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

[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

[flowerwjl]

Hello! I'm facing the same problem, have you found a way to solve it?