Index

_

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

A

aa_comparison() (AAMutPlot 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 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_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 correlation() (AAclustPlot method) CPP (class in aaanalysis) CPPGrid (class in aaanalysis) CPPPlot (class in aaanalysis)

D

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

df_scales (CPP attribute) df_seq dict_num 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 eval() (AAclust method) (AAclustPlot static method) (AAMut method) (CPP method) (CPPGrid method) (CPPPlot static method) (dPULearn static method) (dPULearnPlot static method) (SeqMut method) (ShapModel method) (TreeModel method)

exp_value (ShapModel attribute) 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() (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) fit() (AAclust method) (dPULearn method) (ShapModel method) (TreeModel method)

G

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)

I

ingest() (AnnotationPreprocessor method)

is_medoid_ (AAclust attribute) is_selected_ (TreeModel attribute)

L

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

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

M

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)

N

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

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

O

options (in module aaanalysis)

P

P1 anchor part pca() (dPULearnPlot static method) Plot class 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_rank() (in module aaanalysis)

plot_settings() (in module aaanalysis) pool_embeddings() (EmbeddingPreprocessor method) predict_proba() (TreeModel method) prediction level profile() (CPPPlot method) protein level prune_by_correlation() (SequenceFeature method) prune_by_variance() (SequenceFeature method) pseudo-scale PU labels

R

ranking() (CPPPlot method) read_fasta (class in aaanalysis) redundancy reduction reference construction reference group reference window register_feature() (AnnotationPreprocessor method)

relational / interaction reliable negative residue level residue_mutation_impact() (SeqMutPlot method) run() (AAMut method) (CPP method) (CPPGrid 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_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) SequenceFeature (class in aaanalysis) SequencePreprocessor (class in aaanalysis) shap_values (ShapModel attribute) ShapModel (class in aaanalysis) simplify() (CPP method) single_logo() (AAlogoPlot method) split split_kws (CPP attribute) 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)

U

unit of comparison

update_seq_size() (CPPPlot method)

W

window

Wrapper

Δ

ΔCPP