Trying to run inference script

Start with rf_diffusion/run_inference.py and the config-name and sweep.inference arguments in the reported Singularity command. Then compare config_theoenzyme and the active_site_unindexed_atomic JSON with enzyme_bench_n41.yaml to document which configuration entries are expected and what a successful inference run should produce.

Hello, I'm learning how to run RFdifussion2 and got a little nit confused:

My goal: design a protein from a theoenzyme that contains 4 residues and one coenzyme (FMN).

For my understanding I need to first specify a ORI atom that specifies the center of mass of my coenzyme. (I did this since i converted a cif file to pdb)

Then I need to know what scripts should I modify. For this I created an own json file (active_site_unindexed_atomic.json) that looks like this:

{
    "active_site_unindexed_atomic":                "inference.input_pdb=theoenzyme_ladA_with_ORI.pdb inference.ligand=\\'FMN\\' contigmap.contigs=[\\'16,B17-17,45,B63-63,15,B79-79,58,B138-138,172,B311-311,129\\'] inference.contig_as_guidepost=True contigmap.contig_atoms=\"'{\\'B17\\':\\'CB,CG,ND1,CD2,CE1,NE2\\',\\'B63\\':\\'CB,CG,CD1,CD2,CE1,CE2,CZ,OH\\',\\'B79\\':\\'N,CA,C,O\\',\\'B138\\':\\'CB,CG,ND1,CD2,CE1,NE2\\',\\'B311\\':\\'CB,CG,ND1,CD2,CE1,NE2\\'}'\""
}

From a previous error message I notice the program also asks me to specify a yaml file and I used this yaml file that I modified of the benchmark config file:

defaults:
  - enzyme_bench_n41
  - _self_

in_proc: True
sweep:
  retries: 2
  command_args: >
    --config-name=aa
    inference.deterministic=True
    inference.ckpt_path=REPO_ROOT/rf_diffusion/model_weights/RFD_173.pt
    inference.seed_offset=43
  
  num_per_condition: 1
  num_per_job: 1
  benchmark_json: config_theoenzyme.json

  slurm:
    p: gpu-bf
    gres: gpu:1

stop_step: sweep
outdir: ${hydra:runtime.cwd}/pipeline_outputs/${now:%Y-%m-%d}_${now:%H-%M-%S}_open_source_demo

as it points out to a enzyme_bench_n41.yaml file, I notice maybe I should delete the - enzyme_bench_n41 part of the yaml file isnt it?

This is the script I'm running (I'm using singularity):

program_dir=/opt/RFdiffusion2

singularity exec --nv --env PYTHONPATH=${program_dir} --env MKL_THREADING_LAYER=GNU --env CUDA_VISIBLE_DEVICES=0 \
	-B /opt:/opt ${program_dir}/rf_diffusion/exec/rfdiffusion_sandbox \
    python3 /opt/RFdiffusion2/rf_diffusion/run_inference.py \
    --config-name=config_theoenzyme \
    sweep.inference=active_site_unindexed_atomic \
    inference.num_designs=10

Aditionally, I'm naively passing the name of the config file to sweep.inference . I get an error message that there is no struct called inference. So in addition, how can I provide my config file ?

I know this may look that I'm lost in trying to run this but is my first time using this type of program. just looking for some clarity and feedback on what I'm trying to do.