Serialized Form (overlap-examples-cli-dist 0.3.5 API)

Package com.chemaxon.apidiscovery.linenote
Package com.chemaxon.calculations.io
- Class com.chemaxon.calculations.io.OrderedInputProcessingException extends IllegalArgumentException implements Serializable
  - Serialized Fields
    - inputIndex
```
int inputIndex
```
Package com.chemaxon.calculations.util
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus extends RuntimeException implements Serializable
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus extends RuntimeException implements Serializable
Package com.chemaxon.clustering.framework
- Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk extends Object implements Serializable
- Class com.chemaxon.clustering.framework.RemoveSidechainsSc extends Object implements Serializable
 - Serialized Fields
 - keepUnsaturatedConnections
```
boolean keepUnsaturatedConnections
```
 Keep unsaturated connections.
- Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation extends Object implements Serializable
 - Serialized Fields
 - indexToFramework
```
List<E> indexToFramework
```
 Mapping of cluster index to frameworks.
Package com.chemaxon.descriptors.alignment
- Class com.chemaxon.descriptors.alignment.AbstractShapeComparator extends Object implements Serializable
 - Serialized Fields
 - generator
```
DescriptorGenerator generator
```
- Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator extends Object implements Serializable
 - Serialized Fields
 - parameters
```
AbstractShapeGeneratorParameter parameters
```
- Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter extends Object implements Serializable
 - Serialized Fields
 - atomTyping
```
AtomTyping atomTyping
```
 The setting for available shape coloring methods.
- Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter extends Object implements Serializable
 - Serialized Fields
 - flexibilityMode
```
AlignmentProperties.FlexibilityMode flexibilityMode
```
 - shapeFunction
```
ShapeFunction shapeFunction
```
 - tryCount
```
Optional<T> tryCount
```
- Class com.chemaxon.descriptors.alignment.ShapeComparatorException extends RuntimeException implements Serializable
 
 serialVersionUID:
 
 1L
- Class com.chemaxon.descriptors.alignment.ShapeGeneratorException extends RuntimeException implements Serializable
 
 serialVersionUID:
 
