Get atomic radius#

Extracting atomic van der Waals and effective radii for molecular structures.

The function molsysmt.physchem.get_atomic_radius() retrieves atomic radii using standard element-based van der Waals definitions (definition='vdw') or implicit-hydrogen-aware ProtOr parameter sets (definition='protor').

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.physchem.get_atomic_radius().

Basic usage#

By default (definition='vdw'), MolSysMT extracts standard element-level van der Waals radii tabulated by Bondi and Mantina et al.:

import molsysmt as msm
import pyunitwizard as puw

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

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

Let’s extract standard element-based van der Waals radii for the first residue (group_index==0):

radius_vdw = msm.physchem.get_atomic_radius(molsys, element='atom', selection='group_index==0', definition='vdw')
print('Element-based VdW radii (nm):\n', radius_vdw)

Element-based VdW radii (nm):
 [0.155 0.17 0.17 0.152 0.17 0.17 0.152 0.155 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11] nanometer

Implicit-hydrogen-aware van der Waals radii#

When dealing with united-atom representations or implicit-hydrogen models, the definition='protor' parameter adjusts heavy atom radii depending on the chemical hybridization and number of bonded hydrogens (Tsai et al.):

radius_protor = msm.physchem.get_atomic_radius(molsys, element='atom', selection='group_index==0', definition='protor')
print('ProtOr VdW radii (nm):\n', radius_protor)

ProtOr VdW radii (nm):
 [0.16399999999999998 0.188 0.161 0.142 0.188 0.161 0.142 0.16399999999999998 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11] nanometer

ProtOr atom types and radii#

MolSysMT also provides dedicated helper functions to determine the exact ProtOr atom classification codes (e.g. N3H1, C4H1, C3H0, O1H0) and their corresponding radii directly:

protor_types, provenance = msm.physchem.get_protor_atom_type(molsys, selection='group_index==0')
print('ProtOr atom types:', protor_types)

direct_radii = msm.physchem.get_protor_vdw_radius(molsys, selection='group_index==0')
print('Direct ProtOr radii:', direct_radii)

ProtOr atom types: ['N3H1' 'C4H1' 'C3H0' 'O1H0' 'C4H2' 'C3H0' 'O1H0' 'N3H2' None None None
 None None None None None]
Direct ProtOr radii: [0.16399999999999998 0.188 0.161 0.142 0.188 0.161 0.142 0.16399999999999998 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11] nanometer