MANIFEST.in
README.md
pyproject.toml
onestep_sepal_ppi.egg-info/PKG-INFO
onestep_sepal_ppi.egg-info/SOURCES.txt
onestep_sepal_ppi.egg-info/dependency_links.txt
onestep_sepal_ppi.egg-info/entry_points.txt
onestep_sepal_ppi.egg-info/requires.txt
onestep_sepal_ppi.egg-info/top_level.txt
sepal_ppi/__init__.py
sepal_ppi/cli.py
sepal_ppi/config.py
sepal_ppi/hf_cache.py
sepal_ppi/runtime.py
sepal_ppi/commands/__init__.py
sepal_ppi/commands/predict_cmd.py
sepal_ppi/commands/prepare_cmd.py
sepal_ppi/commands/setup_cmd.py
sepal_ppi/resources/nsp3_env_config.template.ini
sepal_ppi/vendor/mutifeature_tools/extract_features_fast.py
sepal_ppi/vendor/mutifeature_tools/generate_sasa_ss_from_nsp3.py
sepal_ppi/vendor/mutifeature_tools/precompute_multimodal_lmdb.py
sepal_ppi/vendor/src/__init__.py
sepal_ppi/vendor/src/custom_mlp.py
sepal_ppi/vendor/src/data_processing/__init__.py
sepal_ppi/vendor/src/data_processing/auto_bucketed_lmdb.py
sepal_ppi/vendor/src/data_processing/batched_multimodal_loader.py
sepal_ppi/vendor/src/data_processing/bucketed_lmdb_loader.py
sepal_ppi/vendor/src/data_processing/bucketing.py
sepal_ppi/vendor/src/data_processing/cis_data_loader.py
sepal_ppi/vendor/src/data_processing/dynamic_bucketing.py
sepal_ppi/vendor/src/data_processing/fasta_parser.py
sepal_ppi/vendor/src/data_processing/hybrid_bucketing_manager.py
sepal_ppi/vendor/src/data_processing/intelligent_bucketed_loader.py
sepal_ppi/vendor/src/data_processing/lmdb_loader.py
sepal_ppi/vendor/src/data_processing/make_dataset.py
sepal_ppi/vendor/src/data_processing/parallel_lmdb_loader.py
sepal_ppi/vendor/src/data_processing/preprocessing.py
sepal_ppi/vendor/src/data_processing/sequence_dataset.py
sepal_ppi/vendor/src/data_processing/smart_batch_loader.py
sepal_ppi/vendor/src/data_processing/streaming_gpu_cache.py
sepal_ppi/vendor/src/data_processing/unified_cache_loader.py
sepal_ppi/vendor/src/ensemble/__init__.py
sepal_ppi/vendor/src/ensemble/cis_interpretability.py
sepal_ppi/vendor/src/ensemble/ensemble_engine.py
sepal_ppi/vendor/src/ensemble/ensemble_predict_engine.py
sepal_ppi/vendor/src/ensemble/ensemble_runner.py
sepal_ppi/vendor/src/evaluation/__init__.py
sepal_ppi/vendor/src/evaluation/evaluate.py
sepal_ppi/vendor/src/features/__init__.py
sepal_ppi/vendor/src/features/build_features.py
sepal_ppi/vendor/src/inference/__init__.py
sepal_ppi/vendor/src/inference/inference_engine.py
sepal_ppi/vendor/src/models/__init__.py
sepal_ppi/vendor/src/models/classifier.py
sepal_ppi/vendor/src/models/interaction.py
sepal_ppi/vendor/src/models/model.py
sepal_ppi/vendor/src/models/pooling.py
sepal_ppi/vendor/src/models/predict_model.py
sepal_ppi/vendor/src/models/train_model.py
sepal_ppi/vendor/src/models/model_unit/__init__.py
sepal_ppi/vendor/src/models/model_unit/classifier_units.py
sepal_ppi/vendor/src/models/model_unit/input_layer.py
sepal_ppi/vendor/src/models/model_unit/interaction_units.py
sepal_ppi/vendor/src/models/model_unit/model_factory.py
sepal_ppi/vendor/src/models/model_unit/pooling_units.py
sepal_ppi/vendor/src/models/model_unit/prepooling_units.py
sepal_ppi/vendor/src/models/model_unit/preprocessing_units.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/BaseTransformerUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/CrossAttentionEnhancedTransformerUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FeatureConcatUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FeatureCrossAttentionUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FeatureCrossTransformerUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FlashAttentionTransformerUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FlashTransformerDecoderLayer.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/FlashTransformerEncoderLayer.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/GatedFeatureFusionUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/HMMPreprocessingUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/IdentityPreprocessingUnit.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/PositionalEncoding.py
sepal_ppi/vendor/src/models/model_unit/preprocessing/__init__.py
sepal_ppi/vendor/src/onestep_predict/__init__.py
sepal_ppi/vendor/src/onestep_predict/data_preparation.py
sepal_ppi/vendor/src/onestep_predict/embedding_generator.py
sepal_ppi/vendor/src/onestep_predict/ig_attribution.py
sepal_ppi/vendor/src/onestep_predict/predict_engine.py
sepal_ppi/vendor/src/onestep_predict/result_saver.py
sepal_ppi/vendor/src/onestep_predict/test.py
sepal_ppi/vendor/src/onestep_predict/ig_singele/__init__.py
sepal_ppi/vendor/src/onestep_predict/ig_singele/single_lmdb_exporter.py
sepal_ppi/vendor/src/onestep_predict/mutifeature/__init__.py
sepal_ppi/vendor/src/onestep_predict/mutifeature/feature_io.py
sepal_ppi/vendor/src/onestep_predict/mutifeature/netsurfp_features.py
sepal_ppi/vendor/src/onestep_predict/mutifeature/pdb_features.py
sepal_ppi/vendor/src/tools/batch_generate_and_run.py
sepal_ppi/vendor/src/tools/batch_train_datase.py
sepal_ppi/vendor/src/tools/batch_train_datase_new.py
sepal_ppi/vendor/src/tools/collect_ablation_aupr.py
sepal_ppi/vendor/src/tools/collect_metrics.py
sepal_ppi/vendor/src/tools/compare_results.py
sepal_ppi/vendor/src/tools/dataset copy.csv
sepal_ppi/vendor/src/tools/dataset.csv
sepal_ppi/vendor/src/training/training_runner.py
sepal_ppi/vendor/src/utils/__init__.py
sepal_ppi/vendor/src/utils/config_manager.py
sepal_ppi/vendor/src/utils/helpers.py
sepal_ppi/vendor/src/utils/hydra_config_manager.py
sepal_ppi/vendor/src/utils/logger.py
sepal_ppi/vendor/src/visualization/__init__.py
sepal_ppi/vendor/src/visualization/html_generator.py
sepal_ppi/vendor/src/visualization/templates/prediction_results.html