 1L
Package com.chemaxon.descriptors.alignment.drshape
- Class com.chemaxon.descriptors.alignment.drshape.DRShape extends Object implements Serializable
 - Serialized Fields
 - shapeData
```
ShapeData shapeData
```
 - generator
```
DRShapeGenerator generator
```
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter extends BaseShapeComparatorParameter implements Serializable
 - Serialized Fields
 - metrics
```
DRShapeMetrics metrics
```
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator extends Object implements Serializable
 - Serialized Fields
 - parameters
```
DRShapeGeneratorParameter parameters
```
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter extends AbstractShapeGeneratorParameter implements Serializable
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable
 - Serialized Fields
 - comparatorParameter
```
DRShapeComparatorParameter comparatorParameter
```
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable
 - Serialized Fields
 - comparatorParameter
```
DRShapeComparatorParameter comparatorParameter
```
- Class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable
 - Serialized Fields
 - comparatorParameter
```
DRShapeComparatorParameter comparatorParameter
```
Package com.chemaxon.descriptors.alignment.shape
- Class com.chemaxon.descriptors.alignment.shape.Shape extends Object implements Serializable
 - Serialized Fields
 - shapeData
```
ShapeData shapeData
```
 - generator
```
ShapeGenerator generator
```
- Class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter extends BaseShapeComparatorParameter implements Serializable
 - Serialized Fields
 - metrics
```
ShapeMetrics metrics
```
- Class com.chemaxon.descriptors.alignment.shape.ShapeGenerator extends AbstractShapeGenerator<ShapeDescriptor,ShapeGeneratorParameter> implements Serializable
- Class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter extends AbstractShapeGeneratorParameter implements Serializable
- Class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator extends AbstractShapeComparator<ShapeDescriptor> implements Serializable
 - Serialized Fields
 - comparatorParameter
```
ShapeComparatorParameter comparatorParameter
```
- Class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator extends AbstractShapeComparator<ShapeDescriptor> implements Serializable
 - Serialized Fields
 - comparatorParameter
```
ShapeComparatorParameter comparatorParameter
```
Package com.chemaxon.descriptors.common
Package com.chemaxon.descriptors.common.binary
- Class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - comparator
```
BinaryVectorComparator comparator
```
 Underlying comparator.
 - descriptorSerializer
```
DescriptorSerializer descriptorSerializer
```
 Underlying descriptor serializer, also source of the guard object.
 - unguardedContext
```
UnguardedContext<D extends Descriptor,T extends Serializable> unguardedContext
```
 Associated unguarded context.
 - lowerb
```
double lowerb
```
 Lower bound stored.
 - upperb
```
double upperb
```
 Upper bound stored.
 - size
```
int size
```
 Binary vector length.
- Class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl extends Object implements Serializable
 - Serialized Fields
 - fp
```
int[] fp
```
 Represented fingerprint.
 - guardObject
```
Object guardObject
```
 Associated guard object.
 - endianness
```
BinaryVectors.Endianness endianness
```
 Endianness of packing (long-int-byte-binary) operations.
- Class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer extends Object implements Serializable
 - Serialized Fields
 - guardObject
```
Object guardObject
```
 Associated guard object.
 - endianness
```
BinaryVectors.Endianness endianness
```
 Endianness.
 - size
```
int size
```
 Fingerprint size.
Package com.chemaxon.descriptors.common.comparison
Package com.chemaxon.descriptors.common.comparison.impl
- Class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - bitCount
```
int bitCount
```
 Underlying fingerprint length.
 - serializer
```
DescriptorSerializer serializer
```
 Associated serializer.
- Class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - unguardedContext
```
UnguardedContext<D extends Descriptor,T extends Serializable> unguardedContext
```
 Represented unguarded context.
 - descriptorComparator
```
DescriptorComparator<D extends Descriptor> descriptorComparator
```
 Represented descriptor comparator.
 - descriptorSerializer
```
DescriptorSerializer descriptorSerializer
```
 Represented descriptor serializer.
 - guardObject
```
Object guardObject
```
 Associated guard object.
- Class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Number of components.
 - serializer
```
DescriptorSerializer serializer
```
 Associated serializer.
 - defaultMetric
```
FloatVectorMetrics defaultMetric
```
 Default metric.
- Class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Number of components.
 - scaler
```
