files

Path and filename helpers for structure files.

glob_structure_files(input_dir)

Glob for structure files in a directory.

Uses StructureFileExtensions as valid extensions. Does not search recursively.

Parameters:

Name	Type	Description	Default
input_dir	Path	The input directory to search for structure files.	required

Yields:

Type	Description
Generator[Path]	Paths to the found structure files.

locate_structure_file(root, pdb_id)

Locate a structure file for a given PDB ID in the specified directory.

Uses StructureFileExtensions as potential extensions. Also tries different casing of the PDB ID.

Parameters:

Name	Type	Description	Default
root	Path	The root directory to search in.	required
pdb_id	str	The PDB ID to locate.	required

Returns:

Type	Description
Path	The path to the located structure file.

Raises:

Type	Description
FileNotFoundError	If no structure file is found for the given PDB ID.

split_name_and_extension(name)

Split a filename into its name and extension.

.gz is considered part of the extension if present.

Examples:

Some example usages.

>>> from protein_quest.structure.files import split_name_and_extension
>>> split_name_and_extension("1234.pdb")
('1234', '.pdb')
>>> split_name_and_extension("1234.pdb.gz")
('1234', '.pdb.gz')

Parameters:

Name	Type	Description	Default
name	str	The filename to split.	required

Returns:

Type	Description
tuple[str, str]	A tuple containing the name and the extension.