LICENSE
MANIFEST.in
README.rst
pyproject.toml
setup.py
aaanalysis/__init__.py
aaanalysis/_constants.py
aaanalysis/_provenance.py
aaanalysis/_schemas.py
aaanalysis/config.py
aaanalysis/py.typed
aaanalysis/template_classes.py
aaanalysis/utils.py
aaanalysis.egg-info/PKG-INFO
aaanalysis.egg-info/SOURCES.txt
aaanalysis.egg-info/dependency_links.txt
aaanalysis.egg-info/requires.txt
aaanalysis.egg-info/top_level.txt
aaanalysis/_data/__init__.py
aaanalysis/_data/scales.tsv
aaanalysis/_data/scales_cat.tsv
aaanalysis/_data/scales_pc.tsv
aaanalysis/_data/scales_raw.tsv
aaanalysis/_data/subcat.tsv
aaanalysis/_data/top60.tsv
aaanalysis/_data/top60_eval.tsv
aaanalysis/_data/top_explain.tsv
aaanalysis/_data/benchmarks/AA_CASPASE3.tsv
aaanalysis/_data/benchmarks/AA_FURIN.tsv
aaanalysis/_data/benchmarks/AA_LDR.tsv
aaanalysis/_data/benchmarks/AA_MMP2.tsv
aaanalysis/_data/benchmarks/AA_RNABIND.tsv
aaanalysis/_data/benchmarks/AA_SA.tsv
aaanalysis/_data/benchmarks/DOM_GSEC.tsv
aaanalysis/_data/benchmarks/DOM_GSEC_PU.tsv
aaanalysis/_data/benchmarks/Overview.tsv
aaanalysis/_data/benchmarks/SEQ_AMYLO.tsv
aaanalysis/_data/benchmarks/SEQ_CAPSID.tsv
aaanalysis/_data/benchmarks/SEQ_DISULFIDE.tsv
aaanalysis/_data/benchmarks/SEQ_LOCATION.tsv
aaanalysis/_data/benchmarks/SEQ_SOLUBLE.tsv
aaanalysis/_data/benchmarks/SEQ_TAIL.tsv
aaanalysis/_data/features/FEATURES_DOM_GSEC.tsv
aaanalysis/_data/pdb_test/__init__.py
aaanalysis/_utils/__init__.py
aaanalysis/_utils/_utils.py
aaanalysis/_utils/check_data.py
aaanalysis/_utils/check_models.py
aaanalysis/_utils/check_plots.py
aaanalysis/_utils/check_type.py
aaanalysis/_utils/decorators.py
aaanalysis/_utils/metrics.py
aaanalysis/_utils/models.py
aaanalysis/_utils/plotting.py
aaanalysis/_utils/utils_output.py
aaanalysis/_utils/utils_plot_elements.py
aaanalysis/_utils/utils_plot_parts.py
aaanalysis/_utils/utils_types.py
aaanalysis/data_handling/__init__.py
aaanalysis/data_handling/_combine_dict_nums.py
aaanalysis/data_handling/_embed_preproc.py
aaanalysis/data_handling/_get_labels.py
aaanalysis/data_handling/_load_dataset.py
aaanalysis/data_handling/_load_features.py
aaanalysis/data_handling/_load_scales.py
aaanalysis/data_handling/_read_fasta.py
aaanalysis/data_handling/_seq_preproc.py
aaanalysis/data_handling/_to_fasta.py
aaanalysis/data_handling/_backend/__init__.py
aaanalysis/data_handling/_backend/parse_fasta.py
aaanalysis/data_handling/_backend/embed_preproc/__init__.py
aaanalysis/data_handling/_backend/embed_preproc/build_pseudo_scales.py
aaanalysis/data_handling/_backend/embed_preproc/cluster_pseudo_scales.py
aaanalysis/data_handling/_backend/embed_preproc/encode.py
aaanalysis/data_handling/_backend/embed_preproc/fetch.py
aaanalysis/data_handling/_backend/seq_preproc/__init__.py
aaanalysis/data_handling/_backend/seq_preproc/_utils.py
aaanalysis/data_handling/_backend/seq_preproc/encode_integer.py
aaanalysis/data_handling/_backend/seq_preproc/encode_one_hot.py
aaanalysis/data_handling/_backend/seq_preproc/get_aa_window.py
aaanalysis/data_handling/_backend/seq_preproc/get_sliding_aa_window.py
aaanalysis/data_handling_pro/__init__.py
aaanalysis/data_handling_pro/_annot_preproc.py
aaanalysis/data_handling_pro/_struct_preproc.py
aaanalysis/data_handling_pro/_backend/__init__.py
aaanalysis/data_handling_pro/_backend/_fetch.py
aaanalysis/data_handling_pro/_backend/annot_preproc/__init__.py
aaanalysis/data_handling_pro/_backend/annot_preproc/_uniprot.py
aaanalysis/data_handling_pro/_backend/annot_preproc/feature_registry.py
aaanalysis/data_handling_pro/_backend/struct_preproc/__init__.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_afragmenter.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_alphafold.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_chainsaw.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_domain_io.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_extras.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_file_format.py