LinearScaler scaler
```
 Underlying scaler.
 - serializer
```
DescriptorSerializer serializer
```
 Associated serializer.
- Class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Number of components.
 - scaler
```
LinearScaler scaler
```
 Underlying scaler.
 - serializer
```
DescriptorSerializer serializer
```
 Associated descriptor serializer. Source of the guard object.
- Class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - serializer
```
DescriptorSerializer serializer
```
 Descriptor serialzier.
 - comparator
```
DescriptorComparator<D extends Descriptor> comparator
```
 Exposed comparator.
Package com.chemaxon.descriptors.common.realvector
- Class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - comparator
```
FloatVectorComparator comparator
```
 Comparator.
 - descriptorSerializer
```
DescriptorSerializer descriptorSerializer
```
 Associated serializer.
 - unguardedContext
```
UnguardedContext<D extends Descriptor,T extends Serializable> unguardedContext
```
 Associated unguarded context.
 - lenght
```
int lenght
```
 Fingerprint size / dimensionality
- Class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - fp
```
float[] fp
```
 Float array fingerprint.
 - guardObject
```
Object guardObject
```
 Associated guard object.
- Class com.chemaxon.descriptors.common.realvector.LinearScalerImpl extends Object implements Serializable
 - Serialized Fields
 - min
```
double min
```
 Lower bound of scaled range.
 - max
```
double max
```
 Upper bound of scaled range.
- Class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl extends Object implements Serializable
 - Serialized Fields
 - fp
```
byte[] fp
```
 Float array fingerprint.
 - gen
```
ScaledFvDescriptorGenerator gen
```
 Associated scaler, serves also as a guard object.
- Class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor extends Object implements Serializable
 - Serialized Fields
 - fp
```
short[] fp
```
 Float array fingerprint.
 - gen
```
ScaledFvDescriptorGenerator gen
```
 Associated scaler, serves also as a guard object.
Package com.chemaxon.descriptors.common.reflect
- Class com.chemaxon.descriptors.common.reflect.FixedValueInvocationHandler extends Object implements Serializable
 - Serialized Fields
 - ret
```
Object ret
```
 Value to return.
- Class com.chemaxon.descriptors.common.reflect.ForwardingInvocationHandler extends Object implements Serializable
 - Serialized Fields
 - target
```
Object target
```
 Forwarding target.
- Class com.chemaxon.descriptors.common.reflect.GuardedSerializableReturnValue extends Object implements Serializable
 - Serialized Fields
 - guard
```
Object guard
```
 Guard object.
 - base
```
InvocationHandler base
```
 Base handler.
- Class com.chemaxon.descriptors.common.reflect.GuardedSingleArgument extends Object implements Serializable
 - Serialized Fields
 - guard
```
Object guard
```
 Guard object.
 - base
```
InvocationHandler base
```
 Base handler.
- Class com.chemaxon.descriptors.common.reflect.ReturnValueTransformingInvocationHandler extends Object implements Serializable
 - Serialized Fields
 - transformation
```
Function<F,T> transformation
```
 Transformation.
 - base
```
InvocationHandler base
```
 Base handler.
- Class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler extends Object implements Serializable
 - Serialized Fields
 - transformation
```
Function<F,T> transformation
```
 Function to apply.
Package com.chemaxon.descriptors.common.unguarded
Package com.chemaxon.descriptors.common.unguarded.impl
- Class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl extends Object implements Serializable
 - Serialized Fields
 - extractor
```
UnguardedExtractor<D extends Descriptor,T extends Serializable> extractor
```
 Represented extractor.
 - comparator
```
UnguardedDissimilarityCalculator<T> comparator
```
 Represented comparator.
Package com.chemaxon.descriptors.common.unguarded.impl.calc
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - comparator
```
DescriptorComparator<D extends Descriptor> comparator
```
 Underlying comparator.
Package com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitCount
```
int bitCount
```
      Fingerprint length in bits.
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitCount
```
int bitCount
```
      Fingerprint length in bits.
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitCount
```
int bitCount
```
      Fingerprint length in bits.
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitCount
```
int bitCount
```
      Fingerprint length in bits.
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - coeffQuery
```
double coeffQuery
```
      Query side coefficient.
    - coeffTarget
```
double coeffTarget
```
      Target side coefficient.
Package com.chemaxon.descriptors.common.unguarded.impl.calc.floats
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto extends Object implements Serializable
  
