org.openscience.cdk.interfaces.IAtomContainer query
org.openscience.cdk.interfaces.IAtomContainer target
com.google.common.collect.HashBiMap<K,V> mapping
java.util.Map<K,V> mappingIndex
Algorithm algorithmType
double bondSensitiveMcGregorOut
double bondInSensitiveMcGregor
int i
int j
java.util.List<E> compGraphNodes
java.util.List<E> compGraphNodesCZero
java.util.List<E> cEdges
java.util.List<E> dEdges
int cEdgesSize
int dEdgesSize
org.openscience.cdk.interfaces.IAtomContainer source
org.openscience.cdk.interfaces.IAtomContainer target
boolean shouldMatchBonds
boolean shouldMatchRings
boolean matchAtomType
java.util.BitSet fingerprint
long fingerprintAsLong
org.openscience.cdk.interfaces.IAtomContainer container
int max
int counter
int coverage
int limit
java.lang.String sourceDbID
java.util.BitSet rorFp
java.util.BitSet porFp
IPatternFingerprinter cfFp
IPatternFingerprinter ocFp
IPatternFingerprinter stFP
org.openscience.cdk.interfaces.IReaction.Direction direction
java.lang.String pattern
double weight
java.util.Set<E> featureSet
java.lang.String fingerprintID
int fingerprintSize
IPatternFingerprinter reactionFingerprint
java.util.Map<K,V> solution
java.util.Map<K,V> rLabelledAtoms
java.util.Map<K,V> pLabelledAtoms
java.util.Map<K,V> inputRankLabelledAtomsReactant
java.util.Map<K,V> inputRankLabelledAtomsProduct
java.util.Map<K,V> educts
java.util.Map<K,V> products
java.util.List<E> rBonds
java.util.List<E> pBonds
org.openscience.cdk.interfaces.IReaction reactionWithSTOICHIOMETRY
boolean partialMapping
IMappingAlgorithm algorithm
MoleculeMoleculeMapping reactionBlastMolMapping
java.lang.Integer substrateAtomCounter
java.lang.Integer productAtomCounter
int delta
boolean balanceFlag
org.openscience.cdk.interfaces.IReaction reactionWithUniqueSTOICHIOMETRY
boolean removeHydrogen
int delta
MoleculeMoleculeMapping reactionBlastMolMapping
IMappingAlgorithm algorithm
Holder matrixHolder
MoleculeMoleculeMapping reactionBlastMolMapping
java.util.List<E> eductCounter
java.util.List<E> productCounter
org.openscience.cdk.interfaces.IReaction reaction
java.util.Map<K,V> substrateductFPMap
java.util.Map<K,V> productFPMap
FingerprintGenerator fpr
HydrogenFreeFingerPrintContainer hydFreeFPContainer
boolean removeHydrogen
java.lang.String reactionID
ReactionContainer structureMapObj
BestMatch bestMatchContainer
IMappingAlgorithm theory
java.util.List<E> mappingMolPair
EBIMatrix stereoMatrix
EBIMatrix cliqueMatrix
EBIMatrix graphSimilarityMatrix
EBIMatrix fragmentMatrix
EBIMatrix energyMatrix
EBIMatrix fpSimMatrixWithoutHydrogen
int row
int coloumn
ReactionContainer structureInformation
BestMatch bestMatchContainer
java.util.List<E> eductCounter
java.util.List<E> productCounter
java.lang.String reactionID
HydrogenFreeFingerPrintContainer hydFPFree
IMappingAlgorithm theory
int rowSize
int colSize
boolean[][] flagSimilarityMatrix
boolean[][] flagStereoMatrix
boolean isomorphismFlag
Holder matrixHolder
Holder matrixHolderWithSimilarityCheck
Holder matrixHolderWithStereoCheck
boolean ruleMatched
Holder matrixHolder
Holder matrixHolderClone
java.util.Map<K,V> matchedRowColoumn
org.openscience.cdk.interfaces.IAtomContainer smartsWater
org.openscience.cdk.interfaces.IAtomContainer smartsPhosphate
org.openscience.cdk.interfaces.IAtomContainer smartsSulphate
org.openscience.cdk.interfaces.IAtomContainer smartsL_Glutamate
org.openscience.cdk.interfaces.IAtomContainer smartsL_Glutamine
org.openscience.cdk.interfaces.IAtomContainer smartsTwoOxoglutarate
org.openscience.cdk.interfaces.IAtomContainer smartsD_Glutamate
org.openscience.cdk.interfaces.IAtomContainer smartsAcetate
org.openscience.cdk.interfaces.IAtomContainer smartsATP
org.openscience.cdk.interfaces.IAtomContainer smartsADP
org.openscience.cdk.interfaces.IAtomContainer smartsCoA
org.openscience.cdk.interfaces.IAtomContainer smartsAcetyl_CoA
org.openscience.cdk.interfaces.IAtomContainer smartsC00003
org.openscience.cdk.interfaces.IAtomContainer smartsC00006
org.openscience.cdk.interfaces.IAtomContainer smartsC00004
org.openscience.cdk.interfaces.IAtomContainer smartsC00005
int rowSize
int colSize
boolean[][] flagMatrix
java.util.Map<K,V> mcsAtomMap
java.util.Map<K,V> fragmentCount
java.util.Map<K,V> bondBreakingEnergy
java.util.Map<K,V> stereoScore
java.util.Map<K,V> similarity
