molsysmt.physchem.get_atomic_radius

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

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) – Molecular system in any supported MolSysMT format.

• element (str, default='atom') – Structural element level to query (‘atom’, ‘group’, ‘component’, ‘molecule’, ‘chain’, ‘entity’).

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

• definition (str, default='vdw') – Reference dataset used to assign the requested physical property.

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

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

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.