aaanalysis/data_handling_pro/_backend/struct_preproc/_pae_io.py
aaanalysis/data_handling_pro/_backend/struct_preproc/align_dssp_full.py
aaanalysis/data_handling_pro/_backend/struct_preproc/encode_domains.py
aaanalysis/data_handling_pro/_backend/struct_preproc/encode_dssp.py
aaanalysis/data_handling_pro/_backend/struct_preproc/encode_pae.py
aaanalysis/data_handling_pro/_backend/struct_preproc/encode_pdb.py
aaanalysis/data_handling_pro/_backend/struct_preproc/feature_registry.py
aaanalysis/data_handling_pro/_backend/struct_preproc/run_dssp_full.py
aaanalysis/explainable_ai/__init__.py
aaanalysis/explainable_ai/_tree_model.py
aaanalysis/explainable_ai/_backend/__init__.py
aaanalysis/explainable_ai/_backend/check_models.py
aaanalysis/explainable_ai/_backend/tree_model/__init__.py
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aaanalysis/explainable_ai_pro/__init__.py
aaanalysis/explainable_ai_pro/_shap_model.py
aaanalysis/explainable_ai_pro/_shap_model_plot.py
aaanalysis/explainable_ai_pro/_backend/__init__.py
aaanalysis/explainable_ai_pro/_backend/check_models.py
aaanalysis/explainable_ai_pro/_backend/shap_model/__init__.py
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aaanalysis/feature_engineering/__init__.py
aaanalysis/feature_engineering/_aaclust.py
aaanalysis/feature_engineering/_aaclust_plot.py
aaanalysis/feature_engineering/_cpp.py
aaanalysis/feature_engineering/_cpp_grid.py
aaanalysis/feature_engineering/_cpp_plot.py
aaanalysis/feature_engineering/_numerical_feature.py
aaanalysis/feature_engineering/_sequence_feature.py
aaanalysis/feature_engineering/_sequence_feature_transformer.py
aaanalysis/feature_engineering/_backend/__init__.py
aaanalysis/feature_engineering/_backend/check_aaclust.py
aaanalysis/feature_engineering/_backend/check_cpp_plot.py
aaanalysis/feature_engineering/_backend/check_feature.py
aaanalysis/feature_engineering/_backend/cpp_run.py
aaanalysis/feature_engineering/_backend/feature_filter.py
aaanalysis/feature_engineering/_backend/aaclust/__init__.py
aaanalysis/feature_engineering/_backend/aaclust/_utils_aaclust.py
aaanalysis/feature_engineering/_backend/aaclust/aaclust_eval.py
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aaanalysis/feature_engineering/_backend/cpp/__init__.py
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aaanalysis/feature_engineering/_backend/cpp/_simplify.py
aaanalysis/feature_engineering/_backend/cpp/_split.py
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aaanalysis/feature_engineering/_backend/cpp/cpp_plot_ranking.py
aaanalysis/feature_engineering/_backend/cpp/cpp_plot_update_seq_size.py
aaanalysis/feature_engineering/_backend/cpp/sequence_feature.py
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aaanalysis/feature_engineering/_backend/cpp/_filters/__init__.py
aaanalysis/feature_engineering/_backend/cpp/_filters/_add_stat.py
aaanalysis/feature_engineering/_backend/cpp/_filters/_assign.py
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aaanalysis/feature_engineering/_backend/cpp/_filters/_stat_filter.py
aaanalysis/feature_engineering/_backend/cpp/_filters_c/__init__.py
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aaanalysis/feature_engineering/_backend/num_feat/__init__.py
aaanalysis/feature_engineering/_backend/num_feat/extend_alphabet.py
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aaanalysis/feature_engineering_pro/__init__.py
aaanalysis/feature_engineering_pro/_cpp_structure_plot.py
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aaanalysis/feature_engineering_pro/_backend/cpp_struct/__init__.py
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aaanalysis/feature_engineering_pro/_backend/cpp_struct/structure.py
aaanalysis/feature_engineering_pro/_backend/cpp_struct/view.py
aaanalysis/metrics/__init__.py
aaanalysis/metrics/_metrics.py
