confidence

ConfidenceFilterQuery dataclass

Query for filtering AlphaFoldDB structures based on confidence.

Parameters:

Name	Type	Description	Default
confidence	float	The confidence threshold for filtering residues. Residues with a pLDDT (b-factor) above this value are considered high confidence.	required
min_threshold	int	The minimum number of high-confidence residues required to keep the structure.	required
max_threshold	int	The maximum number of high-confidence residues required to keep the structure.	required

ConfidenceFilterResult dataclass

Result of filtering AlphaFoldDB structures based on confidence (pLDDT).

Parameters:

Name	Type	Description	Default
input_file	str	The name of the mmcif/PDB file that was processed.	required
count	int	The number of residues with a pLDDT above the confidence threshold.	required
filtered_file	Path | None	The path to the filtered mmcif/PDB file, if passed filter.	None

filter_file_on_residues(file, query, filtered_dir)

Filter a single AlphaFoldDB structure file based on confidence.

Parameters:

Name	Type	Description	Default
file	Path	The path to the PDB file to filter.	required
query	ConfidenceFilterQuery	The confidence filter query.	required
filtered_dir	Path	The directory to save the filtered PDB file.	required

Returns:

Type	Description
ConfidenceFilterResult	result with filtered_file property set to Path where filtered PDB file is saved.
ConfidenceFilterResult	or None if structure was filtered out.

filter_files_on_confidence(alphafold_pdb_files, query, filtered_dir)

Filter AlphaFoldDB structures based on confidence.

Parameters:

Name	Type	Description	Default
alphafold_pdb_files	list[Path]	List of mmcif/PDB files from AlphaFoldDB to filter.	required
query	ConfidenceFilterQuery	The confidence filter query containing the confidence thresholds.	required
filtered_dir	Path	Directory where the filtered mmcif/PDB files will be saved.	required

Yields:

Type	Description
Generator[ConfidenceFilterResult]	For each mmcif/PDB files yields whether it was filtered or not, and number of residues with pLDDT above the confidence threshold.

filter_out_low_confidence_residues(structure, allowed_residues)

Filter out residues from the structure that do not have high confidence.

Parameters:

Name	Type	Description	Default
structure	Structure	The AlphaFoldDB structure to filter.	required
allowed_residues	set[int]	The set of residue sequence numbers to keep.	required

Returns:

Type	Description
Structure	A new AlphaFoldDB structure with low confidence residues removed.

find_high_confidence_residues(structure, confidence)

Find residues in the structure with pLDDT confidence above the given threshold.

Parameters:

Name	Type	Description	Default
structure	Structure	The AlphaFoldDB structure to search.	required
confidence	float	The confidence threshold (pLDDT) to use for filtering.	required

Yields:

Type	Description
Generator[int]	The sequence numbers of residues with pLDDT above the confidence threshold.