| synthetic | |
| python -m MOAVS.moavs_synthetic --csv_file screening_data/2rgp/2rgp_property_20k.csv --seeds 16 64 42 --outpath moavs_results/moavs_synthetic_chai --docking_model_name chai --prot_fasta screening_data/2rgp/2rgp.fasta --msa_dir screening_data/2rgp/2rgp_msas --init_pose 1 --warmup_ratio 0.01 --n_select 50 --iterations 20 --n_compare 25 --fingerprint_path screening_data/2rgp/fingerprints_20k.npy --prot_path screening_data/2rgp/2rgp.pdb --objectives MW LogP rotBonds --acq qeubo --func_name ackley --n_eval 200 --n_sample 20000 --gp_batch_size 256 --beta 1 | |
| python -m MOAVS.moavs_synthetic --csv_file screening_data/2rgp/2rgp_property_20k.csv --seeds 16 64 42 --outpath moavs_results/moavs_synthetic_edm --docking_model_name edm --init_pose 128 --sampling_batch_size 64 --model_dir ckpts/edm_4M_100k_2rgp --model_ckpt model_99999.pth --warmup_ratio 0.01 --n_select 50 --iterations 20 --n_compare 25 --fingerprint_path screening_data/2rgp/fingerprints_20k.npy --prot_path screening_data/2rgp/2rgp.pdb --objectives MW LogP rotBonds --acq qeubo --func_name hartmann --n_eval 200 --n_sample 20000 --gp_batch_size 256 --beta 1 | |
| HP | |
| python -m MOAVS.moavs_hp --csv_file screening_data/2rgp/2rgp_property_20k.csv --seeds 64 --outpath moavs_results/moavs_hp_20k --docking_model_name theoretical --warmup_ratio 0.01 --n_select 50 --iterations 20 --n_compare 25 --fingerprint_path screening_data/2rgp/fingerprints_20k.npy --prot_path screening_data/2rgp/2rgp.pdb --objectives MW Lipophilicity Half_Life --acq qeubo --n_sample 20000 --gp_batch_size 256 | |
| python -m MOAVS.moavs_hp --csv_file screening_data/2rgp/2rgp_property_100k.csv --seeds 256 --outpath moavs_results/moavs_hp_100k_vina --docking_model_name theoretical --warmup_ratio 0.01 --n_select 500 --iterations 10 --n_compare 200 --fingerprint_path screening_data/2rgp/fingerprints_100k.npy --prot_path screening_data/2rgp/2rgp.pdb --objectives MW Lipophilicity Half_Life --acq qeubo --n_sample 100000 --gp_batch_size 32 --timeout 32 | |
| python -m MOAVS.moavs_hp --csv_file screening_data/2rgp/2rgp_property_100k.csv --seeds 64 --outpath moavs_results/moavs_hp_100k_edm --docking_model_name edm --docking_model_name edm --init_pose 128 --sampling_batch_size 128 --model_dir ckpts/edm_4M_100k_2rgp --model_ckpt model_99999.pth --warmup_ratio 0.01 --n_select 500 --iterations 10 --n_compare 200 --fingerprint_path screening_data/2rgp/fingerprints_100k.npy --prot_path screening_data/2rgp/2rgp.pdb --objectives MW Lipophilicity Half_Life --acq qeubo --n_sample 100000 --gp_batch_size 64 --timeout 32 | |
| AVS | |
| python -m MOAVS.avs --csv_file screening_data/2rgp/2rgp_property_100k.csv --seeds 128 256 --outpath moavs_results/avs_edm_100k --docking_model_name edm --model_dir ckpts/edm_4M_100k_2rgp --model_ckpt model_99999.pth --init_pose 128 --sampling_batch_size 128 --warmup_ratio 0.01 --n_select 500 --iterations 10 --n_compare 200 --fingerprint_path screening_data/2rgp/fingerprints_100k.npy --prot_path screening_data/2rgp/2rgp.pdb --acq ucb --n_sample 100000 --gp_batch_size 64 --beta 1 | |
| python -m MOAVS.avs --csv_file screening_data/2rgp/2rgp_property_100k.csv --seeds 128 --outpath moavs_results/avs_edm_100k --docking_model_name chai --prot_fasta screening_data/2rgp/2rgp.fasta --msa_dir screening_data/2rgp/2rgp_msas --init_pose 1 --warmup_ratio 0.01 --n_select 500 --iterations 10 --n_compare 200 --fingerprint_path screening_data/2rgp/fingerprints_100k.npy --prot_path screening_data/2rgp/2rgp.pdb --acq qeubo --n_sample 100000 --gp_batch_size 32 --beta 1 --timeout 72 | |
| export CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7 | |
| source /lfs/mercury2/0/sttruong/miniconda3/bin/activate | |