Fixed issues with designing in scaffoldguided mode #386
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…gn_ppi_scaffold.sh. The solutions to issues 272 and 273 did not fully address the issue.
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If you run design_ppi_scaffolded.sh, you'll notice a type error for the variable scaffold_list (not a list, but a Boolean). This issue was addressed in errors 272 and 273, and attempts to fix it have been made (Update model_runners.py), but it hasn't been completely resolved (some people still encounter this issue, like me, and I suspect it stems from adding the secondary structure module to RFdiffusion). After much effort, I've modified some of the code (a bit at a time), and my version is the latest version of RFdiffusion (which inherits RFpeptide).