API Documentation

This is the complete generated API reference. Start with the Python library tutorial for the common prediction workflow, then use this page to look up individual classes and methods.

.. automodule:: mhcflurry :members: :show-inheritance: :undoc-members:

Subpackages

.. toctree:: :maxdepth: 4

mhcflurry.affinity mhcflurry.cli mhcflurry.parallelism

Submodules

mhcflurry.allele_encoding module

.. automodule:: mhcflurry.allele_encoding :members: :show-inheritance: :undoc-members:

mhcflurry.amino_acid module

.. automodule:: mhcflurry.amino_acid :members: :show-inheritance: :undoc-members:

mhcflurry.calibrate_percentile_ranks_command module

.. automodule:: mhcflurry.calibrate_percentile_ranks_command :members: :show-inheritance: :undoc-members:

mhcflurry.class1_affinity_predictor module

.. automodule:: mhcflurry.class1_affinity_predictor :members: :show-inheritance: :undoc-members:

mhcflurry.class1_affinity_training_data module

.. automodule:: mhcflurry.class1_affinity_training_data :members: :show-inheritance: :undoc-members:

mhcflurry.class1_encoding module

.. automodule:: mhcflurry.class1_encoding :members: :show-inheritance: :undoc-members:

mhcflurry.class1_neural_network module

.. automodule:: mhcflurry.class1_neural_network :members: :show-inheritance: :undoc-members:

mhcflurry.class1_presentation_predictor module

.. automodule:: mhcflurry.class1_presentation_predictor :members: :show-inheritance: :undoc-members:

mhcflurry.class1_processing_neural_network module

.. automodule:: mhcflurry.class1_processing_neural_network :members: :show-inheritance: :undoc-members:

mhcflurry.class1_processing_predictor module

.. automodule:: mhcflurry.class1_processing_predictor :members: :show-inheritance: :undoc-members:

mhcflurry.class1_training module

.. automodule:: mhcflurry.class1_training :members: :show-inheritance: :undoc-members:

mhcflurry.cluster_parallelism module

.. automodule:: mhcflurry.cluster_parallelism :members: :show-inheritance: :undoc-members:

mhcflurry.cluster_worker_entry_point module

.. automodule:: mhcflurry.cluster_worker_entry_point :members: :show-inheritance: :undoc-members:

mhcflurry.common module

.. automodule:: mhcflurry.common :members: :show-inheritance: :undoc-members:

mhcflurry.custom_loss module

.. automodule:: mhcflurry.custom_loss :members: :show-inheritance: :undoc-members:

mhcflurry.data_dependent_weights_initialization module

.. automodule:: mhcflurry.data_dependent_weights_initialization :members: :show-inheritance: :undoc-members:

mhcflurry.device_footprint module

.. automodule:: mhcflurry.device_footprint :members: :show-inheritance: :undoc-members:

mhcflurry.downloads module

.. automodule:: mhcflurry.downloads :members: :show-inheritance: :undoc-members:

mhcflurry.downloads_command module

.. automodule:: mhcflurry.downloads_command :members: :show-inheritance: :undoc-members:

mhcflurry.encodable_sequences module

.. automodule:: mhcflurry.encodable_sequences :members: :show-inheritance: :undoc-members:

mhcflurry.ensemble_centrality module

.. automodule:: mhcflurry.ensemble_centrality :members: :show-inheritance: :undoc-members:

mhcflurry.fasta module

.. automodule:: mhcflurry.fasta :members: :show-inheritance: :undoc-members:

mhcflurry.flanking_encoding module

.. automodule:: mhcflurry.flanking_encoding :members: :show-inheritance: :undoc-members:

mhcflurry.hyperparameters module

.. automodule:: mhcflurry.hyperparameters :members: :show-inheritance: :undoc-members:

mhcflurry.local_parallelism module

.. automodule:: mhcflurry.local_parallelism :members: :show-inheritance: :undoc-members:

mhcflurry.memory_budget module

.. automodule:: mhcflurry.memory_budget :members: :show-inheritance: :undoc-members:

mhcflurry.model_provenance module

.. automodule:: mhcflurry.model_provenance :members: :show-inheritance: :undoc-members:

mhcflurry.motif_summary module

.. automodule:: mhcflurry.motif_summary :members: :show-inheritance: :undoc-members:

mhcflurry.peptide_reference module

.. automodule:: mhcflurry.peptide_reference :members: :show-inheritance: :undoc-members:

mhcflurry.percent_rank_transform module

.. automodule:: mhcflurry.percent_rank_transform :members: :show-inheritance: :undoc-members:

mhcflurry.predict_command module

.. automodule:: mhcflurry.predict_command :members: :show-inheritance: :undoc-members:

mhcflurry.predict_scan_command module

.. automodule:: mhcflurry.predict_scan_command :members: :show-inheritance: :undoc-members:

mhcflurry.proteome_decoys module

.. automodule:: mhcflurry.proteome_decoys :members: :show-inheritance: :undoc-members:

mhcflurry.pseudosequences module

.. automodule:: mhcflurry.pseudosequences :members: :show-inheritance: :undoc-members:

mhcflurry.pytorch_layers module

.. automodule:: mhcflurry.pytorch_layers :members: :show-inheritance: :undoc-members:

mhcflurry.pytorch_losses module

.. automodule:: mhcflurry.pytorch_losses :members: :show-inheritance: :undoc-members:

mhcflurry.pytorch_sizing module

.. automodule:: mhcflurry.pytorch_sizing :members: :show-inheritance: :undoc-members:

mhcflurry.pytorch_training module

.. automodule:: mhcflurry.pytorch_training :members: :show-inheritance: :undoc-members:

mhcflurry.random_negative_peptides module

.. automodule:: mhcflurry.random_negative_peptides :members: :show-inheritance: :undoc-members:

mhcflurry.regression_target module

.. automodule:: mhcflurry.regression_target :members: :show-inheritance: :undoc-members:

mhcflurry.scoring module

.. automodule:: mhcflurry.scoring :members: :show-inheritance: :undoc-members:

mhcflurry.select_allele_specific_models_command module

.. automodule:: mhcflurry.select_allele_specific_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.select_pan_allele_models_command module

.. automodule:: mhcflurry.select_pan_allele_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.select_processing_models_command module

.. automodule:: mhcflurry.select_processing_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.testing_utils module

.. automodule:: mhcflurry.testing_utils :members: :show-inheritance: :undoc-members:

mhcflurry.train_allele_specific_models_command module

.. automodule:: mhcflurry.train_allele_specific_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.train_pan_allele_models_command module

.. automodule:: mhcflurry.train_pan_allele_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.train_presentation_models_command module

.. automodule:: mhcflurry.train_presentation_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.train_processing_models_command module

.. automodule:: mhcflurry.train_processing_models_command :members: :show-inheritance: :undoc-members:

mhcflurry.training_benchmark module

.. automodule:: mhcflurry.training_benchmark :members: :show-inheritance: :undoc-members:

mhcflurry.version module

.. automodule:: mhcflurry.version :members: :show-inheritance: :undoc-members:

mhcflurry.workload_planning module

.. automodule:: mhcflurry.workload_planning :members: :show-inheritance: :undoc-members: