molsysmt.topology.get_sequence_alignment#

molsysmt.topology.get_sequence_alignment(molecular_system, selection='all', reference_molecular_system=None, reference_selection='all', engine='Biopython', syntax='MolSysMT', prettyprint=False, alignment_index=0, skip_digestion=False)[source]#

Aligning sequences between a query and reference molecular system.

Parameters:

  • molecular_system (molecular system) – Query system providing the sequence to align.

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

  • reference_molecular_system (molecular system, optional) – Reference system to align against.

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

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

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

  • prettyprint (bool, default False) – If True, print a colorized alignment; if False, return aligned sequences.

  • alignment_index (int, default 0) – Alignment index to return when multiple alignments are produced.

  • skip_digestion (bool, default False) – Whether to skip argument digestion.

Returns:

(seq, seq_ref) aligned strings when prettyprint=False; otherwise prints and returns None.

Return type:

tuple of str or None

Raises:

  • NotImplementedError – If an unsupported engine is requested.

  • .. versionadded: – 1.0.0: