neurosnap.database.foldseek module#
Foldseek API helpers.
- neurosnap.database.foldseek.foldseek_search(structure, mode='3diaa', databases=None, max_retries=10, retry_interval=5, output_format='json')[source]#
Perform a protein structure search using the Foldseek API.
- Parameters:
structure (
Union[Structure,StructureEnsemble,StructureStack,str,Path]) – A Neurosnap structure container or a path to a PDB file.mode (
str) – Search mode. Must be one of"3diaa"or"tm-align".databases (
Optional[List[str]]) – Databases to search. Defaults to Foldseek’s common public structure databases.max_retries (
int) – Maximum number of retries when polling job status.retry_interval (
int) – Seconds between job-status polls.output_format (
str) – Output format, either"json"or"dataframe".
- Return type:
Union[str,DataFrame]- Returns:
Search results in the requested format.
- Raises:
RuntimeError – If job submission or retrieval fails.
TimeoutError – If the job does not complete before retries are exhausted.
ValueError – If
output_formatis invalid.