vdw_radius_protor

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

Estimate the Van-der-Waals radius of a heavy 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 heavy atom and the amount of normally bonded hydrogen atoms is taken from the Chemical Component Dictionary.

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:

radiusfloat

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

Van-der-Waals radii for structures with annotated hydrogen atoms.

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