fetch
Module for fetching structures from PDBe.
fetch(ids, save_dir, 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 |
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, 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 |
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. |