DiffDock

https://github.com/gcorso/DiffDock

ほぼそのまま動く

install

code:;

# cd /path/to/DiffDock

conda env create

conda activate diffdock

git clone https://github.com/facebookresearch/esm

cd esm

pip install -e .

1. esmのためのfasta形式のファイルを作る

python datasets/esm_embedding_preparation.py --protein_ligand_csv data/protein_ligand_example_csv.csv --out_file data/prepared_for_esm.fasta

2. fastaの配列からesm2の埋め込みを作る

HOME=esm/model_weights python esm/scripts/extract.py esm2_t33_650M_UR50D data/prepared_for_esm.fasta data/esm2_output --repr_layers 33 --include per_tok

3. 予測する

python -m inference --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_small --inference_steps 20 --samples_per_complex 40 --batch_size 10