openfold.data.tools.hmmbuild

A Python wrapper for hmmbuild - construct HMM profiles from MSA.

Classes

Hmmbuild(*, binary_path[, singlemx])

Python wrapper of the hmmbuild binary.
class Hmmbuild(*, binary_path, singlemx=False)

Python wrapper of the hmmbuild binary.

Parameters:

  • binary_path (str)

  • singlemx (bool)

build_profile_from_a3m(a3m)

Builds a HHM for the aligned sequences given as an A3M string.

Parameters:

a3m (str) – A string with the aligned sequences in the A3M format.

Returns:

A string with the profile in the HMM format.

Raises:

RuntimeError – If hmmbuild fails.

Return type:

str

build_profile_from_sto(sto, model_construction='fast')

Builds a HHM for the aligned sequences given as an A3M string.

Parameters:

  • sto (str) – A string with the aligned sequences in the Stockholm format.

  • model_construction – Whether to use reference annotation in the msa to determine consensus columns (‘hand’) or default (‘fast’).

Returns:

A string with the profile in the HMM format.

Raises:

RuntimeError – If hmmbuild fails.

Return type:

str