filters

FilterStat dataclass

Statistics for filtering files based on residue count in a specific chain.

Parameters:

Name	Type	Description	Default
input_file	Path	The path to the input file.	required
residue_count	int	The number of residues.	required
passed	bool	Whether the file passed the filtering criteria.	required
output_file	Path | None	The path to the output file, if passed.	required

filter_files_on_chain(input_dir, id2chains, output_dir, scheduler_address=None, out_chain='A')

Filter mmcif/PDB files by chain.

Parameters:

Name	Type	Description	Default
input_dir	Path	The directory containing the input mmcif/PDB files.	required
id2chains	dict[str, str]	Which chain to keep for each PDB ID. Key is the PDB ID, value is the chain ID.	required
output_dir	Path	The directory where the filtered files will be written.	required
scheduler_address	str | Cluster | None	The address of the Dask scheduler.	None
out_chain	str	Under what name to write the kept chain.	'A'

Returns:

Type	Description
list[tuple[str, str, Path | None]]	A list of tuples containing the PDB ID, chain ID, and path to the filtered file.
list[tuple[str, str, Path | None]]	Last tuple item is None if something went wrong like chain not present.

filter_files_on_residues(input_files, output_dir, min_residues, max_residues, chain='A')

Filter PDB/mmCIF files by number of residues in given chain.

Parameters:

Name	Type	Description	Default
input_files	list[Path]	The list of input PDB/mmCIF files.	required
output_dir	Path	The directory where the filtered files will be written.	required
min_residues	int	The minimum number of residues in chain.	required
max_residues	int	The maximum number of residues in chain.	required
chain	str	The chain to count residues of.	'A'

Yields:

Type	Description
Generator[FilterStat]	FilterStat objects containing information about the filtering process for each input file.