convert
Convert subcommands for protein-quest.
structures(input_dir, /, *, output_dir=None, output_format='.cif', cache=None, _common=None)
Convert structure files between formats.
Convert structure files between formats.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
input_dir
|
InputDir
|
Directory with structure files. Supported extensions are .pdb, .pdb.gz, .ent, .ent.gz, .cif, .cif.gz, .bcif, .bcif.gz. |
required |
output_dir
|
OutputDir | None
|
Directory to write converted structure files. If not given, files are written to input_dir. |
None
|
output_format
|
CifOutputFormat
|
Output format for converted files. Supported values are .cif and .cif.gz. |
'.cif'
|
cache
|
CacheParameter | None
|
Cache options including no_cache, cache_dir, and copy_method. |
None
|
_common
|
Common | None
|
Common CLI options. |
None
|
uniprot(input_dir, output, /, *, grouped=False, _common=None)
Convert structure files to list of UniProt accessions.
UniProt accessions are read from database reference of each structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
input_dir
|
InputDir
|
Directory with structure files. Supported extensions are .cif, .cif.gz, .pdb, .pdb.gz. |
required |
output
|
OutputFile
|
Output text file with UniProt accessions (one per line). Use '-' for stdout. |
required |
grouped
|
Annotated[bool, Parameter(negative='')]
|
Whether to group accessions by structure file.
If set output changes to |
False
|
_common
|
Common | None
|
Common CLI options. |
None
|