> That would be great. Yes - the previous functions return true. But if
> I understand correctly, they are setting flags used by later
> calculations, and it may be that the problem is already caused at this
> stage?

Indeed. I can't see the exact problem yet, but it's clear that the 
TracePeptideChain is giving different results on the SMILES-only and --gen3d 
structures.

I'll investigate further.
-Geoff
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