aaanalysis/pipe/__init__.py
aaanalysis/pipe/_eval_plot.py
aaanalysis/pipe/_explain_features.py
aaanalysis/pipe/_find_features.py
aaanalysis/pipe/_obtain_samples.py
aaanalysis/pipe/_pipelines.py
aaanalysis/plotting/__init__.py
aaanalysis/plotting/_plot_gcfs.py
aaanalysis/plotting/_plot_get_cdict.py
aaanalysis/plotting/_plot_get_clist.py
aaanalysis/plotting/_plot_get_cmap.py
aaanalysis/plotting/_plot_legend.py
aaanalysis/plotting/_plot_settings.py
aaanalysis/prediction/__init__.py
aaanalysis/prediction/_aa_pred.py
aaanalysis/prediction/_aa_pred_plot.py
aaanalysis/prediction/_model_evaluator.py
aaanalysis/prediction/_model_evaluator_plot.py
aaanalysis/prediction/_reliability_model.py
aaanalysis/prediction/_reliability_model_plot.py
aaanalysis/prediction/_backend/__init__.py
aaanalysis/prediction/_backend/aa_pred/__init__.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_eval.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_fit.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_group.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_plot_clustermap.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_plot_comparison.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_plot_legend.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_plot_rank_scatter.py
aaanalysis/prediction/_backend/aa_pred/aa_pred_plot_ranking.py
aaanalysis/prediction/_backend/model_evaluator/__init__.py
aaanalysis/prediction/_backend/model_evaluator/model_evaluator_eval.py
aaanalysis/prediction/_backend/model_evaluator/model_evaluator_plot.py
aaanalysis/prediction/_backend/reliability/__init__.py
aaanalysis/prediction/_backend/reliability/reliability.py
aaanalysis/prediction/_backend/reliability/reliability_plot.py
aaanalysis/protein_engineering/__init__.py
aaanalysis/protein_engineering/_aamut.py
aaanalysis/protein_engineering/_aamut_plot.py
aaanalysis/protein_engineering/_seqmut.py
aaanalysis/protein_engineering/_seqmut_plot.py
aaanalysis/protein_engineering/_seqopt.py
aaanalysis/protein_engineering/_seqopt_plot.py
aaanalysis/protein_engineering/_backend/__init__.py
aaanalysis/protein_engineering/_backend/aamut/__init__.py
aaanalysis/protein_engineering/_backend/aamut/aamut.py
aaanalysis/protein_engineering/_backend/seqmut/__init__.py
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aaanalysis/protein_engineering/_backend/seqopt/__init__.py
aaanalysis/protein_engineering/_backend/seqopt/genome.py
aaanalysis/protein_engineering/_backend/seqopt/metrics.py
aaanalysis/protein_engineering/_backend/seqopt/nsga2.py
aaanalysis/protein_engineering/_backend/seqopt/penalty.py
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aaanalysis/pu_learning/__init__.py
aaanalysis/pu_learning/_dpulearn.py
aaanalysis/pu_learning/_dpulearn_plot.py
aaanalysis/pu_learning/_backend/__init__.py
aaanalysis/pu_learning/_backend/dpulearn/__init__.py
aaanalysis/pu_learning/_backend/dpulearn/dpul_compare_sets_neg.py
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aaanalysis/pu_learning/_backend/dpulearn/dpul_fit.py
aaanalysis/pu_learning/_backend/dpulearn/dpul_plot.py
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aaanalysis/seq_analysis/__init__.py
aaanalysis/seq_analysis/_aa_window_sampler.py
aaanalysis/seq_analysis/_aalogo.py
aaanalysis/seq_analysis/_aalogo_plot.py
aaanalysis/seq_analysis/_backend/_aalogo/aalogo.py
aaanalysis/seq_analysis/_backend/_aalogo/aalogo_plot.py
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aaanalysis/seq_analysis_pro/_comp_seq_sim.py
aaanalysis/seq_analysis_pro/_filter_seq.py
aaanalysis/seq_analysis_pro/_scan_motif.py
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aaanalysis/seq_analysis_pro/_backend/cd_hit.py
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aaanalysis/seq_analysis_pro/_backend/mmseq2.py
aaanalysis/show_html/__init__.py
aaanalysis/show_html/_display_df.py