public class RDFCalculator extends Object
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(); } } );
IRDFWeightFunction
Constructor and Description |
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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.
|
Modifier and Type | Method and Description |
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double[] |
calculate(IAtomContainer container,
IAtom atom)
Calculates a RDF for
Atom atom in the environment
of the atoms in the AtomContainer . |
public RDFCalculator(double startCutoff, double cutoff, double resolution, double peakWidth)
startCutoff
- radial length in Ångstrom at which the RDF startscutoff
- radial length in Ångstrom at which the RDF stopsresolution
- width of the binspeakWidth
- width of the gaussian applied to the peaks in Ångstrompublic RDFCalculator(double startCutoff, double cutoff, double resolution, double peakWidth, IRDFWeightFunction weightFunction)
startCutoff
- radial length in Ångstrom at which the RDF startscutoff
- radial length in Ångstrom at which the RDF stopsresolution
- width of the binspeakWidth
- width of the gaussian applied to the peaks in ÅngstromweightFunction
- the weight function. If null, then an unweighted RDF is
calculatedpublic double[] calculate(IAtomContainer container, IAtom atom)
Atom
atom in the environment
of the atoms in the AtomContainer
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