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) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • reference_molecular_system (object, default=None) – Argument reference_molecular_system.

  • reference_selection (object, default='all') – Argument reference_selection.

  • engine (object, default='Biopython') – Argument engine.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • prettyprint (object, default=False) – Argument prettyprint.

  • alignment_index (object, default=0) – Argument alignment_index.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

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.

Added in version 1.0.0.