nucleoseeker
nucleoseeker
Index
Index
_
|
A
|
C
|
D
|
E
|
F
|
G
|
M
|
P
|
R
|
S
|
T
|
W
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Y
_
_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)