Merge pull request #2412 from RosettaCommons/JWLabonte/sugars/database
Carbohydrates: H-Placement and Other Topology File Corrections
This merge will correct problems with H-placement that occur when a sugar is not in an ideal chair when loaded in and other blatant topology file errors that have slipped through the cracks.
All sugar `.params` files have been edited/standardized for H-placement, with the following exceptions:
- `to3-alpha-Neup.params` and `to3-beta-Neup.params` — These are chemically impossible sugars and should _not_ be in the database to begin with; however, I am leaving their removal to a future pull request.
- `to8-alpha-Neup.params` and `to4-alpha-Daup.params` — I discovered a `pose_from_saccharide_sequence()` error in loading these two sugars, yet they work fine when loaded from a `.pdb`. The latter is definitely not commonly used; it is only there for a proof-of-concept integration test set up by @everyday847. The former is very common. Please let me know if anyone finds H-placement issues still in the Neup files.
This branch causes integration changes in every sugar test, because I have tweaked all coordinates. I've manually looked at every single one of the ideal structures to make sure that they are correct.