This pull request was triggered by the discussion here.
Summary of the changes:
Move one-to-three protein letter maps into Bio.Data.IUPACData
SeqUtils.seq3 now creates a copy of the imported IUPACData dict
This is to prevent a bug where the IUPACData dict is imported in some other
modules, and the key-value pairs have unexpected values due to seq3's update.
Move Bio.SCOP.three_to_one_dict to Bio.Data.SCOPData
Use SeqUtils.seq1() instead of SCOP.to_one_letter_code().
To avoid breaking scripts that use Bio.SCOP.three_to_one_dict.py, could we add a file at Bio/SCOP/three_to_one_dict.py that simply imports the Bio.Data.SCOPData dictionaries, assigns them to the old names, and issues a DeprecationWarning?
Good idea, Eric :). Added in the latest commit.
Add deprecation warning in place of old SCOP's 3-to-1 dict
Looks good to me. All clear to merge?
Closing this PR since it has been merged into master via cherry-pick (e.g. 8500794)