convert
Conversion orchestration for structure files.
convert_to_cif_file(input_file, output_dir, copy_method, output_format='.cif', pdb2uniprot=None, chain_system='auth')
Convert a single structure file to CIF format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
input_file
|
Path
|
The structure file to convert. See StructureFileExtensions for supported extensions. |
required |
output_dir
|
Path
|
Directory to save the converted file. |
required |
copy_method
|
CopyMethod
|
How to copy when no changes are needed to output file. |
required |
output_format
|
CifOutputFormat
|
Output file format to write. |
'.cif'
|
pdb2uniprot
|
Pdb2UniprotChainsMapping | None
|
Optional dictionary mapping PDB ID to structured UniProt chain mappings. If provided, will not use any shortcuts for copying files and will always read and write the structure to ensure UniProt accessions are verified and injected if necessary. |
None
|
chain_system
|
ChainIdSystem
|
System of chain ids in |
'auth'
|
Returns:
| Type | Description |
|---|---|
Path
|
Path to the converted file. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If the requested output format is not supported. |
convert_to_cif_files(input_files, output_dir, copy_method, output_format='.cif', pdb2uniprot=None, chain_system='auth')
Convert structure files to CIF format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
input_files
|
Iterable[Path]
|
Iterable of structure files to convert. |
required |
output_dir
|
Path
|
Directory to save the converted files. |
required |
copy_method
|
CopyMethod
|
How to copy when no changes are needed to output file. |
required |
output_format
|
CifOutputFormat
|
Output file format to write. |
'.cif'
|
pdb2uniprot
|
Pdb2UniprotChainsMapping | None
|
Optional dictionary mapping PDB ID to structured UniProt chain mappings. If provided, will be used to inject UniProt accessions into structures that lack them. |
None
|
chain_system
|
ChainIdSystem
|
System of chain ids in |
'auth'
|
Yields:
| Type | Description |
|---|---|
Generator[tuple[Path, Path]]
|
A tuple of the input file and the output file. |