IndexError: list index out of range Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

Hello,

I am trying to do the fold conditioning example. I was able to trouble shoot the first example with the adj and ss pt files. But it mentions (although not necessary) you should also generate these files and then gives a script:

./scripts/run_inference.py inference.output_prefix=./scaffold_conditioned_test/test scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=./examples/ppi_scaffolds_subset

I made the necessary changes for Windows:
python .\scripts\run_inference.py inference.output_prefix=.\scaffold_conditioned_test\test scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=.\examples\ppi_scaffolds_subset

BUT it keeps giving me this indexerror?

Error executing job with overrides: ['inference.output_prefix=.\scaffold_conditioned_test\test', 'scaffoldguided.scaffoldguided=True', 'scaffoldguided.target_pdb=False', 'scaffoldguided.scaffold_dir=.\examples\ppi_scaffolds_subset']
Traceback (most recent call last):
File "C:\User\mydir\RFdiffusion\scripts\run_inference.py", line 84, in main
x_init, seq_init = sampler.sample_init()
File "c:\users\mydir\rfdiffusion\rfdiffusion\inference\model_runners.py", line 776, in sample_init
self.L, self.ss, self.adj = self.blockadjacency.get_scaffold()
File "c:\users\mydir\rfdiffusion\rfdiffusion\inference\utils.py", line 891, in get_scaffold
item = random.choice(self.scaffold_list)
File "C:\Users\mydir.conda\envs\SE3nv\lib\random.py", line 346, in choice
return seq[self._randbelow(len(seq))]
IndexError: list index out of range

Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

I am relatively new to coding, can someone help me to correct? Should I add something to the utils.py or random.py?

thanks,
Heather

Start with scripts/run_inference.py and follow sample_init in inference/model_runners.py to inference/utils.py:get_scaffold. Inspect how scaffold_list is populated from the configured scaffold directory and compare it with examples/ppi_scaffolds_subset on Windows. Done means identifying why the list is empty and confirming the fold-conditioning example can proceed without changing Python's random module.