Index

_

_check_and_auto_download() (src.pdb_filter.PDBFilter method)

_check_dataframe() (src.structure_filter.StructureLevelFilter method)

A

alignment_tool (src.dataset_creator.DatasetCreator attribute) (src.polymer_level_filter.PolymerLevelFilter attribute) all_characters_are_n() (src.pdb_filter.PDBFilter method) apply_exptl_method_filter() (src.structure_filter.StructureLevelFilter method), [1] apply_filter_on_df() (src.polymer_level_filter.PolymerLevelFilter method), [1] apply_filters() (src.dataset_creator.DatasetCreator method) (src.structure_filter.StructureLevelFilter method), [1] apply_filters_on_list() (src.polymer_level_filter.PolymerLevelFilter method), [1] apply_filters_on_pdb_id() (src.polymer_level_filter.PolymerLevelFilter method), [1] apply_pdbx_keywords_filter() (src.structure_filter.StructureLevelFilter method), [1]

apply_polymer_entity_count_RNA_filter() (src.structure_filter.StructureLevelFilter method), [1] apply_polymer_entity_instance_count_filter() (src.structure_filter.StructureLevelFilter method), [1] apply_polymer_filters() (src.dataset_creator.DatasetCreator method) apply_resolution_filter() (src.structure_filter.StructureLevelFilter method), [1] apply_selected_polymer_entity_types_filter() (src.structure_filter.StructureLevelFilter method), [1] apply_structure_filters() (src.dataset_creator.DatasetCreator method) apply_year_range_filter() (src.structure_filter.StructureLevelFilter method), [1] auto_download (src.dataset_creator.DatasetCreator attribute) (src.pdb_filter.PDBFilter attribute) (src.polymer_level_filter.PolymerLevelFilter attribute)

C

check_polymer_type() (src.pdb_filter.PDBFilter method), [1] clean_tblout_path (src.dataset_creator.DatasetCreator attribute) cmd (src.dataset_creator.DatasetCreator attribute) cmscan_path (src.dataset_creator.DatasetCreator attribute) contacts_from_pdb() (in module src.utils)

create_combined_fasta_file() (src.polymer_level_filter.PolymerLevelFilter method), [1] create_final_fasta_file() (src.dataset_creator.DatasetCreator method), [1] (src.polymer_level_filter.PolymerLevelFilter method), [1] create_sequence_identity_mat_clustal() (src.polymer_level_filter.PolymerLevelFilter method), [1] create_sequence_identity_mat_emboss() (src.polymer_level_filter.PolymerLevelFilter method), [1]

D

data (src.dataset_creator.DatasetCreator attribute) DATA_API_BASE_URI_GRAPHQL (src.dataset_download.DatasetDownload attribute), [1] data_path (src.dataset_download.DatasetDownload attribute) DATA_PATH (src.polymer_level_filter.PolymerLevelFilter attribute) dataset_files (src.dataset_creator.DatasetCreator attribute) dataset_name (src.dataset_creator.DatasetCreator attribute) DatasetCreator (class in src.dataset_creator) DatasetDownload (class in src.dataset_download) dend (src.dataset_creator.DatasetCreator attribute) (src.dataset_download.DatasetDownload attribute)

df (src.dataset_download.DatasetDownload attribute) download_all (src.dataset_creator.DatasetCreator attribute) download_fasta_file() (in module src.utils) download_fasta_files() (in module src.utils) download_pdb_file() (in module src.utils) download_pdb_files() (in module src.utils) dstart (src.dataset_creator.DatasetCreator attribute) (src.dataset_download.DatasetDownload attribute)

E

e_value_cmscan (src.dataset_creator.DatasetCreator attribute) exptl_method (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute)

extract_sequence_from_combined_fasta() (in module src.utils) extract_sequences_for_pdb_ids() (in module src.utils)

F

final_chain_ids_path (src.dataset_creator.DatasetCreator attribute) final_fams_path (src.dataset_creator.DatasetCreator attribute)

final_fasta_path (src.dataset_creator.DatasetCreator attribute) final_pdb_list_path (src.dataset_creator.DatasetCreator attribute)

