workflow

Workflow steps

WhatRetrieve = Literal['pdbe', 'alphafold'] module-attribute

Types of what to retrieve.

what_retrieve_choices = {'pdbe', 'alphafold'} module-attribute

Set of what can be retrieved.

UniprotSearchResult dataclass

Result of a UniProt search.

Parameters:

Name	Type	Description	Default
nr_uniprot_accessions	int	Number of UniProt accessions found.	required
nr_pdbs	int	Number of PDB structures found.	required
nr_prot2pdb	int	Number of UniProt to PDB mappings found.	required
nr_afs	int	Number of AlphaFold structures found.	required
nr_interaction_partners	int	Number of interaction partners found.	required

async_retrieve_structures(session_dir, what=None, what_af_formats=None) async

Retrieve structure files from PDBe and AlphaFold databases for the Uniprot entries in the session asynchronously.

Parameters:

Name	Type	Description	Default
session_dir	Path	The directory to store downloaded files and the session database.	required
what	set[WhatRetrieve] | None	A set of strings indicating which databases to retrieve files from ("pdbe", "alphafold").	None
what_af_formats	set[DownloadableFormat] | None	A set of formats to download from AlphaFold (e.g., "pdb", "cif"). If None, defaults to {"summary", "cif"}.	None

Returns:

Type	Description
tuple[Path, int, int]	A tuple containing: - The download directory (Path) - The number of PDBe mmCIF files downloaded (int) - The number of AlphaFold files downloaded (int)

filter_structures(session_dir, options, scheduler_address=None)

Filter the structures in the session based on confidence, number of residues, and secondary structure.

Parameters:

Name	Type	Description	Default
session_dir	Path	The directory containing the session data, including structure files.	required
options	FilterOptions	The filter options containing confidence and secondary structure filter queries.	required
scheduler_address	str | Cluster | None	Address of the Dask scheduler for distributed filtering. If None then a local cluster is used.	None

Returns:

Type	Description
tuple[Path, list[FilteredStructure]]	A tuple containing: - The directory with the filtered structures. - A list of FilteredStructure objects containing the filtering results for each structure.

retrieve_structures(session_dir, what=None, what_af_formats=None)

Retrieve structure files from PDBe and AlphaFold databases for the Uniprot entries in the session.

Parameters:

Name	Type	Description	Default
session_dir	Path	The directory to store downloaded files and the session database.	required
what	set[WhatRetrieve] | None	A tuple of strings indicating which databases to retrieve files from.	None
what_af_formats	set[DownloadableFormat] | None	A tuple of formats to download from AlphaFold (e.g., "pdb", "cif").	None

Returns:

Type	Description
Path	A tuple containing the download directory, the number of PDBe mmCIF files downloaded,
int	and the number of AlphaFold files downloaded.

search_structures_in_uniprot(query, session_dir, limit=10000)

Searches for protein structures in UniProt database.

Parameters:

Name	Type	Description	Default
query	UniprotQuery	The search query.	required
session_dir	Path	The directory to store the search results.	required
limit	int	The maximum number of results to return from each database query.	10000

Returns:

Type	Description
UniprotSearchResult	A tuple containing the number of UniProt accessions, the number of PDB structures,
UniprotSearchResult	number of UniProt to PDB mappings,
UniprotSearchResult	and the number of AlphaFold structures found.