molsysmt.structure.get_least_rmsd#

molsysmt.structure.get_least_rmsd(molecular_system, selection='atom_type!="H"', structure_indices='all', reference_molecular_system=None, reference_selection=None, reference_structure_index=0, syntax='MolSysMT', engine='MolSysMT', use_gpu=None, parallel=None, num_threads=None, skip_digestion=False)[source]#

Compute the least-RMSD (optimal superposition RMSD) between structures.

Unlike get_rmsd, this function finds the rotation that minimises the RMSD before measuring it. The algorithm operates in nm and returns a quantity in the MolSysMT standard length unit.

The function handles three broadcasting scenarios:

  • Many query structures vs. one reference — each query frame is aligned to the single reference frame.

  • One query structure vs. many reference frames — the single query is aligned to each reference frame.

  • Equal numbers of frames on both sides — frame-by-frame alignment.

Parameters:

  • molecular_system (molecular system) – Query system in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, default 'atom_type!="H"') – Atoms used for the superposition and RMSD calculation (heavy atoms by default).

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

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

  • reference_selection (str, list, tuple or numpy.ndarray or None, default None) – Atoms in the reference system to superpose onto. When None, the same expression as selection is applied to the reference. The resolved atom count must match selection.

  • reference_structure_index (int, default 0) – Single frame index within the reference system used as the reference structure.

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

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend used for the Kabsch rotation and RMSD computation.

  • parallel (bool or str, optional) – Parallel mode override: True | False | ‘auto’.

  • num_threads (int, optional) – Number of threads override.

Returns:

PyUnitWizard length quantity of shape (n_structures,) containing the least-RMSD values in the standard length unit (nm).

Return type:

quantity

Raises:

  • NotImplementedMethodError – If an unsupported engine is requested.

  • StructuralInconsistencyError – If the number of atoms resolved by selection and reference_selection differ.

  • .. versionadded: – 1.0.0:

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