Peptide Builder v2

General Discussion
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This morning I merged the peptide builder branch. (I forgot that I was going to squash so if you want, you can see the long process along the way in commits.)

I’m sure it’ll have some bugs, so please take a look if you can.

Part of the code implements z-matrix / internal coordinates so there can be some work towards those in the future (e.g., z-matrix editor or input generator features)

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I had various plans to implement additional N-terminus and C-terminus modifications. That’s on the longer term todo list (e.g., post-2.0)