ambit2.groupcontribution.fragmentation

Class Fragmentation

java.lang.Object

ambit2.groupcontribution.fragmentation.Fragmentation

public class Fragmentation
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
List<Double>	correctionFactors
Map<String,Integer>	groupFrequencies

Constructor Summary

Constructors

Constructor and Description
Fragmentation()

Method Summary

Modifier and Type	Method and Description
void	addGroup(String groupDesignation)
static void	calcAtomFragments(Fragmentation fragmentation, DataSetObject dso, Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr, GroupContributionModel gcm)
static Map<org.openscience.cdk.interfaces.IAtom,int[]>	calcAtomLocalDescriptors(org.openscience.cdk.interfaces.IAtomContainer molecule, List<ILocalDescriptor> locDescr)
static void	calcBondFragments(Fragmentation fragmentation, DataSetObject dso, Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr, GroupContributionModel gcm)
static void	calcCorrectionFactors(DataSetObject dso, GroupContributionModel gcm)
static void	calcDGroupFragments(Fragmentation fragmentation, DataSetObject dso, Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr, GroupContributionModel gcm)
static void	calcGGroupFragments(Fragmentation fragmentation, DataSetObject dso, Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr, GroupContributionModel gcm)
static void	calcLGroupFragments(Fragmentation fragmentation, DataSetObject dso, Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr, GroupContributionModel gcm)
static void	calculateLocalDescriptors(DataSetObject dso, GroupContributionModel gcm)
static MatrixDouble	generateCorrectionFactorMatrix(DataSet dataset, GroupContributionModel gcm)
static MatrixDouble	generateFragmentationMatrix(DataSet dataset, GroupContributionModel gcm)
static MatrixDouble	generateMultiplePropertyMatrix(DataSet dataset, List<String> properties)
static MatrixDouble	generateMultiplePropertyMatrix2(DataSet dataset, List<DescriptorInfo> diList)
static MatrixDouble	generatePropertyMatrix(DataSet dataset, String property)
static List<ILocalDescriptor>	getDefaultSecondOrderLocalDescriptors()
static void	makeAtomicFragmenation(DataSetObject dso, GroupContributionModel gcm)
static void	makeBondBasedFragmenation(DataSetObject dso, GroupContributionModel gcm)
static void	makeCustomGroupFragmenation(DataSetObject dso, GroupContributionModel gcm)
static void	makeFragmentation(DataSet dataset, GroupContributionModel gcm)
static void	makeFragmentation(DataSetObject dso, GroupContributionModel gcm)
static void	makeSecondOrderFragmenation(DataSetObject dso, GroupContributionModel gcm)

Methods inherited from class java.lang.Object

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

Field Detail

groupFrequencies

public Map<String,Integer> groupFrequencies

correctionFactors

public List<Double> correctionFactors

Constructor Detail

Fragmentation

public Fragmentation()

Method Detail

addGroup

public void addGroup(String groupDesignation)

makeFragmentation

public static void makeFragmentation(DataSet dataset,
                                     GroupContributionModel gcm)

makeFragmentation

public static void makeFragmentation(DataSetObject dso,
                                     GroupContributionModel gcm)

makeAtomicFragmenation

public static void makeAtomicFragmenation(DataSetObject dso,
                                          GroupContributionModel gcm)

makeBondBasedFragmenation

public static void makeBondBasedFragmenation(DataSetObject dso,
                                             GroupContributionModel gcm)

makeSecondOrderFragmenation

public static void makeSecondOrderFragmenation(DataSetObject dso,
                                               GroupContributionModel gcm)

makeCustomGroupFragmenation

public static void makeCustomGroupFragmenation(DataSetObject dso,
                                               GroupContributionModel gcm)

calcCorrectionFactors

public static void calcCorrectionFactors(DataSetObject dso,
                                         GroupContributionModel gcm)

calcAtomFragments

public static void calcAtomFragments(Fragmentation fragmentation,
                                     DataSetObject dso,
                                     Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr,
                                     GroupContributionModel gcm)

calcBondFragments

public static void calcBondFragments(Fragmentation fragmentation,
                                     DataSetObject dso,
                                     Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr,
                                     GroupContributionModel gcm)

calcDGroupFragments

public static void calcDGroupFragments(Fragmentation fragmentation,
                                       DataSetObject dso,
                                       Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr,
                                       GroupContributionModel gcm)

calcGGroupFragments

public static void calcGGroupFragments(Fragmentation fragmentation,
                                       DataSetObject dso,
                                       Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr,
                                       GroupContributionModel gcm)

calcLGroupFragments

public static void calcLGroupFragments(Fragmentation fragmentation,
                                       DataSetObject dso,
                                       Map<org.openscience.cdk.interfaces.IAtom,int[]> atomLocDescr,
                                       GroupContributionModel gcm)

calculateLocalDescriptors

public static void calculateLocalDescriptors(DataSetObject dso,
                                             GroupContributionModel gcm)

calcAtomLocalDescriptors

public static Map<org.openscience.cdk.interfaces.IAtom,int[]> calcAtomLocalDescriptors(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                                       List<ILocalDescriptor> locDescr)

getDefaultSecondOrderLocalDescriptors

public static List<ILocalDescriptor> getDefaultSecondOrderLocalDescriptors()

generateFragmentationMatrix

public static MatrixDouble generateFragmentationMatrix(DataSet dataset,
                                                       GroupContributionModel gcm)

generateCorrectionFactorMatrix

public static MatrixDouble generateCorrectionFactorMatrix(DataSet dataset,
                                                          GroupContributionModel gcm)

generatePropertyMatrix

public static MatrixDouble generatePropertyMatrix(DataSet dataset,
                                                  String property)
                                           throws Exception

Throws:

Exception

generateMultiplePropertyMatrix

public static MatrixDouble generateMultiplePropertyMatrix(DataSet dataset,
                                                          List<String> properties)
                                                   throws Exception

Throws:

Exception

generateMultiplePropertyMatrix2

public static MatrixDouble generateMultiplePropertyMatrix2(DataSet dataset,
                                                           List<DescriptorInfo> diList)
                                                    throws Exception

Throws:

Exception