public class ReactionSimilarityTool
extends java.lang.Object
Modifier and Type | Method and Description |
---|---|
static double |
getPointWiseMutualInformation(double alpha,
double beta,
IPatternFingerprinter StructFP1,
IPatternFingerprinter BondsCF1,
IPatternFingerprinter BondsOC1,
IPatternFingerprinter BondsST1,
IPatternFingerprinter StructFP2,
IPatternFingerprinter BondsCF2,
IPatternFingerprinter BondsOC2,
IPatternFingerprinter BondsST2) |
static double |
getReactionSimilarity(double alpha,
double beta,
double gamma,
IPatternFingerprinter StructFP1,
IPatternFingerprinter BondsCF1,
IPatternFingerprinter BondsOC1,
IPatternFingerprinter BondsST1,
IPatternFingerprinter StructFP2,
IPatternFingerprinter BondsCF2,
IPatternFingerprinter BondsOC2,
IPatternFingerprinter BondsST2) |
static double |
getReactionSimilarity(double alpha,
double beta,
IPatternFingerprinter StructFP1,
double[] bondFeatures1,
IPatternFingerprinter StructFP2,
double[] bondFeatures2,
boolean oxidationPenalty) |
static double |
getReactionSimilarity(double alpha,
double beta,
IPatternFingerprinter StructFP1,
IPatternFingerprinter BondsCF1,
IPatternFingerprinter BondsOC1,
IPatternFingerprinter BondsST1,
IPatternFingerprinter StructFP2,
IPatternFingerprinter BondsCF2,
IPatternFingerprinter BondsOC2,
IPatternFingerprinter BondsST2) |
static double |
getSimilarity(IPatternFingerprinter fp1,
IPatternFingerprinter fp2) |
static double |
getSimilarityScore(double alpha,
double beta,
double bondSimilarity,
double structuralSimilarity) |
static double |
getSimilarityScore(double alpha,
double beta,
double gamma,
double bondSimilarity,
double structuralSimilarity,
double stereoSimilarity) |
static boolean |
isSubset(double[] query,
double[] target) |
static boolean |
isSubset(double[] BondsCF1,
double[] BondsOC1,
double[] BondsST1,
double[] BondsCF2,
double[] BondsOC2,
double[] BondsST2) |
static boolean |
isSubset(double alpha,
double beta,
double[] StructFP1,
double[] BondsCF1,
double[] BondsOC1,
double[] BondsST1,
double[] StructFP2,
double[] BondsCF2,
double[] BondsOC2,
double[] BondsST2) |
static boolean |
isSubset(IPatternFingerprinter query,
IPatternFingerprinter target) |
public static double getSimilarityScore(double alpha, double beta, double bondSimilarity, double structuralSimilarity) throws org.openscience.cdk.exception.CDKException
alpha
- beta
- bondSimilarity
- structuralSimilarity
- org.openscience.cdk.exception.CDKException
public static double getSimilarityScore(double alpha, double beta, double gamma, double bondSimilarity, double structuralSimilarity, double stereoSimilarity) throws org.openscience.cdk.exception.CDKException
alpha
- beta
- gamma
- bondSimilarity
- structuralSimilarity
- stereoSimilarity
- org.openscience.cdk.exception.CDKException
public static double getReactionSimilarity(double alpha, double beta, IPatternFingerprinter StructFP1, double[] bondFeatures1, IPatternFingerprinter StructFP2, double[] bondFeatures2, boolean oxidationPenalty) throws java.lang.Exception
alpha
- weight for BondFPbeta
- weight for StructuralFPStructFP1
- bondFeatures1
- StructFP2
- bondFeatures2
- oxidationPenalty
- Penalty of 25% on the bond changes if they don't have same similar oxidation type
(oxidation and non-oxidative reactions will face penalty) @Equation (alpha/(alpha+beta)) * BondChange +
(beta/alpha+beta)* StructuralChangejava.lang.Exception
public static double getReactionSimilarity(double alpha, double beta, IPatternFingerprinter StructFP1, IPatternFingerprinter BondsCF1, IPatternFingerprinter BondsOC1, IPatternFingerprinter BondsST1, IPatternFingerprinter StructFP2, IPatternFingerprinter BondsCF2, IPatternFingerprinter BondsOC2, IPatternFingerprinter BondsST2) throws java.lang.Exception
alpha
- weight for BondFPbeta
- weight for StructuralFPStructFP1
- BondsCF1
- Reactant Bond Cleaved/Formed FP for Query ReactionBondsCF2
- Product Bond Cleaved/Formed FP for Target ReactionBondsOC1
- Reactant Bond Order/Change FP for Query ReactionStructFP2
