openfold.data.tools.hmmsearch

A Python wrapper for hmmsearch - search profile against a sequence db.

Classes

Hmmsearch(*, binary_path, ...[, flags])

Python wrapper of the hmmsearch binary.

class Hmmsearch(*, binary_path, hmmbuild_binary_path, database_path, flags=None)

Python wrapper of the hmmsearch binary.

Parameters:

• binary_path (str)

• hmmbuild_binary_path (str)

• database_path (str)

• flags (Sequence[str] | None)

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(msa_sto, output_dir=None)

Queries the database using hmmsearch using a given stockholm msa.

Parameters:

• msa_sto (str)

• output_dir (str | None)

Return type:

str

query_with_hmm(hmm, output_dir=None)

Queries the database using hmmsearch using a given hmm.

Parameters:

• hmm (str)

• output_dir (str | None)

Return type:

str

property input_format: str

property output_format: str