openfold.data.tools.hhblits

Library to run HHblits from Python.

Classes

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

Python wrapper of the HHblits binary.

class HHBlits(*, binary_path, databases, n_cpu=4, n_iter=3, e_value=0.001, maxseq=1000000, realign_max=100000, maxfilt=100000, min_prefilter_hits=1000, all_seqs=False, alt=None, p=20, z=500)

Python wrapper of the HHblits binary.

Parameters:

• binary_path (str)

• databases (Sequence[str])

• n_cpu (int)

• n_iter (int)

• e_value (float)

• maxseq (int)

• realign_max (int)

• maxfilt (int)

• min_prefilter_hits (int)

• all_seqs (bool)

• alt (int | None)

• p (int)

• z (int)

query(input_fasta_path)

Queries the database using HHblits.

Parameters:

input_fasta_path (str)

Return type:

List[Mapping[str, Any]]