Updated "Fixed issues with designing in scaffoldguided mode" original PR 386 (#426)
The original PR for this was #386 from
[OrangeCatzhang](https://github.com/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.<fields> 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.