biotite.structure.info.vdw_radius_protor

biotite.structure.info.vdw_radius_protor(res_name, atom_name)

Estimate the Van-der-Waals radius of an non-hydrogen atom, that includes the radius added by potential bonded hydrogen atoms. The respective radii are taken from the ProtOr dataset. 1

This is especially useful for macromolecular structures where no hydrogen atoms are resolved, e.g. crystal structures. The valency of the non-hydrogen atom and the amount of normally bonded hydrogen atoms is taken from the chemical compound dictionary dataset.

Parameters

res_namestr

The up to 3-letter residue name the non-hydrogen atom belongs to.

atom_namestr

The name of the non-hydrogen atom.

Returns

The Van-der-Waals radius of the given atom.

If the radius cannot be estimated for the atom, None is returned.

See also

vdw_radius_single

References

1

J. Tsai, R. Taylor, C. Chothia, M. Gerstein, “The packing density in proteins: standard radii and volumes,” Journal of Molecular Biology, vol. 290, pp. 253–266, July 1999. doi: 10.1006/jmbi.1999.2829

Examples

>>> print(vdw_radius_protor("GLY", "CA"))
1.88