org.openscience.cdk.interfaces.IReactionSet reactionSet
int moleculeCounter
java.util.Map<K,V> stoichiometryMap
java.util.Map<K,V> fingerprintMap
java.util.Map<K,V> moleculeMap
java.util.Map<K,V> fingerPrintMap
java.util.Map<K,V> reactant_product_mapping_map
java.util.Map<K,V> eAtomContainerMap
java.util.Map<K,V> pAtomContainerMap
java.util.Map<K,V> eFingerPrintMap
java.util.Map<K,V> pFingerPrintMap
java.util.Map<K,V> eductContainerModificationMap
java.util.Map<K,V> productContainerModificationMap
IFingerprintGenerator fpr
int sourceIndex
int targetIndex
java.lang.String mol1
java.lang.String mol2
java.lang.Integer indexI
java.lang.Integer indexJ
java.lang.Integer indexStep
boolean keggMapping
boolean rBLASTMapping
org.openscience.cdk.interfaces.IAtomContainer matchedMol
java.lang.String matchedSMILES
java.util.List<E> _data
int row
int col
org.openscience.cdk.interfaces.IAtomContainer educt
org.openscience.cdk.interfaces.IAtomContainer product
org.openscience.cdk.interfaces.IAtomContainer matchedPart
java.util.Map<K,V> bestAtomMappingList
int fragmentCount
org.openscience.cdk.interfaces.IAtomContainer queryContainer
int targetPosition
org.openscience.cdk.interfaces.IAtomContainer targetContainer
AtomAtomMapping atomatomMapping
int queryPosition
java.lang.Integer stereoScore
java.lang.Integer fragmentSize
java.lang.Double energy
org.openscience.cdk.interfaces.IAtomContainerSet myMoleculeSet
java.util.List<E> bonds
java.util.List<E> atomArray
boolean withoutH
java.util.Map<K,V> mappings
boolean DEBUG
BondChangeAnnotator bondChangeAnnotator
IPatternFingerprinter formedCleavedWFingerprint
IPatternFingerprinter orderChangesWFingerprint
IPatternFingerprinter stereoChangesWFingerprint
IPatternFingerprinter reactionCenterWFingerprint
java.util.Map<K,V> reactionCenterFormedCleavedFingerprint
java.util.Map<K,V> reactionCenterOrderChangeFingerprint
java.util.Map<K,V> reactionCenterStereoChangeFingerprint
java.util.Map<K,V> bondFormedMap
java.util.Map<K,V> bondCleavedMap
java.util.Map<K,V> bondOrderRMap
java.util.Map<K,V> bondOrderPMap
java.util.Map<K,V> AtomStereoRMap
java.util.Map<K,V> AtomStereoPMap
java.util.List<E> reactionCenterFragmentList
java.util.Set<E> reactionMoleculeMoleculePairList
org.openscience.cdk.interfaces.IReaction mappedReaction
int energySum
int energyDelta
int totalSmallestFragmentSize
java.util.HashMap<K,V> matrixMap
java.util.HashMap<K,V> typeMap
java.util.HashMap<K,V> freqMap
IMappingAlgorithm algorithmID
double bondEnergySum
double energyDelta
int totalBondChanges
int totalFragmentChanges
int totalStereoChanges
int smallestFragmentCount
int totalCarbonBondChanges
org.openscience.cdk.interfaces.IReaction reaction
Reactor reactor
int totalChanges
boolean chosen
BondChangeCalculator bondChangeCalculator
boolean generate3D
boolean generate2D
MappingSolution selectedMapping
java.util.Collection<E> allSolutions
BEMatrix reactantBEMatrix
BEMatrix productBEMatrix
AtomAtomMappingContainer myMapping
boolean DEBUG
IStereoAndConformation rAtomStereo
IStereoAndConformation pAtomStereo
org.openscience.cdk.interfaces.IAtom rAtom
org.openscience.cdk.interfaces.IAtom pAtom
java.util.List<E> reactantAtomArray
java.util.List<E> productAtomArray
org.openscience.cdk.interfaces.IAtom reactantAtom
org.openscience.cdk.interfaces.IAtom productAtom
boolean stereoChange
IStereoAndConformation atomStereoR
IStereoAndConformation atomStereoP
org.openscience.cdk.interfaces.IBond reactantBond
org.openscience.cdk.interfaces.IBond productBond
float bondChangeDelta
ReactantProductPair name
ReactantProductPair smarts
ReactantProductPair signature
java.lang.String smirks
ReactantProductPair smarts1
ReactantProductPair signature1
java.lang.String smirks1
ReactantProductPair smarts2
ReactantProductPair signature2
java.lang.String smirks2
ReactantProductPair smarts3
ReactantProductPair signature3
java.lang.String smirks3
java.lang.String query
java.lang.String target
java.lang.String signature
int level
EnumSubstrateProduct rpf
double[][] matrix
int rows
int columns
double[][] L
int n
boolean isspd
int n
boolean issymmetric
double[] d
double[] e
double[][] V
double[][] H
double[] ort
double[][] LU
int m
int n
int pivsign
int[] piv
double[][] QR
int m
int n
double[] Rdiag
double[][] U
double[][] V
double[] s
int m
int n