04_MPNN.sh

#!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=50g
#SBATCH --gres=gpu:titan:1
#SBATCH -c 3
#SBATCH --output=mpnn_run.out

/software/containers/mlfold.sif /home/apillai1/switchable_ring_pipeline/MPNN/MPNN_redesign_C2/mpnn-master/mpnn_run.py        --max_length 10000         --checkpoint_path '/projects/ml/struc2seq/data_for_complexes/training_scripts/paper_experiments/model_outputs/p10/checkpoints/epoch51_step255000.pt'         --hidden_dim 192         --num_layers 3         --protein_features 'full'         --jsonl_path='pdbs_test.jsonl'         --fixed_positions_jsonl 'fixed_pos.jsonl'         --out_folder='MPNN_outputs'         --num_seq_per_target 4         --sampling_temp="0.1"         --batch_size 4         --backbone_noise 0.01         --decoding_order 'random'         --num_connections 64 	--chain_id_jsonl 'pdbs_masked.jsonl' --omit_AAs 'X'