deepfold.data.tools.hhsearch.HHSearch

class deepfold.data.tools.hhsearch.HHSearch(*, binary_path: str, databases: Sequence[str], n_cpu: int = 2, maxseq: int = 1000000)[source]

Python wrapper of the HHsearch binary.

__init__(*, binary_path: str, databases: Sequence[str], n_cpu: int = 2, maxseq: int = 1000000)[source]

Initializes the Python HHsearch wrapper.

Parameters:

  • binary_path – The path to the HHsearch executable.

  • databases – A sequence of HHsearch database paths. This should be the common prefix for the database files (i.e. up to but not including _hhm.ffindex etc.)

  • n_cpu – The number of CPUs to use

  • maxseq – The maximum number of rows in an input alignment. Note that this parameter is only supported in HHBlits version 3.1 and higher.

Raises:

RuntimeError – If HHsearch binary not found within the path.

Methods

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

Initializes the Python HHsearch wrapper.

get_template_hits(output_string, input_sequence)

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

query(a3m[, output_dir])

Queries the database using HHsearch using a given a3m.

Attributes

input_format

output_format