Get atomic radius#

This tool extracts the van der Waals or physical radius of atoms in a molecular system. MolSysMT supports two primary radius definitions:

  • 'vdw': Standard element-based van der Waals radii.

  • 'protor': ProtOr implicit-hydrogen-aware van der Waals radii, which are optimized for proteins and are independent of whether explicit hydrogens are physically present in the input system.

import molsysmt as msm

Let’s load the classic Trp-Cage system to demonstrate both radius definitions:

molecular_system = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'])

1. Element-Based VdW Radii#

Using the default definition='vdw', the atomic radii are looked up purely by the chemical element of each atom:

radius_vdw = msm.physchem.get_atomic_radius(molecular_system, element='atom', selection='group_id==4',
                                           definition='vdw')

radius_vdw
Magnitude
[0.155 0.17 0.17 0.152 0.17 0.17 0.17 0.17 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11]
Unitsnanometer

2. ProtOr Implicit-Hydrogen-Aware VdW Radii#

By specifying definition='protor', MolSysMT calculates the ProtOr atom types for protein heavy atoms, mapping them to the proper implicit-hydrogen-aware radii in nanometers (nm). Non-protein elements cleanly fall back to standard VdW values.

radius_protor = msm.physchem.get_atomic_radius(molecular_system, element='atom', selection='group_id==4',
                                              definition='protor')

radius_protor
Magnitude
[0.16399999999999998 0.188 0.161 0.142 0.188 0.188 0.188 0.188 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11]
Unitsnanometer

3. Direct ProtOr Type and Radii Helpers#

For advanced physical chemistry workflows, you can also directly call the underlying service functions get_protor_atom_type and get_protor_vdw_radius from the molsysmt.physchem namespace.

protor_types, provenance = msm.physchem.get_protor_atom_type(molecular_system, selection='group_id==0')

protor_types, provenance

(array([], dtype=object), array([], dtype=object))

direct_radii = msm.physchem.get_protor_vdw_radius(molecular_system, selection='group_id==0')

direct_radii
Magnitude
[]
Unitsnanometer