├── .dockerignore ├── .github └── workflows │ ├── build.yml │ ├── ci.yml │ ├── release.yml │ └── release_testpypi.yml ├── .gitignore ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── code-of-conduct.md ├── docs ├── Makefile ├── README.md ├── api.rst ├── commandline_tools.rst ├── commandline_tutorial.rst ├── conf.py ├── doctest.sh ├── environment.yml ├── example.fasta ├── index.rst ├── intro.rst ├── python_tutorial.rst └── requirements.txt ├── downloads-generation ├── README.md ├── allele_sequences │ ├── GENERATE.sh │ ├── class1_pseudosequences.csv │ ├── filter_sequences.py │ ├── make_allele_sequences.py │ └── select_alleles_to_disambiguate.py ├── analysis_predictor_info │ ├── GENERATE.sh │ ├── cluster_submit_script_header.mssm_hpc.lsf │ ├── generate_artifacts.py │ ├── generate_model_selection_with_decoys.py │ ├── predict_on_model_selection_data.py │ └── requirements.txt ├── data_curated │ ├── GENERATE.sh │ ├── README.md │ ├── curate.py │ ├── curate_ms_by_pmid.py │ └── requirements.txt ├── data_evaluation │ ├── GENERATE.sh │ ├── cluster_submit_script_header.mssm_hpc.lsf │ ├── join_with_precomputed.py │ ├── make_benchmark.py │ └── split_by_sample.py ├── data_iedb │ ├── GENERATE.sh │ └── README.md ├── data_mass_spec_annotated │ ├── GENERATE.sh │ ├── annotate.py │ └── requirements.txt ├── data_predictions │ ├── GENERATE.WITH_HPC_CLUSTER.sh │ ├── GENERATE.sh │ ├── cluster_submit_script_header.mssm_hpc.gpu.lsf │ ├── cluster_submit_script_header.mssm_hpc.nogpu.lsf │ ├── requirements.txt │ ├── run_predictors.py │ ├── write_allele_list.py │ └── write_proteome_peptides.py ├── data_published │ ├── GENERATE.sh │ └── README.md ├── data_references │ ├── GENERATE.sh │ ├── README.md │ ├── process.py │ └── requirements.txt ├── data_systemhcatlas │ ├── GENERATE.sh │ └── README.md ├── models_class1 │ ├── GENERATE.sh │ ├── README.md │ └── write_validation_data.py ├── models_class1_kim_benchmark │ ├── GENERATE.sh │ ├── README.md │ ├── class1_pseudosequences.csv │ ├── curate.py │ ├── generate_hyperparameters.py │ └── write_validation_data.py ├── models_class1_minimal │ ├── GENERATE.sh │ ├── README.md │ └── write_validation_data.py ├── models_class1_pan │ ├── GENERATE.WITH_HPC_CLUSTER.sh │ ├── GENERATE.sh │ ├── README.md │ ├── additional_alleles.txt │ ├── cluster_submit_script_header.mssm_hpc.lsf │ ├── generate_hyperparameters.py │ └── reassign_mass_spec_training_data.py ├── models_class1_pan_variants │ ├── GENERATE.WITH_HPC_CLUSTER.sh │ ├── GENERATE.sh │ ├── cluster_submit_script_header.mssm_hpc.gpu.lsf │ ├── exclude_data_from_training.py │ ├── generate_hyperparameters.production.py │ ├── generate_hyperparameters.py │ └── reassign_mass_spec_training_data.py ├── models_class1_presentation │ ├── GENERATE.sh │ ├── cluster_submit_script_header.mssm_hpc.lsf │ └── make_train_data.py ├── models_class1_processing │ ├── GENERATE.WITH_HPC_CLUSTER.sh │ ├── GENERATE.sh │ ├── annotate_hits_with_expression.py │ ├── cluster_submit_script_header.mssm_hpc.lsf │ ├── generate_hyperparameters.base.py │ ├── generate_hyperparameters.variants.py │ ├── make_train_data.py │ └── write_proteome_peptides.py ├── models_class1_selected_no_mass_spec │ ├── GENERATE.sh │ └── write_validation_data.py ├── models_class1_trained_with_mass_spec │ ├── GENERATE.sh │ └── write_validation_data.py ├── models_class1_unselected │ ├── GENERATE.sh │ ├── README.md │ ├── class1_pseudosequences.csv │ └── generate_hyperparameters.py ├── models_class1_unselected_with_mass_spec │ ├── GENERATE.sh │ ├── README.md │ ├── class1_pseudosequences.csv │ └── generate_hyperparameters.py └── random_peptide_predictions │ ├── GENERATE.sh │ └── random_predictions.py ├── lint.sh ├── mhcflurry ├── __init__.py ├── allele_encoding.py ├── amino_acid.py ├── calibrate_percentile_ranks_command.py ├── class1_affinity_predictor.py ├── class1_neural_network.py ├── class1_presentation_predictor.py ├── class1_processing_neural_network.py ├── class1_processing_predictor.py ├── cluster_parallelism.py ├── common.py ├── custom_loss.py ├── data_dependent_weights_initialization.py ├── downloads.py ├── downloads.yml ├── downloads_command.py ├── encodable_sequences.py ├── ensemble_centrality.py ├── fasta.py ├── flanking_encoding.py ├── hyperparameters.py ├── local_parallelism.py ├── percent_rank_transform.py ├── predict_command.py ├── predict_scan_command.py ├── random_negative_peptides.py ├── regression_target.py ├── scoring.py ├── select_allele_specific_models_command.py ├── select_pan_allele_models_command.py ├── select_processing_models_command.py ├── testing_utils.py ├── train_allele_specific_models_command.py ├── train_pan_allele_models_command.py ├── train_presentation_models_command.py ├── train_processing_models_command.py └── version.py ├── notebooks ├── example1.ipynb └── mhcflurry-colab.ipynb ├── pylintrc ├── readthedocs.yml ├── requirements.txt ├── setup.py ├── test-environment.yml └── test ├── __init__.py ├── data ├── data_10mer.csv ├── data_8mer.csv ├── data_9mer.csv ├── example.fasta ├── hpv_predictions.csv ├── multiallelic.benchmark.small.csv.bz2 └── multiallelic_ms.benchmark1.csv.bz2 ├── expensive_verify_pretrain_optimizable.py ├── test_allele_encoding.py ├── test_amino_acid.py ├── test_calibrate_percentile_ranks_command.py ├── test_changing_allele_representations.py ├── test_class1_affinity_predictor.py ├── test_class1_neural_network.py ├── test_class1_pan.py ├── test_class1_presentation_predictor.py ├── test_class1_processing_neural_network.py ├── test_class1_processing_predictor.py ├── test_custom_loss.py ├── test_doctest.py ├── test_download_models_class1.py ├── test_ensemble_centrality.py ├── test_hyperparameters.py ├── test_multi_output.py ├── test_network_merging.py ├── test_percent_rank_transform.py ├── test_predict_command.py ├── test_predict_scan_command.py ├── test_random_negative_peptides.py ├── test_regression_target.py ├── test_released_predictors_on_hpv_dataset.py ├── test_released_predictors_well_correlated.py ├── test_speed.py ├── 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