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This repository was archived by the owner on Dec 8, 2025. It is now read-only.
This repository was archived by the owner on Dec 8, 2025. It is now read-only.

how to define given protein pockets for sampling molecules in command line #2

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@MachineGUN001

hi,

thanks for your higly interesting work.

could you please provide some instruction how to define given protein pockets for sampling molecules in command line?

python scripts/sample_diffusion_decomp.py configs/sampling_drift.yml  \
  --outdir $SAMPLE_OUT_DIR -i $DATA_ID --prior_mode {ref_prior, beta_prior}

and I tried to see the related parameters -h

usage: sample_diffusion_decomp.py [-h] [--ori_data_path ORI_DATA_PATH]
                                  [--index_path INDEX_PATH]
                                  [--beta_prior_path BETA_PRIOR_PATH]
                                  [--natom_models_path NATOM_MODELS_PATH]
                                  [--ckpt_path CKPT_PATH] [--outdir OUTDIR]
                                  [-i DATA_ID] [--device DEVICE]
                                  [--batch_size BATCH_SIZE]
                                  [--prior_mode {subpocket,ref_prior,beta_prior}]
                                  [--num_atoms_mode {prior,ref,ref_large}]
                                  [--bp_num_atoms_mode {old,stat,v2}]
                                  [--suffix SUFFIX]
                                  [--recon_with_bond RECON_WITH_BOND]
                                  config

I didnot find where I input the info of protein pocket. many thanks for your help!

Best,
Sh-Y

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