Metapredict

Changes:
Updated to require V1.0 of alphaPredict for pLDDT scores. This improves accuracy from over 9% per residue to about 8% per residue for pLDDT score predictions. Documentation was updated for this change.

Changes:
Fixed bug causing some functions to fail when getting sequences from Uniprot.
Added information on citing metapredict because the final publication went live.

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*.

Change:
Added functionality to generate predicted AlphaFold2 pLDDT confidence scores. Can get scores or generate graphs from Python or command-line. Can also generate graphs with both predicted disorder and predicted pLDDT confidence scores. Also added functionality to predict disorder domains using scores from a different disorder predictor.

Change:
Major update. Changed some basic functionality. Made it such that you don't need to specify to save (for disorder prediction values or graphs). Rather, if a file path is specified, the files will be saved. Updated graphing functionality to allow for specifying the disorder cutoff line and to allow users to highlight various regions of the graph. Changed import such that you can now just use import metapredict as meta in Python (as opposed to import metapredict and then from metapredict import meta). Lots of backend changes to make metapredict more stable. Added additional testing. Updated documentation. Standardized file reading/writing. Made it so user can specify file type of saved graphs. Added backend meta_tools.py to handle the busywork. Changed version numbering for networks. Updated code to avoid OMPLIB issue (known bug in previous versions). Updated all command-line tools to match backend code.

Change:
Fixed some bugs.