fetch
Module for fetching structures from PDBe.
fetch(ids, save_dir, /, *, archived=False, max_parallel_downloads=5, cacher=None)
async
Fetches mmCIF files from the PDBe database.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ids
|
Iterable[str]
|
A set of PDB IDs to fetch. |
required |
save_dir
|
Path
|
The directory to save the fetched mmCIF files to. |
required |
archived
|
bool
|
Whether to fetch archived versions of the files or default updated version. The updated version is generated with standardisation of vocabularies, and addition of connectivity information for every chemical compound present in the PDB entry. |
False
|
max_parallel_downloads
|
int
|
The maximum number of parallel downloads. |
5
|
cacher
|
Cacher | None
|
An optional cacher to use for caching downloaded files. |
None
|
Returns:
| Type | Description |
|---|---|
Mapping[str, Path]
|
A dict of id and paths to the downloaded mmCIF files. |
read_pdb_ids_from_csv(file)
Reads PDB IDs from a CSV file.
The CSV file can provide PDB IDs in the pdb_id column. It can also
provide generic identifiers through the model_provider and
model_identifier columns. In that case, only rows with
model_provider == "pdbe" are used. If the CSV contains only one
column, every value in that column is treated as an ID, including the
first row.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file
|
Path
|
A path to a file containing the CSV data. |
required |
Returns:
| Type | Description |
|---|---|
set[str]
|
A set of PDB IDs extracted from the CSV file. |
sync_fetch(ids, save_dir, /, *, archived=False, max_parallel_downloads=5)
Synchronously fetches mmCIF files from the PDBe database.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ids
|
Iterable[str]
|
A set of PDB IDs to fetch. |
required |
save_dir
|
Path
|
The directory to save the fetched mmCIF files to. |
required |
archived
|
bool
|
Whether to fetch archived versions of the files or default updated version. The updated version is generated with standardisation of vocabularies, and addition of connectivity information for every chemical compound present in the PDB entry. |
False
|
max_parallel_downloads
|
int
|
The maximum number of parallel downloads. |
5
|
Returns:
| Type | Description |
|---|---|
Mapping[str, Path]
|
A dict of id and paths to the downloaded mmCIF files. |