molsysmt.topology.get_sequence_identity#

molsysmt.topology.get_sequence_identity(molecular_system, selection='all', reference_molecular_system=None, reference_selection='all', syntax='MolSysMT', engine='Biopython')[source]#

Calculating sequence identity between two molecular systems.

Parameters:

  • molecular_system (molecular system) – Query system containing the sequence to compare.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Group-level selection in the query system (MolSysMT syntax or indices).

  • reference_molecular_system (molecular system, optional) – Reference system against which identity is computed.

  • reference_selection (str, list, tuple or numpy.ndarray, default 'all') – Group-level selection in the reference system.

  • syntax (str, default 'MolSysMT') – Selection syntax when using string selections.

  • engine ({'Biopython'}, default 'Biopython') – Alignment engine to use.

Returns:

  • float – Sequence identity percentage (0–100).

  • list of int – Group indices in the query sequence that matched.

  • list of int – Group indices in the reference sequence that matched.

Raises:

NotImplementedError – If an unsupported engine is requested.

Notes

  • Uses get_sequence_alignment to align the two selections and counts identical, aligned positions.

Added in version 1.0.0.