molsysmt.structure.least_rmsd_align#

molsysmt.structure.least_rmsd_align(molecular_system, selection='atom_name=="CA"', structure_indices='all', reference_molecular_system=None, reference_selection=None, reference_structure_index=0, syntax='MolSysMT', engine_sequence_alignment='Biopython', engine_least_rmsd_fit='MolSysMT', in_place=False, use_gpu=None, gpu_backend=None, precision=None, skip_digestion=False)[source]#

Align a molecular system to a reference using sequence alignment followed by least-RMSD fitting.

This is a two-step procedure:

  1. Sequence alignment — the topology of both systems is aligned using molsysmt.topology.get_sequence_identity (via engine_sequence_alignment) to identify structurally equivalent residue groups.

  2. Least-RMSD fit — least_rmsd_fit is called on the equivalent atoms to compute the optimal rotation/translation (Kabsch algorithm) and apply it to all atoms in the selected components.

This function is suitable for aligning homologous proteins whose sequences differ, where a simple atom-by-atom correspondence cannot be assumed.

Parameters:

  • molecular_system (molecular system) – Query system to be aligned, in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, default 'atom_name=="CA"') – Atoms (typically C-alpha carbons) used for sequence alignment and fitting. The entire component(s) containing the selected atoms are translated and rotated.

  • structure_indices ('all' or array-like, default 'all') – Frame indices of the query system to align.

  • reference_molecular_system (molecular system or None, default None) – Reference system. When None, molecular_system itself is used.

  • reference_selection (str, list, tuple or numpy.ndarray or None, default None) – Atoms in the reference used for sequence alignment. When None, the same expression as selection is applied to the reference.

  • reference_structure_index (int, default 0) – Single frame index in the reference system to align to.

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

  • engine_sequence_alignment ({'Biopython'}, default 'Biopython') – Backend used for pairwise sequence alignment.

  • engine_least_rmsd_fit ({'MolSysMT'}, default 'MolSysMT') – Backend used for the Kabsch rotation / RMSD minimisation.

  • in_place (bool, default False) – If True the molecular system is modified in-place and None is returned. If False a new copy is returned with the aligned coordinates.

  • skip_digestion (bool, default False) – Whether to skip argument digestion (for internal use on trusted hot paths).

Returns:

A new molecular system with the aligned coordinates when in_place=False; None when in_place=True.

Return type:

molecular system or None

Raises:

  • NotImplementedMethodError – If an unsupported sequence-alignment engine or least-RMSD-fit engine is requested.

  • .. versionadded: – 1.0.0:

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