LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
src/plants_sm/__init__.py
src/plants_sm/setup_logger.py
src/plants_sm.egg-info/PKG-INFO
src/plants_sm.egg-info/SOURCES.txt
src/plants_sm.egg-info/dependency_links.txt
src/plants_sm.egg-info/not-zip-safe
src/plants_sm.egg-info/requires.txt
src/plants_sm.egg-info/top_level.txt
src/plants_sm/alignments/__init__.py
src/plants_sm/alignments/alignment.py
src/plants_sm/data_standardization/__init__.py
src/plants_sm/data_standardization/padding_enumerators.py
src/plants_sm/data_standardization/truncation.py
src/plants_sm/data_standardization/x_padder.py
src/plants_sm/data_standardization/compounds/__init__.py
src/plants_sm/data_standardization/compounds/_presets.py
src/plants_sm/data_standardization/compounds/deepmol_standardizers.py
src/plants_sm/data_standardization/compounds/padding.py
src/plants_sm/data_standardization/proteins/__init__.py
src/plants_sm/data_standardization/proteins/padding.py
src/plants_sm/data_standardization/proteins/standardization.py
src/plants_sm/data_structures/__init__.py
src/plants_sm/data_structures/dataset/__init__.py
src/plants_sm/data_structures/dataset/_utils.py
src/plants_sm/data_structures/dataset/dataset.py
src/plants_sm/data_structures/dataset/multi_input_dataset.py
src/plants_sm/data_structures/dataset/single_input_dataset.py
src/plants_sm/data_structures/dataset/batch_manager/__init__.py
src/plants_sm/data_structures/dataset/batch_manager/batch_manager.py
src/plants_sm/design_patterns/__init__.py
src/plants_sm/design_patterns/observer.py
src/plants_sm/estimation/__init__.py
src/plants_sm/estimation/_utils.py
src/plants_sm/estimation/estimator.py
src/plants_sm/featurization/__init__.py
src/plants_sm/featurization/_utils.py
src/plants_sm/featurization/featurizer.py
src/plants_sm/featurization/compounds/__init__.py
src/plants_sm/featurization/compounds/_presets.py
src/plants_sm/featurization/compounds/deepmol_descriptors.py
src/plants_sm/featurization/compounds/map4_fingerprint.py
src/plants_sm/featurization/encoding/__init__.py
src/plants_sm/featurization/encoding/encoder.py
src/plants_sm/featurization/encoding/label_encoder.py
src/plants_sm/featurization/encoding/one_hot_encoder.py
src/plants_sm/featurization/proteins/__init__.py
src/plants_sm/featurization/proteins/bio_embeddings/__init__.py
src/plants_sm/featurization/proteins/bio_embeddings/_utils.py
src/plants_sm/featurization/proteins/bio_embeddings/constants.py
src/plants_sm/featurization/proteins/bio_embeddings/esm.py
src/plants_sm/featurization/proteins/bio_embeddings/esm_models.py
src/plants_sm/featurization/proteins/bio_embeddings/prot_bert.py
src/plants_sm/featurization/proteins/bio_embeddings/unirep.py
src/plants_sm/featurization/proteins/encodings/__init__.py
src/plants_sm/featurization/proteins/encodings/_constants.py
src/plants_sm/featurization/proteins/encodings/blosum.py
src/plants_sm/featurization/proteins/encodings/nlf.py
src/plants_sm/featurization/proteins/encodings/z_scale.py
src/plants_sm/featurization/proteins/propythia/__init__.py
src/plants_sm/featurization/proteins/propythia/propythia.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/__init__.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/_constants.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/_utils.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/amino_acid_composition.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/composition_transition_distribution.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/correlation.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/presets.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/pseudo_amino_acid_composition.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/psycho_chemical.py
src/plants_sm/featurization/proteins/propythia/propythia_descriptors/sequence_order.py
src/plants_sm/hyperparameter_optimization/__init__.py
src/plants_sm/hyperparameter_optimization/experiment.py
src/plants_sm/hyperparameter_optimization/nni_searcher.py
src/plants_sm/hyperparameter_optimization/trial.py
src/plants_sm/io/__init__.py
src/plants_sm/io/commons.py
src/plants_sm/io/csv.py
src/plants_sm/io/excel.py
src/plants_sm/io/h5.py
src/plants_sm/io/json.py
src/plants_sm/io/pickle.py
src/plants_sm/io/reader.py
src/plants_sm/io/writer.py
src/plants_sm/io/yaml.py
src/plants_sm/mixins/__init__.py
src/plants_sm/mixins/mixins.py
src/plants_sm/models/__init__.py
src/plants_sm/models/_esm.py
src/plants_sm/models/_utils.py
src/plants_sm/models/constants.py
src/plants_sm/models/enumerators.py
src/plants_sm/models/lightning_model.py
src/plants_sm/models/model.py
src/plants_sm/models/pytorch_model.py
src/plants_sm/models/tensorflow_model.py
src/plants_sm/models/cnn/__init__.py
src/plants_sm/models/cnn/cnn.py
src/plants_sm/models/ec_number_prediction/__init__.py
src/plants_sm/models/ec_number_prediction/_clean_distance_maps.py
src/plants_sm/models/ec_number_prediction/_clean_utils.py
src/plants_sm/models/ec_number_prediction/_esm_model_architectures.py
src/plants_sm/models/ec_number_prediction/clean.py
src/plants_sm/models/ec_number_prediction/d_space.py
src/plants_sm/models/ec_number_prediction/deepec.py
src/plants_sm/models/ec_number_prediction/esm.py
src/plants_sm/models/ec_number_prediction/hdmlf.py
src/plants_sm/models/fc/__init__.py
src/plants_sm/models/fc/fc.py
src/plants_sm/models/interaction/__init__.py
src/plants_sm/models/interaction/baseline_model.py
src/plants_sm/models/interaction/deep_conv_dti.py
src/plants_sm/models/interaction/deep_dta.py
src/plants_sm/parallelisation/__init__.py
src/plants_sm/parallelisation/torch_spawner.py
src/plants_sm/pipeline/__init__.py
src/plants_sm/pipeline/pipeline.py
src/plants_sm/reports/__init__.py
src/plants_sm/reports/model_report.py
src/plants_sm/tokenisation/__init__.py
src/plants_sm/tokenisation/tokeniser.py
src/plants_sm/tokenisation/compounds/__init__.py
src/plants_sm/tokenisation/compounds/smilespe.py
src/plants_sm/transformation/__init__.py
src/plants_sm/transformation/_utils.py
src/plants_sm/transformation/transformer.py
src/plants_sm/unsupervised/__init__.py
src/plants_sm/unsupervised/kmeans.py
src/plants_sm/unsupervised/model.py
src/plants_sm/unsupervised/pca.py
src/plants_sm/unsupervised/tsne.py
src/plants_sm/utilities/__init__.py
src/plants_sm/utilities/utils.py
src/plants_sm/validation/__init__.py