io

ProteinPdbRow dataclass

Info about PDB entry and its relation to an Uniprot entry

Parameters:

Name	Type	Description	Default
id	str	The PDB ID of the entry.	required
uniprot_chains	str	The UniProt chains associated with the PDB entry.	required
uniprot_acc	str	The UniProt accession number associated with the PDB entry.	required
mmcif_file	Path | None	The path to the mmCIF file for the PDB entry, or None if not retrieved yet.	required

SingleChainQuery dataclass

Query for writing single chain PDB files.

Parameters:

Name	Type	Description	Default
min_residues	int	Minimum number of residues that must be in chain.	required
max_residues	int	Maximum number of residues that must be in chain.	required

SingleChainResult dataclass

Result of writing a single chain PDB file.

Parameters:

Name	Type	Description	Default
uniprot_acc	str	The UniProt accession.	required
pdb_id	str	The PDB ID of the entry.	required
output_file	Path | None	The path to the output PDB file with just the first chain (renamed to A) belonging to given Uniprot accession. Only set when passed is True.	required
nr_residues	int	The number of residues in the chain that was written.	required
passed	bool	Whether the chain passed the number of residue filter.	required

filter_and_write_single_chain_pdb_file(mmcif_file, chain2keep, output_file, min_residues, max_residues, out_chain='A')

Saves a specific protein chain from a mmCIF file to a new PDB file.

Parameters:

Name	Type	Description	Default
mmcif_file	Path | str	Path to the input mmCIF file.	required
chain2keep	str	Chain to keep.	required
output_file	Path | str	Path to the output PDB file.	required
min_residues	int	Minimum number of residues in the chain to write.	required
max_residues	int	Maximum number of residues in the chain to write.	required
out_chain	str	Chain identifier for the saved chain in the output file.	'A'

Returns:

Type	Description
bool	A tuple containing a boolean indicating whether
int	chain is in the residue range and the file was written successfully,
tuple[bool, int]	and the number of residues in the chain.

first_chain_from_uniprot_chains(uniprot_chains)

Extracts the first chain identifier from a UniProt chains string.

The UniProt chains string is formatted (with EBNF notation) as follows:

chain_group(=range)?(,chain_group(=range)?)*

where

chain_group := chain_id(/chain_id)* chain_id := [A-Za-z]+ range := start-end start, end := integer

Parameters:

Name	Type	Description	Default
uniprot_chains	str	A string representing UniProt chains, For example "B/D=1-81".	required

Returns: The first chain identifier from the UniProt chain string. For example "B".

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 keep.	'A'

Returns:

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

write_single_chain_pdb_file(proteinpdb, session_dir, single_chain_dir, query)

Process a ProteinPdbRow to write a single chain PDB file if possible, returning the result.

Parameters:

Name	Type	Description	Default
proteinpdb	ProteinPdbRow	A ProteinPdbRow object.	required
session_dir	Path	The directory where the session files are stored.	required
single_chain_dir	Path	The directory where the single chain PDB files will be saved.	required
query	SingleChainQuery	The query containing the minimum and maximum number of residues.	required

Returns:

Type	Description
SingleChainResult	Result object containing the output file path and whether the chain passed the residue filter.

write_single_chain_pdb_files(proteinpdbs, session_dir, single_chain_dir, query)

Writes single chain PDB files from the provided protein PDB rows.

Parameters:

Name	Type	Description	Default
proteinpdbs	list[ProteinPdbRow]	A list of ProteinPdbRow objects.	required
session_dir	Path	The directory where the session files are stored.	required
single_chain_dir	Path	The directory where the single chain PDB files will be saved.	required
query	SingleChainQuery	The query containing the minimum and maximum number of residues.	required

Yields:

Type	Description
Generator[SingleChainResult]	SingleChainResult objects containing the output file path and whether the chain passed the residue filter.