Index

A

AAS (in module polyclonal.alphabets) AAS_WITHGAP (in module polyclonal.alphabets) AAS_WITHSTOP (in module polyclonal.alphabets) AAS_WITHSTOP_WITHGAP (in module polyclonal.alphabets) activity_wt_barplot() (in module polyclonal.plot) (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method)

activity_wt_df (polyclonal.polyclonal.Polyclonal property) (polyclonal.polyclonal_collection.PolyclonalCollection property) activity_wt_df_replicates (polyclonal.polyclonal_collection.PolyclonalCollection property) alphabet (polyclonal.polyclonal.Polyclonal attribute) (polyclonal.polyclonal_collection.PolyclonalCollection attribute)

B

biochem_order_aas() (in module polyclonal.alphabets)

C

color_gradient_hex() (in module polyclonal.plot) corr_heatmap() (in module polyclonal.plot) create_bootstrap_sample() (in module polyclonal.polyclonal_collection) curve_specs_df (polyclonal.polyclonal.Polyclonal property) (polyclonal.polyclonal_collection.PolyclonalCollection property)

curve_specs_df_replicates (polyclonal.polyclonal_collection.PolyclonalCollection property) curves_plot() (in module polyclonal.plot) (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method)

D

data_to_fit (polyclonal.polyclonal.Polyclonal attribute) default_avg_to_plot (polyclonal.polyclonal_collection.PolyclonalCollection attribute) DEFAULT_NEGATIVE_COLOR (in module polyclonal.plot)

DEFAULT_POSITIVE_COLORS (in module polyclonal.plot) DEFAULT_SCIPY_MINIMIZE_KWARGS (polyclonal.polyclonal.Polyclonal attribute) descriptor_names (polyclonal.polyclonal_collection.PolyclonalCollection attribute) distance_matrix (polyclonal.polyclonal.Polyclonal attribute)

E

epitope_colors (polyclonal.polyclonal.Polyclonal attribute) (polyclonal.polyclonal_collection.PolyclonalCollection attribute) epitope_harmonized_model() (polyclonal.polyclonal.Polyclonal method)

epitopes (polyclonal.polyclonal.Polyclonal attribute) (polyclonal.polyclonal_collection.PolyclonalCollection attribute) extract_atom_locations() (in module polyclonal.pdb_utils)

F

filter_variants_by_seen_muts() (polyclonal.polyclonal.Polyclonal method) fit() (polyclonal.polyclonal.Polyclonal method)

fit_models() (in module polyclonal.polyclonal_collection) (polyclonal.polyclonal_collection.PolyclonalBootstrap method)

H

hill_coefficient_df (polyclonal.polyclonal.Polyclonal property) (polyclonal.polyclonal_collection.PolyclonalCollection property)

hill_coefficient_df_replicates (polyclonal.polyclonal_collection.PolyclonalCollection property)

I

icXX() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method)

icXX_replicates() (polyclonal.polyclonal_collection.PolyclonalCollection method) inter_residue_distances() (in module polyclonal.pdb_utils)

L

lineplot_and_heatmap() (in module polyclonal.plot)

M

model_descriptors (polyclonal.polyclonal_collection.PolyclonalCollection attribute) models (polyclonal.polyclonal_collection.PolyclonalCollection attribute) module polyclonal polyclonal.alphabets polyclonal.pdb_utils polyclonal.plot polyclonal.polyclonal polyclonal.polyclonal_collection polyclonal.utils mut_escape_corr() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_escape_corr_heatmap() (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_escape_df (polyclonal.polyclonal.Polyclonal property) (polyclonal.polyclonal_collection.PolyclonalCollection property) mut_escape_df_replicates (polyclonal.polyclonal_collection.PolyclonalCollection property)

mut_escape_df_w_model_values (polyclonal.polyclonal_collection.PolyclonalCollection property) mut_escape_pdb_b_factor() (polyclonal.polyclonal.Polyclonal method) mut_escape_plot() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_escape_site_summary_df() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_escape_site_summary_df_replicates() (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_icXX_df() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_icXX_df_replicates() (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_icXX_df_w_model_values() (polyclonal.polyclonal_collection.PolyclonalCollection method) mut_icXX_plot() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) MutationParser (class in polyclonal.utils) mutations (polyclonal.polyclonal.Polyclonal attribute) mutations_times_seen (polyclonal.polyclonal.Polyclonal attribute)

N

n_models_by_site (polyclonal.polyclonal_collection.PolyclonalCollection attribute) n_threads (polyclonal.polyclonal_collection.PolyclonalBootstrap attribute)

non_neutralized_frac_df (polyclonal.polyclonal.Polyclonal property) (polyclonal.polyclonal_collection.PolyclonalCollection property) non_neutralized_frac_df_replicates (polyclonal.polyclonal_collection.PolyclonalCollection property)

P

parse_mut() (polyclonal.utils.MutationParser method) polyclonal module Polyclonal (class in polyclonal.polyclonal) polyclonal.alphabets module polyclonal.pdb_utils module polyclonal.plot module polyclonal.polyclonal module polyclonal.polyclonal_collection module

polyclonal.utils module PolyclonalAverage (class in polyclonal.polyclonal_collection) PolyclonalBootstrap (class in polyclonal.polyclonal_collection) PolyclonalCollection (class in polyclonal.polyclonal_collection) PolyclonalCollectionFitError PolyclonalConcentrationError PolyclonalFitError PolyclonalHarmonizeError prob_escape() (polyclonal.polyclonal.Polyclonal method) (polyclonal.polyclonal_collection.PolyclonalCollection method) prob_escape_replicates() (polyclonal.polyclonal_collection.PolyclonalCollection method)

R

reassign_b_factor() (in module polyclonal.pdb_utils)

regions (polyclonal.polyclonal_collection.PolyclonalCollection attribute) root_polyclonal (polyclonal.polyclonal_collection.PolyclonalBootstrap attribute)

S

sequential_integer_sites (polyclonal.polyclonal.Polyclonal attribute) (polyclonal.polyclonal_collection.PolyclonalCollection attribute) shift_mut_site() (in module polyclonal.utils) site_level_model() (polyclonal.polyclonal.Polyclonal method)

site_level_variants() (in module polyclonal.utils) sites (polyclonal.polyclonal.Polyclonal attribute) (polyclonal.polyclonal_collection.PolyclonalCollection attribute) spatial_distances (polyclonal.polyclonal.Polyclonal attribute)

T

TAB10_COLORS_NOGRAY (in module polyclonal.plot)

tidy_to_corr() (in module polyclonal.utils)

U

unique_descriptor_names (polyclonal.polyclonal_collection.PolyclonalCollection attribute)

W

wts (polyclonal.polyclonal.Polyclonal attribute)