molsysmt.physchem.get_protor_vdw_radius#

molsysmt.physchem.get_protor_vdw_radius(molecular_system, selection='all', syntax='MolSysMT', skip_digestion=False)[source]#

Calculating the ProtOr atomic van der Waals radius for selected atoms.

Computes the implicit-hydrogen-aware ProtOr radii in nanometers, applying specific protein heavy-atom definitions or standard element-level fallbacks.

Parameters:

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

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

  • 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 van der Waals radii as a PyUnitWizard quantity in nm. Shape: (n_atoms,).

Return type:

quantity

Notes

Standard ProtOr radii are defined in Ångstroms and converted to nanometers (nm) for integration with MolSysMT’s default unit framework. Non-protein atoms or unrecognized residues utilize standard element fallbacks or global default values.

Added in version 1.0.0.