├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── deploy.sh ├── develop.sh ├── lint.sh ├── pepdata ├── __init__.py ├── amino_acid.py ├── amino_acid_alphabet.py ├── amino_acid_properties.py ├── blosum.py ├── chou_fasman.py ├── common.py ├── iedb │ ├── __init__.py │ ├── alleles.py │ ├── columns.py │ ├── common.py │ ├── memoize.py │ ├── mhc.py │ └── tcell.py ├── matrices │ ├── BLOSUM30 │ ├── BLOSUM50 │ ├── BLOSUM62 │ ├── __init__.py │ ├── amino_acid_properties.txt │ ├── helix_vs_coil.txt │ ├── helix_vs_strand.txt │ ├── pmbec.mat │ └── strand_vs_coil.txt ├── peptide_vectorizer.py ├── pmbec.py ├── reduced_alphabet.py ├── residue_contact_energies.py ├── static_data.py └── version.py ├── pylintrc ├── requirements.txt ├── setup.py ├── test.sh └── tests ├── test_amino_acids.py ├── test_blosum.py ├── test_iedb_alleles.py ├── test_iedb_mhc.py ├── test_iedb_tcell.py ├── test_ngram.py └── test_pmbec.py /.gitignore: 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