Merge pull request #543 from RosettaCommons/JWLabonte/sugars/input
PDB Input/Output: Allowing for alternative 3-letter codes
This will allow Rosetta to handle alternative 3-letter codes, a list of which are provided in simple text files.
Usage of this new feature is described on our user-facing documentation wiki here:
http://www.rosettacommons.org/docs/wiki/Preparing-PDB-files-for-non-peptide-polymers#Alternate-3-Letter-Codes-Files
Thank you to all those who provided feedback during the pull request process!
:rat:
Testing:
All unit tests passed, with the exception of a PyRosetta unit test, which I've seen randomly fail in the past. If it turns out it was something I did after all, I'll revert.
carbohydrate integration test change expected: renamed an atom type and added loading of sugar with GLYCAM 3-letter codes as an example/test
code_duplication test change expected: deleted commented-out code, thus changing reported line numbers of duplications
All other tests were already broken.