Index

A

add_structure() (PANDORA.Database.Database.Database method) align() (PANDORA.Pandora.Pandora.Pandora method)

anchor_contacts() (PANDORA.Pandora.Pandora.Pandora method) archive_and_remove() (in module PANDORA.Wrapper.Wrapper)

C

calc_anchor_contacts() (PANDORA.PMHC.PMHC.Target method) (PANDORA.PMHC.PMHC.Template method) calc_anchors() (PANDORA.PMHC.PMHC.Template method) calc_contacts() (PANDORA.PMHC.PMHC.Target method) (PANDORA.PMHC.PMHC.Template method) check_allele_name() (PANDORA.PMHC.PMHC.Target method) (PANDORA.PMHC.PMHC.Template method) clean_MHCI_file() (PANDORA.Database.Database.Database method)

clean_MHCII_file() (PANDORA.Database.Database.Database method) construct_blast_db() (PANDORA.Database.Database.Database method) construct_both_blast_db() (PANDORA.Database.Database.Database method) construct_database() (PANDORA.Database.Database.Database method) Contacts (class in PANDORA.Contacts.Contacts) copy_template() (PANDORA.Pandora.Pandora.Pandora method) create_db_folders() (in module PANDORA.Database.Database) create_initial_model() (PANDORA.Pandora.Pandora.Pandora method)

D

Database (class in PANDORA.Database.Database)

download_data() (PANDORA.Database.Database.Database method)

F

fetch_database() (in module PANDORA.Database.Database) fill_allele_seq_info() (PANDORA.PMHC.PMHC.Target method)

find_chain_contacts() (PANDORA.Contacts.Contacts.Contacts method) find_pept_chain_contacts() (PANDORA.Contacts.Contacts.Contacts method) find_template() (PANDORA.Pandora.Pandora.Pandora method)

G

get_pdb_path() (PANDORA.PMHC.PMHC.Template method)

I

info() (PANDORA.PMHC.PMHC.Target method) (PANDORA.PMHC.PMHC.Template method)

install_database() (in module PANDORA.Database.Database)

L

load() (in module PANDORA.Database.Database)

M

make_output_dir() (PANDORA.PMHC.PMHC.Target method) model() (PANDORA.Pandora.Pandora.Pandora method) module PANDORA.Contacts.Contacts PANDORA.Database PANDORA.Database.Database PANDORA.Pandora PANDORA.Pandora.Pandora PANDORA.PMHC PANDORA.PMHC.PMHC PANDORA.Wrapper PANDORA.Wrapper.Wrapper

P

Pandora (class in PANDORA.Pandora.Pandora) PANDORA.Contacts.Contacts module PANDORA.Database module PANDORA.Database.Database module PANDORA.Pandora module PANDORA.Pandora.Pandora module

PANDORA.PMHC module PANDORA.PMHC.PMHC module PANDORA.Wrapper module PANDORA.Wrapper.Wrapper module parse_pdb() (PANDORA.PMHC.PMHC.Template method) PMHC (class in PANDORA.PMHC.PMHC) prep_collective_output_dir() (PANDORA.Wrapper.Wrapper.Wrapper method)

R

remove_B2M() (PANDORA.Pandora.Pandora.Pandora method) remove_structure() (PANDORA.Database.Database.Database method)

retrieve_MHC_refseq() (PANDORA.PMHC.PMHC.Target method) run_case() (in module PANDORA.Wrapper.Wrapper) run_modeller() (PANDORA.Pandora.Pandora.Pandora method)

S

save() (PANDORA.Database.Database.Database method)

set_reverse() (PANDORA.Database.Database.Database method) show() (PANDORA.Contacts.Contacts.Contacts method)

T

Target (class in PANDORA.PMHC.PMHC)

Template (class in PANDORA.PMHC.PMHC)

U

update_ref_sequences() (PANDORA.Database.Database.Database method)

W

Wrapper (class in PANDORA.Wrapper.Wrapper) write_db_into_fasta() (PANDORA.Database.Database.Database method)

write_ini_script() (PANDORA.Pandora.Pandora.Pandora method) write_modeller_script() (PANDORA.Pandora.Pandora.Pandora method)