structure

Module for querying and modifying [gemmi structures][gemmi.Structure].

ChainNotFoundError

Bases: IndexError

Exception raised when a chain is not found in a structure.

chains_in_structure(structure)

Get a list of chains in a structure.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi structure to get chains from.	required

Returns:

Type	Description
set[Chain]	A set of chains in the structure.

find_chain_in_model(model, wanted_chain)

Find a chain in a model.

Parameters:

Name	Type	Description	Default
model	Model	The gemmi model to search in.	required
wanted_chain	str	The chain identifier to search for.	required

Returns:

Type	Description
Chain | None	The found chain or None if not found.

find_chain_in_structure(structure, wanted_chain)

Find a chain in a structure.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi structure to search in.	required
wanted_chain	str	The chain identifier to search for.	required

Returns:

Type	Description
Chain | None	The found chain or None if not found.

nr_residues_in_chain(file, chain='A')

Returns the number of residues in a specific chain from a structure file.

Parameters:

Name	Type	Description	Default
file	Path	Path to the input structure file.	required
chain	str	Chain to count residues of.	'A'

Returns:

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

structure2uniprot_accessions(structure)

Extract UniProt accessions from a gemmi Structure object.

Logs a warning and returns an empty set if no accessions are found in structure.

Parameters:

Name	Type	Description	Default
structure	Structure	The gemmi Structure object to extract UniProt accessions from.	required

Returns:

Type	Description
set[str]	A set of UniProt accessions found in the structure.

write_single_chain_structure_file(input_file, chain2keep, output_dir, out_chain='A', copy_method='copy')

Write a single chain from a structure file to a new structure file.

Also

• removes ligands and waters
• renumbers atoms ids
• removes chem_comp section from cif files
• adds provenance information to the header like software and input file+chain

This function is equivalent to the following gemmi commands:

gemmi convert --remove-lig-wat --select=B --to=cif chain-in/3JRS.cif - | \
gemmi convert --from=cif --rename-chain=B:A - chain-out/3JRS_B2A.gemmi.cif

Parameters:

Name	Type	Description	Default
input_file	Path	Path to the input structure 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'
copy_method	CopyMethod	How to copy when no changes are needed to output file.	'copy'

Returns:

Type	Description
Path	Path to the output structure file

Raises:

Type	Description
FileNotFoundError	If the input file does not exist.
ChainNotFoundError	If the specified chain is not found in the input file.