convert
Conversion orchestration for structure files.
ConversionStatistics
dataclass
¶
Statistics for a single file conversion.
Attributes:
| Name | Type | Description |
|---|---|---|
input_file |
Path
|
Path to the input file. |
output_file |
Path
|
Path to the output file. |
uniprot_chain_mappings |
UniprotChainMappings
|
Set of UniprotChainMapping that were injected, empty set if none. |
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 |
|---|---|
ConversionStatistics
|
ConversionStatistics with details about the conversion. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If the requested output format is not supported. |
write_conversion_stats(results, output_file)
¶
Write conversion statistics to a CSV file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
results
|
Iterable[ConversionStatistics]
|
Iterable of ConversionStatistics to write. |
required |
output_file
|
Path
|
Path to write the CSV file. Use '-' for stdout. |
required |