ambit2.model.structure

Class DataCoverageFingerprintsTanimoto

java.lang.Object

ambit2.model.numeric.DataCoverage<List<BitSet>>

ambit2.model.structure.DataCoverageFingerprints

ambit2.model.structure.DataCoverageFingerprintsTanimoto

All Implemented Interfaces:

IDataCoverage<List<BitSet>>, Serializable

public class DataCoverageFingerprintsTanimoto
extends DataCoverageFingerprints

See Also:

Serialized Form

Field Summary

Fields inherited from class ambit2.model.structure.DataCoverageFingerprints

consensusFingerprint, fingerPrintLength, fingerprintsCalculated, fpProfile

Fields inherited from class ambit2.model.numeric.DataCoverage

appDomainMethodType, logger, object, pThreshold, threshold

Constructor Summary

Constructors

Constructor and Description
DataCoverageFingerprintsTanimoto()

Method Summary

Modifier and Type	Method and Description
protected double	estimateThresholdValues(double percent, double[] values, int npoints)
void	evaluate(List<BitSet> bitsets)
String	getDomainName()
String	getMetricName()
String	getName()
double[]	predict(List<BitSet> data)
protected double	tanimoto(BitSet bs1, BitSet bs2) Returns (1-Tanimoto distance) where Tanimoto = ( bc / (b1.cardinality() + b2.cardinality() - bc) bc = bs1.and(bs2).cardinality (the number of common bits set to 1) (1- Tanimoto) is used to make it compatible with distances approach (the larger the distance value, the more dissimilar the compounds
protected double[]	tanimoto(List<BitSet> data)

Methods inherited from class ambit2.model.structure.DataCoverageFingerprints

arrayToString, build, buildStart, clear, clearProfile, estimateConsensusFP, getDomain, getDomain, getFingerPrintLength, getFingerprintsCalculated, histToString, isEmpty, profileToHistogram, profileToString, setFingerPrintLength

Methods inherited from class ambit2.model.numeric.DataCoverage

clone, getAppDomainMethodType, getId, getPoints, getPThreshold, setAppDomainMethodType, setDomainName, setMetricName, setMode, setParameters, setPThreshold, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

DataCoverageFingerprintsTanimoto

public DataCoverageFingerprintsTanimoto()

Method Detail

evaluate

public void evaluate(List<BitSet> bitsets)

Specified by:

evaluate in class DataCoverageFingerprints

tanimoto

protected double tanimoto(BitSet bs1,
                          BitSet bs2)

Returns (1-Tanimoto distance) where Tanimoto = ( bc / (b1.cardinality() + b2.cardinality() - bc) bc = bs1.and(bs2).cardinality (the number of common bits set to 1) (1- Tanimoto) is used to make it compatible with distances approach (the larger the distance value, the more dissimilar the compounds

Parameters:

bs1 - fingerprint 1

bs2 - fingerprint 2

Returns:

(1-Tanimoto distance)

tanimoto

protected double[] tanimoto(List<BitSet> data)

estimateThresholdValues

protected double estimateThresholdValues(double percent,
                                         double[] values,
                                         int npoints)

predict

public double[] predict(List<BitSet> data)

getName

public String getName()

Overrides:

getName in class DataCoverageFingerprints

getDomainName

public String getDomainName()

Specified by:

getDomainName in interface IDataCoverage<List<BitSet>>

Overrides:

getDomainName in class DataCoverage<List<BitSet>>

getMetricName

public String getMetricName()

Specified by:

getMetricName in interface IDataCoverage<List<BitSet>>

Overrides:

getMetricName in class DataCoverage<List<BitSet>>