From e77cc376aaff8ca481fdace6d5795c5b5feb0e87 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 14:45:20 +0100 Subject: Added pc descriptor calc service --- java/docs/feature/RadialDistributionFunction.html | 230 ++++++++++++++++++++++ 1 file changed, 230 insertions(+) create mode 100644 java/docs/feature/RadialDistributionFunction.html (limited to 'java/docs/feature/RadialDistributionFunction.html') diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html new file mode 100644 index 0000000..09d9600 --- /dev/null +++ b/java/docs/feature/RadialDistributionFunction.html @@ -0,0 +1,230 @@ +

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 rij is the geometrical distance between the atoms +i and atom j, wi +and wj are the atom properties of the atoms i and +j. B is the smoothing parameter +(fuzziness of the distance rij) 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 rij 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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