molsysmt.structure.get_center#

molsysmt.structure.get_center(molecular_system, selection='all', weights=None, structure_indices='all', syntax='MolSysMT', engine='MolSysMT', heavy_mode='auto', parallel=None, num_threads=None, skip_digestion=False)[source]#

Computing centers (centroids or weighted centers) of atom selections.

Parameters:

  • molecular_system (molecular system) – Input system.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms (or groups of atoms) to center; nested iterables are treated as groups.

  • weights (array-like or 'masses', optional) – Non-negative weights per atom (or per group) when computing centers. Use 'masses' to compute centers of mass. Every group must have a positive total weight.

  • structure_indices ('all' or array-like, default 'all') – Structures/frames over which centers are computed.

  • syntax (str, default 'MolSysMT') – Selection syntax when using strings.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend.

  • heavy_mode (str, default 'auto') – Chunked execution mode: ‘auto’ | ‘force’ | ‘off’.

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

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

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

Returns:

Centers as a PyUnitWizard quantity in length units.

Return type:

quantity

Raises:

  • ArgumentError – If the atom or frame selection is empty, or weights are non-finite, negative, or have zero total weight.

  • ArgumentLengthError – If the number of weights does not match the selected atoms.

  • NotImplementedMethodError – If an unsupported engine is requested.

Examples

>>> import molsysmt as msm
>>> molsys = msm.convert(msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm'], to_form='molsysmt.MolSys')
>>> msm.structure.get_center(molsys, weights='masses').shape
(1, 1, 3)

Added in version 1.0.0.

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