Updated "Fixed issues with designing in scaffoldguided mode" original PR 386 #426
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…gn_ppi_scaffold.sh. The solutions to issues 272 and 273 did not fully address the issue.
…oldguided=True instead of scaffoldguided_enabled
… Sampler and ScaffoldedSampler
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The original PR for this was #386 from OrangeCatzhang. This PR is to fix the error "AttributeError: 'bool' object has no attribute 'scaffold_list'" when running in scaffoldguided mode.
The first error is fixed by passing the full composed config object (conf) into BlockAdjacency instead of passing the scaffoldguided sub-node. BlockAdjacency expects the full config and to access conf.scaffoldguided. internally, so passing the sub-node caused self.conf.scaffoldguided to resolve to the nested boolean field (scaffoldguided.scaffoldguided), which produced the AttributeError when code tried to read .scaffold_list. Passing teh full conf fixes that mismatch.
The other fix is to add initialization of cyclic_reses to ScaffoldedSampler. I have slightly updated what was in the original PR to avoid code duplication. I added a helper function to the Sampler class and then call that in both Sampler and ScaffoldedSampler to initialize cyclic_reses. I also removed the changes to the scaffoldedguided flag from the original PR, so the CLI stays the same.