├── .gitignore ├── LICENSE ├── README.md ├── docs ├── api │ ├── biology.md │ ├── descriptors.md │ ├── encoding.md │ └── tokenizer.md ├── assets │ ├── molml_logo.png │ └── peptidy_logo.png ├── index.md ├── javascripts │ └── mathjax.js └── stylesheets │ └── style.css ├── examples ├── amp_prediction_with_CNN.ipynb ├── amp_prediction_with_xgboost.ipynb ├── peptide_generation_with_LSTM.ipynb └── subsample_AMP.csv ├── mkdocs.yml ├── peptidy ├── __init__.py ├── biology.py ├── data │ ├── aromatic_aas.json │ ├── blosum62_scores.json │ ├── descriptor_per_aas.json │ ├── formulas.json │ ├── hydrophobic_aas.json │ ├── instabilities.json │ ├── n_h_acceptors.json │ ├── n_h_donors.json │ ├── n_rotatable_bonds.json │ ├── neg_pks.json │ ├── pos_pks.json │ ├── token_to_label.json │ ├── tpsas.json │ ├── weights.json │ └── x_logps.json ├── descriptors.py ├── encoding.py └── tokenizer.py ├── setup.py └── tests ├── encoding_matrices ├── blosum62_0.txt ├── blosum62_1.txt ├── blosum62_2.txt ├── blosum62_3.txt ├── blosum62_4.txt ├── one_hot_0.txt ├── one_hot_1.txt └── one_hot_2.txt ├── results ├── biology.xml ├── descriptors.xml ├── encoder_tests_1.xml ├── encoder_tests_2.xml ├── encoding.xml └── tokenizer.xml ├── run_tests.sh ├── test_encodings_1.py └── test_encodings_2.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/peptidy/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/peptidy/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/peptidy/HEAD/README.md -------------------------------------------------------------------------------- /docs/api/biology.md: 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