  serialVersionUID:
  
  0L
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - coeffQuery
```
double coeffQuery
```
      Query side coefficient.
    - coeffTarget
```
double coeffTarget
```
      Target side coefficient.
Package com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - scaler
```
LinearScaler scaler
```
      Underlying scaler.
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto extends Object implements Serializable
  
  serialVersionUID:
  
  0L
Package com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv
- Class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - scaler
```
LinearScaler scaler
```
      Underlying scaler.
    - length
```
int length
```
      Dimensionality.
Package com.chemaxon.descriptors.common.unguarded.impl.extractors
- Class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - fplength
```
int fplength
```
 Expected length in longs.
 - guardObj
```
Object guardObj
```
 Expected guard object.
- Class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Length.
 - guardObj
```
Object guardObj
```
 Guard object.
- Class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Length.
 - guardObj
```
Object guardObj
```
 Associated guard object.
- Class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - length
```
int length
```
 Length.
 - guardObj
```
Object guardObj
```
 Associated guard object.
- Class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - serializer
```
DescriptorSerializer serializer
```
 Underlying serializer.
Package com.chemaxon.descriptors.fingerprints.cfp
- Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitsPerPattern
```
int bitsPerPattern
```
      Bits set for each pattern.
    - length
```
int length
```
      Fingerprint length (bit count).
    - bondCount
```
int bondCount
```
      Max pattern length considered (bond count).
    - rings
```
boolean rings
```
      Consider rings in fingerprint generation.
Package com.chemaxon.descriptors.fingerprints.ecfp
- Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - diameter
```
int diameter
```
 Diameter parameter.
 - length
```
int length
```
 Fingerprint length (bit count).
 - atomTypizer
```
EcfpAtomTypizers atomTypizer
```
 Atom typizer to use.
 - identifierConfigurationXml
```
Optional<T> identifierConfigurationXml
```
 Identifier configuration for custom XML mode.
- Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - params
```
EcfpParameters params
```
 Delegated parameters.

Package com.chemaxon.descriptors.fingerprints.maccs

Class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp extends Object implements Serializable

Serialized Fields

bit1
```
GsSearch bit1
```
bit2
```
GsSearch bit2
```
bit8
```
GsSearch bit8
```
bit11
```
GsSearch bit11
```
bit13
```
GsSearch bit13
```
bit14
```
GsSearch bit14
```
bit15
```
GsSearch bit15
```
bit16
```
GsSearch bit16
```
bit17
```
GsSearch bit17
```
bit19
```
GsSearch bit19
```
bit21
```
GsSearch bit21
```
bit22
```
GsSearch bit22
```
bit23
```
GsSearch bit23
```
bit24
```
GsSearch bit24
```
bit25
```
GsSearch bit25
```
bit26
```
GsSearch bit26
```
bit28
```
GsSearch bit28
```
bit30
```
GsSearch bit30
```
bit31
```
GsSearch bit31
```
bit32
```
GsSearch bit32
```
bit33
```
GsSearch bit33
```
bit34
```
GsSearch bit34
```
bit36
```
GsSearch bit36
```
bit37
```
GsSearch bit37
```
bit38
```
GsSearch bit38
```
