Merge pull request #3354 from RosettaCommons/JWLabonte/sugars/output
GlycanTree: Adding a method to output the IUPAC sequence for an individual glycan
This merge will add a function `Pose::glycan_tree_sequence` that will output a string representation of a glycan in IUPAC format. Currently, `Pose::chain_sequence` will output the IUPAC sequence for a polysaccharide chain, but this is simply a linear sequence. The new function will give the branches and their connectivity using the standard IUPAC bracket notation.
In the process of writing this code, I made a few modifications to `CarbohydrateInfo` in regards to nomenclature:
* Reducing-end residues now include their anomeric form as part of their name. (They usually don't in the literature, but that's because of ignorance because of their instability. In a modeling case, we absolutely know which anomer we have.)
* A bug is fixed regarding sugar-modification abbreviations as suffixes in short-form names. Reducing-end GlcpNAc, for example, no longer outputs as GlcpN.
I have also corrected input files for use with the 'glycosylate_pose()` functions, reordering their branches so that Rosetta no longer gets confused.
CCD_loop_closure and carbohydrate integration test changes expected, because of the bulleted changed noted above. All unit tests pass.
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Merge pull request #3319 from RosettaCommons/vmullig/parametric_rna_fix
Fix for parametrically-generated RNA helices.
The parametric code wrongly assumed that the first N atoms of a polymer type are always the mainchain atoms. Correcting this assumption with explicit lookups from ResidueType::mainchain_atom().
Labonte 6 years I think you broke PyRosetta with this merge.
Vikram K. Mulligan 6 years Both of those tests are showing intermittent failures before and after this commit. I don't know what's causing those, but I'm pretty sure that it wasn't this pull request.[list]
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