Index

A

add_domain() (alphafragment.classes.Protein method) add_fragment() (alphafragment.classes.Protein method) add_fragment_sequences() (alphafragment.classes.Protein method) alphafragment.alphafold_db_domain_identification module alphafragment.classes module alphafragment.domain_compilation module alphafragment.fragment_file_creation module

alphafragment.fragment_protein module alphafragment.fragmentation_methods module alphafragment.long_domains module alphafragment.plot_fragments module alphafragment.process_proteins_csv module alphafragment.uniprot_fetch module

B

break_in_half() (in module alphafragment.fragmentation_methods)

C

calculate_tick_freq() (in module alphafragment.plot_fragments)

check_valid_cutpoint() (in module alphafragment.fragmentation_methods) compile_domains() (in module alphafragment.domain_compilation)

D

Domain (class in alphafragment.classes)

domains_from_manual_pae() (in module alphafragment.process_proteins_csv) draw_label() (in module alphafragment.plot_fragments)

F

fetch_uniprot_info() (in module alphafragment.uniprot_fetch) find_domain_by_res() (in module alphafragment.alphafold_db_domain_identification) find_domains_from_pae() (in module alphafragment.alphafold_db_domain_identification) find_next_start() (in module alphafragment.fragmentation_methods)

find_uniprot_domains() (in module alphafragment.uniprot_fetch) find_user_specified_domains() (in module alphafragment.process_proteins_csv) fragment_protein() (in module alphafragment.fragment_protein) fragments_from_csv() (in module alphafragment.process_proteins_csv)

G

get_protein_combinations() (in module alphafragment.fragment_file_creation)

H

handle_long_domains() (in module alphafragment.long_domains)

I

initialize_proteins_from_csv() (in module alphafragment.process_proteins_csv)

M

merge_overlapping_domains() (in module alphafragment.fragmentation_methods) module alphafragment.alphafold_db_domain_identification alphafragment.classes alphafragment.domain_compilation alphafragment.fragment_file_creation alphafragment.fragment_protein alphafragment.fragmentation_methods alphafragment.long_domains alphafragment.plot_fragments alphafragment.process_proteins_csv alphafragment.uniprot_fetch

O

output_fastas() (in module alphafragment.fragment_file_creation)

output_pulldown() (in module alphafragment.fragment_file_creation)

P

plot_domain() (in module alphafragment.plot_fragments) plot_fragment() (in module alphafragment.plot_fragments)

plot_fragmentation_output() (in module alphafragment.plot_fragments) Protein (class in alphafragment.classes) ProteinSubsection (class in alphafragment.classes)

R

read_afdb_json() (in module alphafragment.alphafold_db_domain_identification)

recursive_fragmentation() (in module alphafragment.fragmentation_methods) reinitialize_proteins_from_csv() (in module alphafragment.process_proteins_csv)

U

update_csv_with_fragments() (in module alphafragment.process_proteins_csv)

V

validate_fragmentation_parameters() (in module alphafragment.fragmentation_methods)