Index

_

__init__() (ProtACon.config_parser.Config method) (ProtACon.modules.basics.CA_Atom method) (ProtACon.modules.utils.Logger method)

A

append_frequency_and_total() (in module ProtACon.manage_tot_ds)

average_matrices_together() (in module ProtACon.modules.attention)

B

binarize_contact_map() (in module ProtACon.modules.contact)

C

CA_Atom (class in ProtACon.modules.basics) clean_attention() (in module ProtACon.modules.attention) compute_att_align_on_heads() (in module ProtACon.modules.attention)

compute_att_align_on_layers() (in module ProtACon.modules.attention) compute_attention_similarity() (in module ProtACon.modules.attention) Config (class in ProtACon.config_parser) create() (in module ProtACon.manage_tot_ds)

D

distance_between_atoms() (in module ProtACon.modules.contact)

download_pdb() (in module ProtACon.modules.basics)

E

extract_CA_atoms() (in module ProtACon.modules.basics)

F

fetch_pdb_entries() (in module ProtACon.modules.basics)

find_best_nrows() (in module ProtACon.modules.plot_functions)

G

generate_distance_map() (in module ProtACon.modules.contact) get_amino_acid_pos() (in module ProtACon.modules.attention) get_attention_to_amino_acid() (in module ProtACon.modules.attention) get_cutoffs() (ProtACon.config_parser.Config method)

get_logger() (ProtACon.modules.utils.Logger method) get_model_structure() (in module ProtACon.modules.basics) get_paths() (ProtACon.config_parser.Config method) get_proteins() (ProtACon.config_parser.Config method) get_sequence_to_tokenize() (in module ProtACon.modules.basics)

I

include_att_to_missing_aa() (in module ProtACon.modules.attention)

K

keep_nonzero() (in module ProtACon.manage_tot_ds)

L

load_Bert() (in module ProtACon.modules.basics)

Loading() (in module ProtACon.modules.utils) Logger (class in ProtACon.modules.utils)

M

main() (in module ProtACon.align_with_contact) (in module ProtACon.compute_on_set) (in module ProtACon.preprocess) (in module ProtACon.process_contact) module ProtACon.align_with_contact ProtACon.compute_on_set ProtACon.config_parser ProtACon.manage_tot_ds ProtACon.modules.attention ProtACon.modules.basics ProtACon.modules.contact ProtACon.modules.plot_functions ProtACon.modules.utils ProtACon.plotting ProtACon.preprocess ProtACon.process_contact

N

normalize_array() (in module ProtACon.modules.basics)

P

plot_attention_matrices() (in module ProtACon.modules.plot_functions) plot_attention_to_amino_acids_alone() (in module ProtACon.modules.plot_functions) plot_attention_to_amino_acids_together() (in module ProtACon.modules.plot_functions) plot_bars() (in module ProtACon.modules.plot_functions) plot_distance_and_contact() (in module ProtACon.modules.plot_functions) plot_heatmap() (in module ProtACon.modules.plot_functions) plot_on_chain() (in module ProtACon.plotting) plot_on_set() (in module ProtACon.plotting) ProtACon.align_with_contact module ProtACon.compute_on_set module ProtACon.config_parser module ProtACon.manage_tot_ds module

ProtACon.modules.attention module ProtACon.modules.basics module ProtACon.modules.contact module ProtACon.modules.plot_functions module ProtACon.modules.utils module ProtACon.plotting module ProtACon.preprocess module ProtACon.process_contact module

S

sum_attention_on_columns() (in module ProtACon.modules.attention)

sum_attention_on_heads() (in module ProtACon.modules.attention)

T

threshold_attention() (in module ProtACon.modules.attention)

Timer() (in module ProtACon.modules.utils)

U

update() (in module ProtACon.manage_tot_ds)