Index

_

__getattr__() (modelarchive.modelcif.access.MABlock method)

__iter__() (modelarchive.modelcif.access.MABlock method)

A

add_category() (in module modelarchive.modelcif.edit) (modelarchive.modelcif.access.MABlock method) add_column() (in module modelarchive.modelcif.edit) add_data_from_json_files() (in module modelarchive.modelcif.fix_af3)

add_per_residue_plddt() (in module modelarchive.modelcif.fix_af3) add_row_to_category_dict() (in module modelarchive.modelcif.ma_dict) add_rows() (in module modelarchive.modelcif.edit) add_to_category() (modelarchive.modelcif.access.MABlock method) assemble_modelcif_software() (in module modelarchive.modelcif.fix_af2)

B

block (modelarchive.modelcif.access.MABlock attribute)

C

category (modelarchive.modelcif.edit.NotFoundCategoryError attribute) (modelarchive.modelcif.fix_af3.NotIdentifiedContextRecordError attribute) (modelarchive.modelcif.fix_af3.NotIdentifiedDuplicatedRecordError attribute) (modelarchive.modelcif.fix_af3.NotIdentifiedSingleRecordError attribute)

D

doc (modelarchive.modelcif.access.MABlock attribute)

E

entry_status (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

entry_version (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

F

find_strict() (modelarchive.modelcif.access.MABlock method) first_appearance (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) fix_citation() (in module modelarchive.modelcif.fix_af3)

fix_model_name() (in module modelarchive.modelcif.fix_af3) fix_modelcif_issues() (in module modelarchive.modelcif.fix_af3) fix_protocol() (in module modelarchive.modelcif.fix_af3) fix_software_location() (in module modelarchive.modelcif.fix_af3)

G

get() (modelarchive.databases.uniprotkb.UniProtKBEntryCache method) get_af2_config() (in module modelarchive.modelcif.fix_af2) get_af2_sequence_dbs() (in module modelarchive.modelcif.fix_af2) get_af2_software() (in module modelarchive.modelcif.fix_af2) get_and_check_ncbi_data() (in module modelarchive.databases.ncbi) get_and_check_ncbi_species_names() (in module modelarchive.databases.ncbi) get_category() (modelarchive.modelcif.access.MABlock method) get_cf_config() (in module modelarchive.modelcif.fix_af2) get_cf_db_versions() (in module modelarchive.modelcif.fix_af2) get_cf_sequence_dbs() (in module modelarchive.modelcif.fix_af2)

get_cf_sw_plus_params() (in module modelarchive.modelcif.fix_af2) get_colabfold_software() (in module modelarchive.modelcif.fix_af2) get_galaxy_software() (in module modelarchive.modelcif.fix_af2) get_localcolabfold_software() (in module modelarchive.modelcif.fix_af2) get_mmseqs2_software() (in module modelarchive.modelcif.fix_af2) get_sequence() (in module modelarchive.modelcif.fix_af2) (modelarchive.modelcif.access.MABlock method) get_table() (in module modelarchive.modelcif.access) GlobalConfRankMultimer (class in modelarchive.modelcif.fix_af2) GlobalIpTM (class in modelarchive.modelcif.fix_af2)

H

has_category() (modelarchive.modelcif.access.MABlock method)

I

item (modelarchive.modelcif.edit.NotFoundItemError attribute) (modelarchive.modelcif.fix_af3.NotIdentifiedContextRecordError attribute) (modelarchive.modelcif.fix_af3.NotIdentifiedSingleRecordError attribute)

L

last_change (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

last_seq_change (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

M

MABlock (class in modelarchive.modelcif.access) make_copy_value_in_row() (in module modelarchive.modelcif.edit) make_res_per_chain_counter() (in module modelarchive.modelcif.edit) match_sequence() (modelarchive.databases.uniprotkb.UniProtKBEntryCache method) modelarchive.databases.ncbi module modelarchive.databases.uniprotkb module modelarchive.modelcif.access module modelarchive.modelcif.edit module modelarchive.modelcif.fix_af2 module

modelarchive.modelcif.fix_af3 module modelarchive.modelcif.ma_dict module module modelarchive.databases.ncbi modelarchive.databases.uniprotkb modelarchive.modelcif.access modelarchive.modelcif.edit modelarchive.modelcif.fix_af2 modelarchive.modelcif.fix_af3 modelarchive.modelcif.ma_dict move_category() (in module modelarchive.modelcif.edit) MoveIdxToFarError

N

name (modelarchive.modelcif.fix_af2.GlobalConfRankMultimer attribute) (modelarchive.modelcif.fix_af2.GlobalIpTM attribute) ncbi_taxid (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) NotFoundCategoryError NotFoundError

NotFoundItemError NotIdentifiedContextRecordError NotIdentifiedDuplicatedRecordError NotIdentifiedRecordError NotIdentifiedSingleRecordError

O

organism_species (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

P

polymer_targets (modelarchive.modelcif.access.MABlock property)

S

seq_version (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) seqlen (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) software (modelarchive.modelcif.fix_af2.GlobalConfRankMultimer attribute) (modelarchive.modelcif.fix_af2.GlobalIpTM attribute)

sort() (in module modelarchive.modelcif.edit) source (modelarchive.modelcif.access.MABlock attribute) store_as_modelcif() (in module modelarchive.modelcif.fix_af2)

T

targets (modelarchive.modelcif.access.MABlock property) to_json() (modelarchive.databases.uniprotkb.UniProtKBEntry method) (modelarchive.databases.uniprotkb.UniProtKBEntryCache method)

translate_upkb_date_string() (in module modelarchive.databases.uniprotkb)

U

UniProtKBEntry (class in modelarchive.databases.uniprotkb) UniProtKBEntryCache (class in modelarchive.databases.uniprotkb) unp_ac (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

unp_crc64 (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) unp_details_full (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) unp_id (modelarchive.databases.uniprotkb.UniProtKBEntry attribute) unp_seq (modelarchive.databases.uniprotkb.UniProtKBEntry attribute)

W

write_file() (modelarchive.modelcif.access.MABlock method)