- BondsOC2
- Product Bond Order/Change FP for Target ReactionBondsST1
- Reactant Bond Stereo FP for Query ReactionBondsST2
- Product Bond Stereo FP for Query Reactionjava.lang.Exception
public static double getReactionSimilarity(double alpha, double beta, double gamma, IPatternFingerprinter StructFP1, IPatternFingerprinter BondsCF1, IPatternFingerprinter BondsOC1, IPatternFingerprinter BondsST1, IPatternFingerprinter StructFP2, IPatternFingerprinter BondsCF2, IPatternFingerprinter BondsOC2, IPatternFingerprinter BondsST2) throws java.lang.Exception
alpha
- weight for BondFPbeta
- weight for StructuralFPgamma
- weight for Bond Stereo FPStructFP1
- BondsCF1
- Reactant Bond Cleaved/Formed FP for Query ReactionBondsCF2
- Product Bond Cleaved/Formed FP for Target ReactionBondsOC1
- Reactant Bond Order/Change FP for Query ReactionStructFP2
- BondsOC2
- Product Bond Order/Change FP for Target ReactionBondsST1
- Reactant Bond Stereo FP for Query ReactionBondsST2
- Product Bond Stereo FP for Query Reactionjava.lang.Exception
public static double getPointWiseMutualInformation(double alpha, double beta, IPatternFingerprinter StructFP1, IPatternFingerprinter BondsCF1, IPatternFingerprinter BondsOC1, IPatternFingerprinter BondsST1, IPatternFingerprinter StructFP2, IPatternFingerprinter BondsCF2, IPatternFingerprinter BondsOC2, IPatternFingerprinter BondsST2) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
alpha
- weight for BondFPbeta
- weight for StructuralFPStructFP1
- BondsCF1
- Reactant Bond Cleaved/Formed FP for Query ReactionBondsCF2
- Product Bond Cleaved/Formed FP for Target ReactionBondsOC1
- Reactant Bond Order/Change FP for Query ReactionStructFP2
- BondsOC2
- Product Bond Order/Change FP for Target ReactionBondsST1
- Reactant Bond Stereo FP for Query ReactionBondsST2
- Product Bond Stereo FP for Query Reactionorg.openscience.cdk.exception.CDKException
java.lang.Exception
public static boolean isSubset(double alpha, double beta, double[] StructFP1, double[] BondsCF1, double[] BondsOC1, double[] BondsST1, double[] StructFP2, double[] BondsCF2, double[] BondsOC2, double[] BondsST2) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
alpha
- weight for BondFPbeta
- weight for StructuralFPStructFP1
- BondsCF1
- Reactant Bond Cleaved/Formed FP for Query ReactionBondsCF2
- Product Bond Cleaved/Formed FP for Target ReactionBondsOC1
- Reactant Bond Order/Change FP for Query ReactionStructFP2
- BondsOC2
- Product Bond Order/Change FP for Target ReactionBondsST1
- Reactant Bond Stereo FP for Query ReactionBondsST2
- Product Bond Stereo FP for Query Reactionorg.openscience.cdk.exception.CDKException
java.lang.Exception
public static boolean isSubset(double[] BondsCF1, double[] BondsOC1, double[] BondsST1, double[] BondsCF2, double[] BondsOC2, double[] BondsST2) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
BondsCF1
- Reactant Bond Cleaved/Formed FP for Query ReactionBondsCF2
- Product Bond Cleaved/Formed FP for Target ReactionBondsOC1
- Reactant Bond Order/Change FP for Query ReactionBondsOC2
- Product Bond Order/Change FP for Target ReactionBondsST1
- Reactant Bond Stereo FP for Query ReactionBondsST2
- Product Bond Stereo FP for Query Reactionorg.openscience.cdk.exception.CDKException
java.lang.Exception
public static boolean isSubset(double[] query, double[] target) throws org.openscience.cdk.exception.CDKException
query
- target
- @Equation Unweighted comparison of patternsorg.openscience.cdk.exception.CDKException
public static boolean isSubset(IPatternFingerprinter query, IPatternFingerprinter target) throws org.openscience.cdk.exception.CDKException
query
- target
- @Equation Unweighted comparison of patternsorg.openscience.cdk.exception.CDKException
public static double getSimilarity(IPatternFingerprinter fp1, IPatternFingerprinter fp2) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
fp1
- fp2
- org.openscience.cdk.exception.CDKException
java.lang.Exception