binder design shell script error

[ppxwwtaking]

1. design_ppi.sh and design_ppi_flexible_peptide.sh
   assert any(x is not None for x in (conf.contigmap.inpaint_str_helix, conf.contigmap.inpaint_str_strand, conf.contigmap.inpaint_str_loop))
   AssertionError
   This means we need to provide these configs in the shell scripts.
2. design_ppi_flexible_peptide_with_secondarystructure_specification.sh
   works.
3. design_ppi_scaffolded.sh
   config error, solved by following Error in latest commit #273.
4. All partial design shell scripts fail to work with same error as in 1.

RFdiffusion/rfdiffusion/inference/model_runners.py", line 745, in init
assert any(x is not None for x in (conf.contigmap.inpaint_str_helix, conf.contigmap.inpaint_str_strand, conf.contigmap.inpaint_str_loop))

I believe scripts in 1 are simple uses for binder design without specifying the secondary structure. But now they don't work as expected. I don't want to change every design to something like 3. Possibly some changes globally affected the parse or some if statements. Please check.

[matteoferla]

To recap for other users like me who don't wish to spend an hour going through comments:

• In the file $CONDA_PREFIX/lib/python3.9/site-packages/rfdiffusion/inference/model_runners.py (or wherever you keep rfdiffusion/inference/model_runners.py), the assert in line 750 needs to be commented out and the next line changed to
  self.blockadjacency = iu.BlockAdjacency(conf, conf.inference.num_designs)
  (difference: conf.scaffoldguided --> conf)
• scaffoldguided.target_path is optional, but is not causing issues
• The hardcoded 1qys.pdb example needs to exist as providing inference.input_pdb will cause havoc
• The solution scaffoldguided.scaffold_list=[] does not work for my aims, at least, but gets mentioned somewhere as a fix.
• The usual things like the need of inference.output_prefix to have a folder even if hydra.output_subdir is supplied etc etc