Index

_

__init__() (AAclust method) (AAclustPlot method) (AAlogo method) (AAlogoPlot method) (AAMut method) (AAMutPlot method) (AAPred method) (AAPredPlot method) (AAWindowSampler method) (AnnotationPreprocessor method) (CPP method) (CPPGrid method) (CPPPlot method) (CPPStructurePlot method) (dPULearn method) (dPULearnPlot method) (EmbeddingPreprocessor method) (ReliabilityModel method) (SeqMut method) (SeqMutPlot method) (SeqOpt method) (SeqOptPlot method) (SequenceFeature method) (ShapModel method) (StructurePreprocessor method) (TreeModel method)

A

aa_comparison() (AAMutPlot method) aa_composition() (SequenceFeature method) aaanalysis.py module AAclust (class in aaanalysis) AAclustPlot (class in aaanalysis) AAlogo (class in aaanalysis) AAlogoPlot (class in aaanalysis) AAMut (class in aaanalysis)

AAMutPlot (class in aaanalysis) AAontology AAPred (class in aaanalysis) AAPredPlot (class in aaanalysis) AAWindowSampler (class in aaanalysis) add_feat_impact() (ShapModel method) add_feat_importance() (TreeModel method) add_sample_mean_dif() (ShapModel static method) AnnotationPreprocessor (class in aaanalysis)

B

build_cat() (AnnotationPreprocessor method) (EmbeddingPreprocessor method) (StructurePreprocessor method)

build_scales() (AnnotationPreprocessor method) (EmbeddingPreprocessor method) (StructurePreprocessor method)

C

centers() (AAclustPlot method) centers_ (AAclust attribute) combine() (SeqMut method) combine_dict_nums (class in aaanalysis) comp_auc_adjusted() (in module aaanalysis) comp_bic_score() (in module aaanalysis) comp_bootstrap_ci() (in module aaanalysis) comp_centers() (AAclust static method) comp_correlation() (AAclust static method) comp_coverage() (AAclust static method) comp_detection_metrics() (in module aaanalysis) comp_kld() (in module aaanalysis)

comp_medoids() (AAclust static method) comp_per_protein_ap() (in module aaanalysis) comp_seq_sim (class in aaanalysis) comp_smooth_scores() (in module aaanalysis) compare_sets_negatives() (dPULearn static method) compositional vs positional convergence() (SeqOptPlot method) correlation() (AAclustPlot method) CPP (class in aaanalysis) CPPGrid (class in aaanalysis) CPPPlot (class in aaanalysis) CPPStructurePlot (class in aaanalysis)

D

design / engineering determinant discovery df_feat df_parts df_pu_ (dPULearn attribute) df_seq

dict_num dipeptide_composition() (SequenceFeature method) display_df() (in module aaanalysis) domain level dPULearn (class in aaanalysis) dPULearnPlot (class in aaanalysis)

E

EmbeddingPreprocessor (class in aaanalysis) encode() (AnnotationPreprocessor method) (EmbeddingPreprocessor method) encode_domains() (StructurePreprocessor method) encode_dssp() (StructurePreprocessor method) encode_integer() (SequencePreprocessor static method) encode_one_hot() (SequencePreprocessor static method) encode_pae() (StructurePreprocessor method) encode_pdb() (StructurePreprocessor method) entry epistasis() (SeqMutPlot method) eval() (AAclust method) (AAclustPlot static method) (AAMut method) (AAPred method) (AAPredPlot static method) (CPP method) (CPPGrid method) (CPPPlot static method) (dPULearn static method) (dPULearnPlot static method) (ReliabilityModel method) (SeqMut method) (SeqOpt method) (ShapModel method) (TreeModel method)

exp_value (ShapModel attribute) explain_features() (in module aaanalysis.pipe) explore() (CPPStructurePlot method) extend_alphabet() (NumericalFeature static method)

F

feat_importance (TreeModel attribute) feat_importance_std (TreeModel attribute) feature feature impact feature importance feature pruning feature selection feature simplification feature() (CPPPlot method) feature_importances_ (TreeModel property) feature_map() (CPPPlot method) feature_matrix() (NumericalFeature static method) (SequenceFeature method)

fetch_alphafold() (StructurePreprocessor method) fetch_embeddings() (EmbeddingPreprocessor method) fetch_uniprot() (AnnotationPreprocessor method) filter_correlation() (NumericalFeature static method) filter_coverage() (AAclust method) filter_seq (class in aaanalysis) find_features() (in module aaanalysis.pipe) fit() (AAclust method) (AAPred method) (dPULearn method) (ReliabilityModel method) (ShapModel method) (TreeModel method)

