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
`archived`	`Annotated[bool, Parameter(negative='')]`	Retrieve archived versions. By default downloads an updated version of the PDB archive mmCIF format file. 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`	`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`