molsysmt.structure.get_rmsf#

molsysmt.structure.get_rmsf(molecular_system, selection='atom_type!="H"', structure_indices='all', syntax='MolSysMT', engine='MolSysMT', heavy_mode='auto', parallel=None, num_threads=None, skip_digestion=False)[source]#

Computing root-mean-square fluctuations per atom over a set of structures.

The RMSF of atom i is defined as:

\[\mathrm{RMSF}_i = \sqrt{\frac{1}{T} \sum_{t=1}^{T} \left| \mathbf{r}_i(t) - \langle \mathbf{r}_i \rangle \right|^2}\]

where \(\langle \mathbf{r}_i \rangle\) is the time-averaged position of atom i and T is the number of structures.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

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

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

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

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

  • heavy_mode (object, default='auto') – Argument heavy_mode.

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

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

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

Returns:

RMSF per selected atom as a PyUnitWizard quantity in length units. Shape: (n_atoms,).

Return type:

quantity

Raises:

  • ArgumentError – If the atom or frame selection is empty.

  • NotImplementedMethodError – If an unsupported engine is requested.

Notes

All structures must be pre-aligned to a common reference frame before calling this function if positional fluctuations relative to a reference are intended. Use molsysmt.structure.least_rmsd_align() to align first.

Examples

>>> import molsysmt as msm
>>> molsys = msm.convert(msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm'], to_form='molsysmt.MolSys')
>>> msm.structure.get_rmsf(molsys, selection='all').shape[0] == msm.get(molsys, n_atoms=True)
True

Added in version 1.0.0.

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