Descriptor

Radial distribution function (RDF)

The radial distribution function (RDF) [msg99,wfz04b] can be interpreted as the probability distribution of finding an atom in a spherical volume of radius r.

Equation 1. Radial distribution function

where r_ij is the geometrical distance between the atoms i and atom j, w_i and w_j are the atom properties of the atoms i and j. B is the smoothing parameter (fuzziness of the distance r_ij) for the interatomic distance and f the scaling factor.

If B aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness of the distance r_ij vanishes. So the RDF code can be treated as a generalized autocorrelation function.

The RDF user parameters can be defined in the joelib.properties-file, otherwise the default parameters will be used:

jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2
joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0
joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2
joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25

Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.

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