}${struc##*/}"
if [[ "$ab" == "g6" ]]; then
chain_modeled="$([ "$chain" == "H" ] && echo "hc" || echo "lc")"
out_file="${out_file%_fvar.pdb}_${chain_modeled}_scores.csv"
else
out_file="${out_file%_fvar.pdb}_scores.csv"
fi
if [[ ! -f "$out_file" ]]; then
python model/score_log_likelihoods.py "$struc" --chain "$chain" --seqpath "${ab_dir_path}${ab_fasta}" --outpath "$out_file"
else
echo "$out_file already exists. Skipping..."
fi
done
done
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