openfold.data.tools.hhsearch

Library to run HHsearch from Python.

Classes

HHSearch(*, binary_path, databases[, n_cpu, ...])

Python wrapper of the HHsearch binary.

class HHSearch(*, binary_path, databases, n_cpu=2, maxseq=1000000)

Python wrapper of the HHsearch binary.

Parameters:

• binary_path (str)

• databases (Sequence[str])

• n_cpu (int)

• maxseq (int)

static get_template_hits(output_string, input_sequence)

Gets parsed template hits from the raw string output by the tool

Parameters:

• output_string (str)

• input_sequence (str)

Return type:

Sequence[TemplateHit]

query(a3m, output_dir=None)

Queries the database using HHsearch using a given a3m.

Parameters:

• a3m (str)

• output_dir (str | None)

Return type:

str

property input_format: str

property output_format: str