Change:
For clarity, previous functions that used the term 'confidence' such as *graph_confidence_uniprot()* were changed to use the term pLDDT rather than confidence. This is to clarify that the confidence scores are AlphaFold2 pLDDT confidence scores and not scores to reflect the confidence that the user should have in the metapredict disorder prediction. For command-line usage where confidence scores are optional (such as metapredict-graph-disorder), when a *-c* or *--confidence* flag used to be used, now a *-p* or *--pLDDT* flag is used to graph confidence scores. This is similarly reflected in Python where now you must use *pLDDT_scores=True* instead of *confidence_scores=True*.