io

glob_structure_files(input_dir)

Glob for structure files in a directory.

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.

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.

nr_residues_in_chain(file, chain='A')

Returns the number of residues in a specific chain from a mmCIF/pdb file.

Parameters:

Name	Type	Description	Default
file	Path | str	Path to the input mmCIF/pdb file.	required
chain	str	Chain to count residues of.	'A'

Returns:

Type	Description
int	The number of residues in the specified chain.

write_single_chain_pdb_file(input_file, chain2keep, output_dir, out_chain='A')

Write a single chain from a mmCIF/pdb file to a new mmCIF/pdb file.

Parameters:

Name	Type	Description	Default
input_file	Path	Path to the input mmCIF/pdb file.	required
chain2keep	str	The chain to keep.	required
output_dir	Path	Directory to save the output file.	required
out_chain	str	The chain identifier for the output file.	'A'

Returns:

Type	Description
Path | None	Path to the output mmCIF/pdb file or None if not created.

write_structure(structure, path)

Write a gemmi structure to a file.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi structure to write.	required
path	Path	The file path to write the structure to. The format depends on the file extension. Supported extensions are .pdb, .pdb.gz, .cif, .cif.gz.	required

Raises:

Type	Description
ValueError	If the file extension is not supported.