raghavagps/cbtope2 ? reverse-engineered prompt

Build me a simple Python tool for predicting antibody interacting residues in protein sequences, like the CBTOPE2 standalone app.

I want to paste in one or more protein or peptide sequences, either as a FASTA file or one sequence per line, then get a clear prediction for which residues are likely to be part of a conformational B cell epitope. Let me choose between two modes, one basic model and one better ensemble model, and let me set a probability threshold from 0 to 1, with 0.5 as the default.

The result should be easy to read, showing the sequence, the predicted interacting residues, and the scores or labels for each position. If possible, make it work as a command line script first, but keep it clean enough that it could also be used as a small standalone package later. Use the existing data and model files in the repository, and look up any current setup details online if you need to.