RFE Protocol - disallow mappings instead on the fly fixing constrained bond mappings

[IAlibay]

For v2.0 - we should consider just failing when a constrained bond is encountered and should be demapped.

[mikemhenry]

Since we know the protocol at network generation time, I think the error or warning should be raised at that point so you don't get an error at runtime when you submit a job to an HPC queue.

[jthorton]

I agree we want to fail early, I would love to have some validation run when constructing a Transformation so we know it at least has a valid setup and will attempt to run. I think requiring each protocol to have a validate method that is called during the construction of the Transformation should be flexible enough for many of these issues. The Transformation could also handle a lot of general validation of the components before performing protocol specific validation.