bit39
```
GsSearch bit39
```
bit40
```
GsSearch bit40
```
bit41
```
GsSearch bit41
```
bit43
```
GsSearch bit43
```
bit44
```
GsSearch bit44
```
bit45
```
GsSearch bit45
```
bit47
```
GsSearch bit47
```
bit48
```
GsSearch bit48
```
bit49
```
GsSearch bit49
```
bit50
```
GsSearch bit50
```
bit51
```
GsSearch bit51
```
bit52
```
GsSearch bit52
```
bit53
```
GsSearch bit53
```
bit54
```
GsSearch bit54
```
bit55
```
GsSearch bit55
```
bit56
```
GsSearch bit56
```
bit57
```
GsSearch bit57
```
bit58
```
GsSearch bit58
```
bit59
```
GsSearch bit59
```
bit60
```
GsSearch bit60
```
bit61
```
GsSearch bit61
```
bit62
```
GsSearch bit62
```
bit63
```
GsSearch bit63
```
bit64
```
GsSearch bit64
```
bit65
```
GsSearch bit65
```
bit66
```
GsSearch bit66
```
bit67
```
GsSearch bit67
```
bit68
```
GsSearch bit68
```
bit69
```
GsSearch bit69
```
bit70
```
GsSearch bit70
```
bit71
```
GsSearch bit71
```
bit72
```
GsSearch bit72
```
bit73
```
GsSearch bit73
```
bit74
```
GsSearch bit74
```
bit75
```
GsSearch bit75
```
bit76
```
GsSearch bit76
```
bit77
```
GsSearch bit77
```
bit78
```
GsSearch bit78
```
bit79
```
GsSearch bit79
```
bit80
```
GsSearch bit80
```
bit81
```
GsSearch bit81
```
bit82
```
GsSearch bit82
```
bit83
```
GsSearch bit83
```
bit84
```
GsSearch bit84
```
bit85
```
GsSearch bit85
```
bit86
```
GsSearch bit86
```
bit87
```
GsSearch bit87
```
bit89
```
GsSearch bit89
```
bit90
```
GsSearch bit90
```
bit91
```
GsSearch bit91
```
bit92
```
GsSearch bit92
```
bit93
```
GsSearch bit93
```
bit94
```
GsSearch bit94
```
bit95
```
GsSearch bit95
```
bit96
```
GsSearch bit96
```
bit97
```
GsSearch bit97
```
bit98
```
GsSearch bit98
```
bit99
```
GsSearch bit99
```
bit100
```
GsSearch bit100
```
bit101
```
GsSearch bit101
```
bit102
```
GsSearch bit102
```
bit104
```
GsSearch bit104
```
bit105
```
GsSearch bit105
```
bit106
```
GsSearch bit106
```
bit107
```
GsSearch bit107
```
bit108
```
GsSearch bit108
```
bit109
```
GsSearch bit109
```
bit110
```
GsSearch bit110
```
bit111
```
GsSearch bit111
```
bit112
```
GsSearch bit112
```
bit113
```
GsSearch bit113
```
bit114
```
GsSearch bit114
```
bit115
```
GsSearch bit115
```
bit116
```
GsSearch bit116
```
bit117
```
GsSearch bit117
```
bit118
```
GsSearch bit118
```
bit119
```
GsSearch bit119
```
bit120
```
GsSearch bit120
```
bit121
```
GsSearch bit121
```
bit122
```
GsSearch bit122
```
bit123
```
GsSearch bit123
```
bit124
```
GsSearch bit124
```
bit126
```
GsSearch bit126
```
bit127
```
GsSearch bit127
```
bit128
```
GsSearch bit128
```
bit129
```
GsSearch bit129
```
bit131
```
GsSearch bit131
```
bit132
```
GsSearch bit132
```
bit133
```
GsSearch bit133
```
bit135
```
GsSearch bit135
```
bit136
```
GsSearch bit136
```
bit138
```
GsSearch bit138
```
bit139
```
GsSearch bit139
```
bit140
```
GsSearch bit140
```
bit141
```
GsSearch bit141
```
bit142
```
GsSearch bit142
```
bit144
```
GsSearch bit144
```
bit145
```
GsSearch bit145
```
bit147
```
GsSearch bit147
```
bit148
```
GsSearch bit148
```
bit149
```
GsSearch bit149
```
bit150
```
GsSearch bit150
```
bit151
```
GsSearch bit151
```
bit152
```
GsSearch bit152
```
bit154
```
GsSearch bit154
```
bit155
```
GsSearch bit155
```
bit156
```
GsSearch bit156
```
bit157
```
GsSearch bit157
```
bit158
```
GsSearch bit158
```
bit162
```
GsSearch bit162
```
bit163
```
GsSearch bit163
```
bit165
```
GsSearch bit165
```

