retrieve

Retrieve subcommands for protein-quest.

`alphafold(alphafold_csv, output_dir, /, *, format_=None, db_version=None, gzip_files=False, all_isoforms=False, max_parallel_downloads=5, cache=None, _=None)`

Retrieve AlphaFold files for IDs in CSV.

Retrieve AlphaFold files from the AlphaFold Protein Structure Database.

Parameters:

Name	Type	Description	Default
`alphafold_csv`	`InputFile`	CSV file with an `af_id` column, or with `model_provider` and `model_identifier` columns. When using `model_provider`, only rows with `model_provider == 'alphafold'` are used. Single-column CSV files are also accepted, and the first row is treated as an ID. Use `-` for stdin.	required
`output_dir`	`OutputDir`	Directory to store downloaded AlphaFold files.	required
`format_`	`Annotated[set[DownloadableFormat], Parameter(name=--format, negative='')] \| None`	Formats to retrieve. Defaults to [`cif`]. Repeat parameter for multiple formats, for example `--format cif --format pdb`.	`None`
`db_version`	`str \| None`	AlphaFold database version.	`None`
`gzip_files`	`Annotated[bool, Parameter(negative='')]`	Gzip downloaded files.	`False`
`all_isoforms`	`Annotated[bool, Parameter(negative='')]`	Return all isoforms.	`False`
`max_parallel_downloads`	`BatchSize`	Maximum number of parallel downloads.	`5`
`cache`	`CacheParameter \| None`	Cache options including no_cache, cache_dir, and copy_method.	`None`
`_`	`Common \| None`	Common CLI options.	`None`

Retrieve EMDB volume files for EMDB IDs in CSV.

Retrieve volume files from Electron Microscopy Data Bank (EMDB) website for unique EMDB IDs listed in a CSV file.

Parameters:

Name	Type	Description	Default
`emdb_csv`	`InputFile`	CSV file with `emdb_id` column. Other columns are ignored. Single-column CSV files are also accepted, and the first row is treated as an ID. Use `-` for stdin.	required
`output_dir`	`OutputDir`	Directory to store downloaded EMDB volume files.	required
`cache`	`CacheParameter \| None`	Cache options including no_cache, cache_dir, and copy_method.	`None`
`_`	`Common \| None`	Common CLI options.	`None`

Retrieve mmCIF files from PDBe for PDB IDs in CSV.

Retrieve mmCIF files from Protein Data Bank in Europe Knowledge Base (PDBe) website for unique PDB IDs listed in a CSV file.

Parameters:

Name	Type	Description	Default
`pdbe_csv`	`InputFile`	CSV file with a `pdb_id` column, or with `model_provider` and `model_identifier` columns. When using `model_provider`, only rows with `model_provider == 'pdbe'` are used. Single-column CSV files are also accepted, and the first row is treated as an ID. Use `-` for stdin.	required
`output_dir`	`OutputDir`	Directory to store downloaded PDBe mmCIF files.	required
`max_parallel_downloads`	`BatchSize`	Maximum number of parallel downloads.	`5`
`cache`	`CacheParameter \| None`	Cache options including no_cache, cache_dir, and copy_method.	`None`
`_`	`Common \| None`	Common CLI options.	`None`

Retrieve structure files from search structure CSV output.

Retrieve structure files from model URLs listed in search structure CSV output.

Parameters:

Name	Type	Description	Default
`structures_csv`	`InputFile`	CSV file with `provider`, `model_identifier`, `model_url`, and `model_format` columns. Use `-` for stdin.	required
`output_dir`	`OutputDir`	Directory to store retrieved structure files.	required
`raw`	`Annotated[bool, Parameter(negative='')]`	Download in native format from CSV.	`False`
`max_parallel_downloads`	`BatchSize`	Maximum number of parallel downloads.	`5`
`cache`	`CacheParameter \| None`	Cache options including no_cache, cache_dir, and copy_method.	`None`
`_`	`Common \| None`	Common CLI options.	`None`