add mpnn msd submission script

cc_msd/mpnn_msd.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+#$ -S /bin/bash
+#$ -o /wynton/home/kortemme/scrilly/ProteinMPNN/vanilla_proteinmpnn/my_mpnn
+#$ -e /wynton/home/kortemme/scrilly/ProteinMPNN/vanilla_proteinmpnn/my_mpnn
+#$ -pe smp 10
+#$ -cwd
+#$ -l mem_free=4G
+#$ -l h_rt=02:00:00
+
+conda activate mlfold
+trap 'conda deactivate' EXIT
+#source /wynton/home/kortemme/scrilly/mpnn_test_env/bin/activate
+
+folder_with_pdbs="/wynton/home/kortemme/scrilly/helix_sliding/20240515_pilot_pdbs_for_msd"
+
+output_dir="/wynton/home/kortemme/scrilly/helix_sliding/20240515_pilot_pdbs_for_msd/temp_03"
+
+if [ ! -d $output_dir ]
+then
+    mkdir -p $output_dir
+fi
+
+
+path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl"
+path_for_assigned_chains=$output_dir"/assigned_pdbs.jsonl"
+path_for_tied_positions=$output_dir"/tied_pdbs.jsonl"
+path_for_fixed_positions=$output_dir"/fixed_positions.jsonl"
+
+chains_to_design="A B"
+pos_neg_chain_list="A,B"
+chain_betas="1.0,1.0"
+
+fixed_positions="52 53 54 55 56 57 58 59 60 61 62 63 64, 52 53 54 55 56 57 58 59 60 61 62 63 64"
+
+python ../helper_scripts/parse_multiple_chains.py --input_path=$folder_with_pdbs --output_path=$path_for_parsed_chains
+
+#python ../helper_scripts/assign_fixed_chains.py --input_path=$path_for_parsed_chains --output_path=$path_for_assigned_chains --chain_list "$chains_to_design"
+
+python ../helper_scripts/make_pos_neg_tied_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_tied_positions --homooligomer 1 --pos_neg_chain_list $pos_neg_chain_list --pos_neg_chain_betas $chain_betas
+
+python ../helper_scripts/make_fixed_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_fixed_positions --chain_list "$chains_to_design" --position_list "$fixed_positions"
+
+python ../protein_mpnn_run.py \
+        --jsonl_path $path_for_parsed_chains \
+        --tied_positions_jsonl $path_for_tied_positions \
+        --fixed_positions_jsonl $path_for_fixed_positions \
+        --out_folder $output_dir \
+        --num_seq_per_target 1000 \
+        --sampling_temp "0.3" \
+        --batch_size 1 \
+        --omit_AAs 'CHX' \
+        --save_probs 1
+        #--chain_id_jsonl $path_for_assigned_chains \