G

genealogy() (SeqOptPlot method) get_aa_window() (SequencePreprocessor static method) get_conservation() (AAlogo static method) get_df_feat() (SequenceFeature method) get_df_logo() (AAlogo method) get_df_logo_info() (AAlogo method) get_df_parts() (SequenceFeature method) get_df_parts_from_windows() (SequenceFeature static method) get_df_pos() (SequenceFeature static method) get_domains() (StructurePreprocessor method) get_dssp() (StructurePreprocessor method)

get_feature_descriptions() (SequenceFeature static method) get_feature_names() (SequenceFeature static method) get_feature_positions() (SequenceFeature static method) get_features() (SequenceFeature method) get_labels_ovo() (SequenceFeature static method) get_labels_ovr() (SequenceFeature static method) get_labels_quantile() (SequenceFeature static method) get_labels_tiered() (SequenceFeature static method) get_parts() (NumericalFeature static method) get_seq_kws() (SequenceFeature method) get_sliding_aa_window() (SequencePreprocessor static method) get_split_kws() (SequenceFeature static method)

H

heatmap() (CPPPlot method)

hypervolume() (SeqOptPlot method)

I

ingest() (AnnotationPreprocessor method) interactive() (CPPStructurePlot method)

is_medoid_ (AAclust attribute) is_selected_ (TreeModel attribute)

K

kmer_composition() (SequenceFeature method)

L

labels_ (AAclust attribute) (dPULearn attribute) labels_centers_ (AAclust attribute) labels_medoids_ (AAclust attribute)

last_filter_stats_ (CPP attribute) list_models_ (TreeModel attribute) load_dataset (class in aaanalysis) load_features (class in aaanalysis) load_scales (class in aaanalysis)

M

map_structure() (CPPStructurePlot method) medoid medoid_ind_ (AAclust attribute) medoid_names_ (AAclust attribute) medoids() (AAclustPlot method) medoids_ (AAclust attribute)

model (AAclust attribute) module aaanalysis.py multi_logo() (AAlogoPlot method) mutate() (SeqMut method) mutation_landscape() (SeqMutPlot method) mutation_map() (SeqOptPlot method)

N

n_clusters (AAclust attribute) name_clusters() (AAclust static method)

norm_params_ (EmbeddingPreprocessor attribute) numerical CPP NumericalFeature (class in aaanalysis)

O

obtain_samples() (in module aaanalysis.pipe)

ood_hist() (ReliabilityModelPlot static method) options (in module aaanalysis)

P

P1 anchor pad_parts() (SequencePreprocessor static method) parallel_coordinates() (SeqOptPlot method) pareto_front() (SeqOptPlot method) part pca() (dPULearnPlot static method) Plot class plot_combined() (CPPStructurePlot method) plot_eval() (in module aaanalysis.pipe) plot_gcfs() (in module aaanalysis) plot_get_cdict() (in module aaanalysis) plot_get_clist() (in module aaanalysis) plot_get_cmap() (in module aaanalysis) plot_legend() (in module aaanalysis) plot_linked() (CPPStructurePlot method) plot_settings() (in module aaanalysis)

pool_embeddings() (EmbeddingPreprocessor method) pre_select_scales() (AAclust method) predict() (AAPred method) (ReliabilityModel method) predict_group() (AAPredPlot static method) predict_proba() (TreeModel method) predict_sample() (AAPredPlot static method) predict_samples() (in module aaanalysis.pipe) prediction level profile() (CPPPlot method) project() (dPULearn method) protein level prune_by_correlation() (SequenceFeature method) prune_by_variance() (SequenceFeature method) pseudo-scale PU labels

R

ranking() (CPPPlot method) (ReliabilityModelPlot static method) read_fasta (class in aaanalysis) redundancy reduction reference construction reference group reference window register_feature() (AnnotationPreprocessor method) relational / interaction reliability_diagram() (ReliabilityModelPlot static method)

ReliabilityModel (class in aaanalysis) ReliabilityModelPlot (class in aaanalysis) reliable negative residue level residue_mutation_impact() (SeqMutPlot method) run() (AAMut method) (CPP method) (CPPGrid method) (SeqOpt method) run_composit() (CPP method) run_num() (CPP method)

S

sample_benchmark_set() (AAWindowSampler method) sample_different_protein() (AAWindowSampler method) sample_motif_matched() (AAWindowSampler method) sample_same_protein() (AAWindowSampler method) sample_synthetic() (AAWindowSampler method) scale scale_composition() (SequenceFeature method) scale_ranking() (AAMutPlot method) scan() (SeqMut method) scan_motif (class in aaanalysis) select_features() (TreeModel method) select_proteins() (AAclust method) select_scales() (AAclust method)

SeqMut (class in aaanalysis) SeqMutPlot (class in aaanalysis) SeqOpt (class in aaanalysis) SeqOptPlot (class in aaanalysis) SequenceFeature (class in aaanalysis) SequencePreprocessor (class in aaanalysis) shap_values (ShapModel attribute) ShapModel (class in aaanalysis) simplify() (CPP method) single_logo() (AAlogoPlot method) split StructurePreprocessor (class in aaanalysis) substitution_matrix() (AAMutPlot method) suggest() (SeqMut method)

T

test group to_df_seq() (AnnotationPreprocessor method) to_fasta (class in aaanalysis)

Tool TreeModel (class in aaanalysis) trust_map() (ReliabilityModelPlot static method)

U

unit of comparison

update_seq_size() (CPPPlot method)

V

variant_impact() (SeqMutPlot method)

W

window

Wrapper

Δ

ΔCPP