org.openscience.cdk.geometry

Class RDFCalculator

java.lang.Object

org.openscience.cdk.geometry.RDFCalculator

public class RDFCalculator
extends Object

Calculator of radial distribution functions. The RDF has bins defined around a point, i.e. the first bin starts at 0 Å and ends at 0.5*resolution Å, and the second bins ends at 1.5*resolution Å.

By default, the RDF is unweighted. By implementing and registering a RDFWeightFunction, the RDF can become weighted. For example, to weight according to partial charge interaction, this code could be used:

 RDFCalculator calculator = new RDFCalculator(0.0, 5.0, 0.1, 0.0,
     new RDFWeightFunction() {
         public double calculate(Atom atom, Atom atom2) {
             return atom.getCharge()*atom2.getCharge();
         }
     }
 );
 

Author:

Egon Willighagen

See Also:

IRDFWeightFunction

Source code:

master

Belongs to CDK module:

extra

Keywords:

radial distribution function, RDF

Created on:

2005-01-10

Constructor Summary

Constructors

Constructor and Description
RDFCalculator(double startCutoff, double cutoff, double resolution, double peakWidth) Constructs a RDF calculator that calculates a unweighted, digitized RDF function.
RDFCalculator(double startCutoff, double cutoff, double resolution, double peakWidth, IRDFWeightFunction weightFunction) Constructs a RDF calculator that calculates a digitized RDF function.

Method Summary

Modifier and Type	Method and Description
double[]	calculate(IAtomContainer container, IAtom atom) Calculates a RDF for Atom atom in the environment of the atoms in the AtomContainer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RDFCalculator

public RDFCalculator(double startCutoff,
                     double cutoff,
                     double resolution,
                     double peakWidth)

Constructs a RDF calculator that calculates a unweighted, digitized RDF function.

Parameters:

startCutoff - radial length in Ångstrom at which the RDF starts

cutoff - radial length in Ångstrom at which the RDF stops

resolution - width of the bins

peakWidth - width of the gaussian applied to the peaks in Ångstrom

RDFCalculator

public RDFCalculator(double startCutoff,
                     double cutoff,
                     double resolution,
                     double peakWidth,
                     IRDFWeightFunction weightFunction)

Constructs a RDF calculator that calculates a digitized RDF function.

Parameters:

startCutoff - radial length in Ångstrom at which the RDF starts

cutoff - radial length in Ångstrom at which the RDF stops

resolution - width of the bins

peakWidth - width of the gaussian applied to the peaks in Ångstrom

weightFunction - the weight function. If null, then an unweighted RDF is calculated

Method Detail

calculate

public double[] calculate(IAtomContainer container,
                          IAtom atom)

Calculates a RDF for Atom atom in the environment of the atoms in the AtomContainer.