RosettaCommons / RosettaCommons/RFdiffusion

why there is no example for design binder for protein complex

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Python
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Description

I got error with paras like this, i wonder if it is a incompatible problem that i try to design binder for more than one molecule? ['contigmap.contigs=[C/0 F/0 100-120]', 'ppi.hotspot_res=[C80,C82,C86,C87,C90,C92,C93,E128,C138,C185,C187]', 'denoiser.noise_scale_ca=0', 'denoiser.noise_scale_frame=0'
Traceback (most recent call last):
File "/Share/app/RFdiffusion/scripts/run_inference.py", line 194, in
main()
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/main.py", line 94, in decorated_main
_run_hydra(
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/utils.py", line 394, in _run_hydra
_run_app(
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/utils.py", line 457, in _run_app
run_and_report(
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/utils.py", line 223, in run_and_report
raise ex
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/utils.py", line 220, in run_and_report
return func()
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/utils.py", line 458, in
lambda: hydra.run(
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/_internal/hydra.py", line 132, in run
_ = ret.return_value
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/core/utils.py", line 260, in return_value
raise self._return_value
File "/Share/app/miniconda3.9/envs/SE3nv/lib/python3.9/site-packages/hydra/core/utils.py", line 186, in run_job
ret.return_value = task_function(task_cfg)
File "/Share/app/RFdiffusion/scripts/run_inference.py", line 84, in main
x_init, seq_init = sampler.sample_init()
File "/Share/app/RFdiffusion/rfdiffusion/inference/model_runners.py", line 278, in sample_init
self.contig_map = self.construct_contig(self.target_feats)
File "/Share/app/RFdiffusion/rfdiffusion/inference/model_runners.py", line 240, in construct_contig
return ContigMap(target_feats, **self.contig_conf)
File "/Share/app/RFdiffusion/rfdiffusion/contigs.py", line 78, in init
) = self.expand_sampled_mask()
File "/Share/app/RFdiffusion/rfdiffusion/contigs.py", line 225, in expand_sampled_mask
int(subcon.split("-")[0][1:]), int(subcon.split("-")[1]) + 1
ValueError: invalid literal for int() with base 10: ''

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the command and traceback through scripts/run_inference.py, then inspect rfdiffusion/inference/model_runners.py and rfdiffusion/contigs.py, especially expand_sampled_mask. Determine whether the shown multi-chain contig syntax is supported and identify the expected behavior or an actionable error message. Done means the supported input is clear and the reported failure is resolved or documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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