G

generate_contact_map_from_mmcif_file() (in module src.utils) generate_contact_map_from_pdb_file() (in module src.utils) get_data_as_df() (src.dataset_download.DatasetDownload method), [1] get_data_for_each_pdb() (src.dataset_download.DatasetDownload method), [1] get_final_df() (src.dataset_creator.DatasetCreator method) get_final_fam_pdb_chain_csv() (in module src.utils) get_final_families() (src.dataset_creator.DatasetCreator method) get_final_pdb_list() (src.dataset_creator.DatasetCreator method)

get_graphql_query() (src.dataset_download.DatasetDownload method), [1] get_pdb_list() (src.dataset_download.DatasetDownload method), [1] get_polymer_filtered_df() (src.dataset_creator.DatasetCreator method) get_search_api_query() (src.dataset_download.DatasetDownload method), [1] get_sequence_identity_df_clustal() (src.polymer_level_filter.PolymerLevelFilter method), [1] get_sequence_identity_df_emboss() (src.polymer_level_filter.PolymerLevelFilter method), [1] get_structure_filtered_df() (src.dataset_creator.DatasetCreator method) get_without_filter_df() (src.dataset_creator.DatasetCreator method)

M

main() (in module src.dataset_creator) module src src.columns src.dataset_creator src.dataset_download src.pdb_filter src.polymer_level_filter src.structure_filter src.utils

P

parse_fasta() (in module src.utils) pdb_file (src.pdb_filter.PDBFilter attribute) pdb_id (src.pdb_filter.PDBFilter attribute) pdb_parser (src.pdb_filter.PDBFilter attribute) (src.polymer_level_filter.PolymerLevelFilter attribute) PDBFilter (class in src.pdb_filter) pdbx_keywords (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute)

polymer_entity_count_RNA (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute) polymer_entity_instance_count (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute) polymer_level_filter (src.dataset_creator.DatasetCreator attribute) polymer_type (src.dataset_creator.DatasetCreator attribute) (src.pdb_filter.PDBFilter attribute) (src.polymer_level_filter.PolymerLevelFilter attribute) PolymerLevelFilter (class in src.polymer_level_filter)

R

rcsb_entity_polymer_type (src.dataset_creator.DatasetCreator attribute) (src.dataset_download.DatasetDownload attribute) remove_backbone_contacts() (in module src.utils) resolution (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute)

rfam_cm_path (src.dataset_creator.DatasetCreator attribute) run() (src.dataset_creator.DatasetCreator method) run_cmscan() (src.dataset_creator.DatasetCreator method)

S

save (src.dataset_creator.DatasetCreator attribute) save_data_as_csv() (src.dataset_download.DatasetDownload method), [1] save_dataframe() (src.dataset_creator.DatasetCreator method), [1] save_filtered_data() (src.dataset_creator.DatasetCreator method) save_pdb_list() (src.dataset_creator.DatasetCreator method), [1] save_sequences() (in module src.utils) SEARCH_API_BASE_URI (src.dataset_download.DatasetDownload attribute), [1] selected_polymer_entity_types (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute) sequence_identity (src.dataset_creator.DatasetCreator attribute) (src.polymer_level_filter.PolymerLevelFilter attribute) sequence_identity_mat_file (src.polymer_level_filter.PolymerLevelFilter attribute) sequence_identity_mat_path (src.polymer_level_filter.PolymerLevelFilter attribute) sequence_length (src.dataset_creator.DatasetCreator attribute) (src.pdb_filter.PDBFilter attribute) (src.polymer_level_filter.PolymerLevelFilter attribute) src module

src.columns module src.dataset_creator module src.dataset_download module src.pdb_filter module src.polymer_level_filter module src.structure_filter module src.utils module structure_determination_methodology (src.dataset_creator.DatasetCreator attribute) (src.dataset_download.DatasetDownload attribute) structure_dict (src.pdb_filter.PDBFilter attribute) structure_filter (src.dataset_creator.DatasetCreator attribute) StructureLevelFilter (class in src.structure_filter)

T

tblout (src.dataset_creator.DatasetCreator attribute)

W

write_sequences_to_files() (in module src.utils)

Y

year_range (src.dataset_creator.DatasetCreator attribute) (src.structure_filter.StructureLevelFilter attribute)