molsysmt.physchem.get_atomic_radius#

molsysmt.physchem.get_atomic_radius(molecular_system, element='atom', selection='all', definition='vdw', syntax='MolSysMT', skip_digestion=False)[source]#

Atomic radius for each selected atom.

Returns a tabulated radius value for each atom based on its element type and the requested radius definition (e.g. van der Waals radius). Values are returned as a PyUnitWizard quantity in nm.

Parameters:

  • molecular_system (molecular system) – Input system in any supported form.

  • element ({'atom'}, default 'atom') – Hierarchical element for which the radius is returned. Currently only 'atom' level is meaningful.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Selection of atoms to include in the output.

  • definition ({'vdw', 'protor'}, default 'vdw') – Radius definition to use. 'vdw' returns the van der Waals radius for each element. 'protor' returns the implicit-hydrogen-aware ProtOr van der Waals radius for protein heavy atoms.

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

  • skip_digestion (bool, default False) – If True, bypass argument validation (for internal use only).

Returns:

Atomic radii as a PyUnitWizard quantity in nm. Shape: (n_atoms,).

Return type:

quantity

Raises:

NotImplementedError – If an unsupported definition is requested.

Notes

Van der Waals radii are sourced from standard reference tables covering all elements of the periodic table. When using definition='protor', standard ProtOr radii are assigned to protein heavy atoms, falling back to element defaults where applicable.

Added in version 1.0.0.

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