filter

Module dealing with filtering of protein structures.

In protein_quest package the filters are more granular, here we combine them into coarse grained methods.

FilterOptions dataclass

Filter query containing confidence and secondary structure filters.

Parameters:

Name	Type	Description	Default
confidence	ConfidenceFilterQuery	The confidence filter query.	required
secondary_structure	SecondaryStructureFilterQuery	The secondary structure filter query.	required

FilteredStructure dataclass

Filter result of a single uniprot+[pdb] entry.

Parameters:

Name	Type	Description	Default
uniprot_accession	str	The UniProt accession.	required
pdb_id	str | None	The PDB ID if applicable.	None
confidence	ConfidenceFilterResult | None	The confidence filter result if applicable.	None
chain	ChainFilterStatistics | None	The chain filter result if applicable.	None
residue	ResidueFilterStatistics | None	The residue filter result if applicable.	None
secondary_structure	tuple[Path, SecondaryStructureFilterResult, Path | None] | None	A tuple containing: - The input file path for the secondary structure filter. - The secondary structure filter result. - The output file path for the secondary structure filter, if passed.	None

output_file property writable

Get the output file of the last filter that was applied

Only valid if the structure passed all filters.

passed property

Whether the structure passed all filters.

make_relative_to(session_dir)

Make all file paths relative to the given session directory.

Parameters:

Name	Type	Description	Default
session_dir	Path	The session directory to make paths relative to.	required

Returns:

Type	Description
FilteredStructure	A new FilterResultRow object with paths made relative to the session directory.

filter_alphafold_structures(afs, session_dir, options, final_dir)

Filter AlphaFold structures in the session directory based on confidence and secondary structure.

Parameters:

Name	Type	Description	Default
afs	list[AlphaFoldEntry]	The list of AlphaFold entries to filter.	required
session_dir	Path	The directory containing the session data, including AlphaFold structure files.	required
options	FilterOptions	The filter options containing confidence and secondary structure filter queries.	required
final_dir	Path	The directory to store the final filtered structures.	required

Returns:

Type	Description
FilterResults	A dictionary mapping (uniprot_accession, pdb_id) to FilteredStructure objects

Raises:

Type	Description
ValueError	If there are inconsistencies in the filtering results.

filter_pdbe_structures(proteinpdbs, session_dir, options, final_dir, scheduler_address)

Filter PDBe structures in the session directory based on chain, number of residues, and secondary structure.

Parameters:

Name	Type	Description	Default
proteinpdbs	list[ProteinPdbRow]	The list of ProteinPdbRow entries to filter.	required
session_dir	Path	The directory containing the session data, including PDBe structure files.	required
options	FilterOptions	The filter options containing confidence and secondary structure filter queries.	required
final_dir	Path	The directory to store the final filtered structures.	required
scheduler_address	str | Cluster | None	Address of the Dask scheduler for distributed filtering. If None then local cluster is used.	required

Returns:

Type	Description
FilterResults	A dictionary mapping (uniprot_accession, pdb_id) to FilteredStructure objects