Class com.chemaxon.descriptors.fingerprints.maccs.GsSearch extends Object implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - log
```
org.apache.commons.logging.Log log
```
    Logger to use.
  - sma
```
String sma
```
    The input SMARTS string
  - queries
```
Molecule[] queries
```
    The query molecule or array if the SMARTS is not represented correctly.
Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters extends Object implements Serializable
Class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs extends BitSet implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - mol
```
Molecule mol
```
  - ringAtoms
```
BitSet ringAtoms
```
Class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs extends BitSet implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - mol
```
Molecule mol
```
  - ringBonds
```
BitSet ringBonds
```

Package com.chemaxon.descriptors.fingerprints.maccs.cli
- Class com.chemaxon.descriptors.fingerprints.maccs.cli.GSearch extends GsSearch implements Serializable
  
  serialVersionUID:
  
  0L
Package com.chemaxon.descriptors.fingerprints.pf2d
- Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl extends Object implements Serializable
- Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - xmlConfig
```
Optional<T> xmlConfig
```
 XML configuration string.
- Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl extends FloatVectorDescriptorImpl implements Serializable
 - Serialized Fields
 - fingerprint
```
PharmacophoreFingerprint fingerprint
```
 Exposed fingerprint.
- Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - xmlConfig
```
Optional<T> xmlConfig
```
 XML configuration string.
Package com.chemaxon.descriptors.metrics
- Class com.chemaxon.descriptors.metrics.TverskyParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - coeffTarget
```
double coeffTarget
```
      Coefficient for target only part.
    - coeffQuery
```
double coeffQuery
```
      Coefficient for query only part.
Package com.chemaxon.descriptors.vectors.binary
- Class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - parameters
```
BvParameters parameters
```
      Parameter object for the represented settings.
- Class com.chemaxon.descriptors.vectors.binary.BvParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - length
```
int length
```
      Fingerprint length (bit count).
    - stringFormat
```
BvParameters.StringFormat stringFormat
```
      String format to use.
    - endianness
```
BinaryVectors.Endianness endianness
```
      Endianness of long-int-byte-binary packing operations.
Package com.chemaxon.descriptors.vectors.floats
- Class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - parameters
```
FvParameters parameters
```
      Parameter object for the represented settings.
- Class com.chemaxon.descriptors.vectors.floats.FvParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - length
```
int length
```
      Fingerprint length (bit count).
    - numericRepresentation
```
FvParameters.NumericRepresentation numericRepresentation
```
      Numeric representation.
    - scaledMin
```
double scaledMin
```
      Minimum value for scaling.
    - scaledMax
```
double scaledMax
```
      Maximum value for scaling.
    - sparseCompression
```
FvParameters.SparseCompression sparseCompression
```
      Optimization for sparse vectors.
Package com.chemaxon.overlap.bruteforce
- Class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - storage
```
UnguardedPagedStorage<T extends Serializable> storage
```
 Paged storage.
 - comparator
```
UnguardedDissimilarityCalculator<T> comparator
```
 Descriptor comparator to use.
Package com.chemaxon.overlap.cli
- Class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - context
```
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> context
```
 Associated context.
 - queries
```
DescriptorsWithMols<T extends Serializable> queries
```
 Queries.
 - targets
```
DescriptorsWithMols<T extends Serializable> targets
```
 Targets.
 - metrics
```
Optional<T> metrics
```
 Metrics used when specified.
 - results
```
KnnResults results
```
 Results of query-target overlap analysis.
 - name
```
String name
```
 Human readable comparison name.
 - descName
```
String descName
```
 Human readable descriptor name.
 - queryName
```
String queryName
```
 Human readable query name.
 - targetName
```
String targetName
```
 Human readable target name.
- Class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - context
```
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> context
```
 Associated context.
 - desc
```
UnguardedPagedOverlap<T extends Serializable> desc
```
 Descriptors.
 - idp
```
IndexProjector idp
```
 Storage id projector.
 - mms
```
MasterMoleculeStorage mms
```
 Master molecule storage.
 - mids
```
MasterStorage<T> mids
```
 Master ID storage.
 - selfKnn
```
KnnResults selfKnn
```
 Self knn.
Package com.chemaxon.overlap.cli.util
- Class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl extends Object implements Serializable
 - Serialized Fields
 - idstorage
```
MasterStringStorage idstorage
```
 Exposed IDs.
 - descriptors
```
UnguardedPagedOverlap<T extends Serializable> descriptors
```
 Exposed descriptors.
 - context
```
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> context
```
 Represented context.
 - indexProjector
```
IndexProjector indexProjector
```
 Projector for the descriptor storage.
- Class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl extends Object implements Serializable
 - Serialized Fields
 - idstorage
```
MasterStringStorage idstorage
```
 Exposed IDs.
 - descriptors
```
UnguardedPagedOverlap<T extends Serializable> descriptors
```
 Exposed descriptors.
 - mms
```
MasterMoleculeStorage mms
```
 Represented MMS.
 - context
```
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> context
```
 Represented context.
 - indexProjector
```
IndexProjector indexProjector
```
 Projector for the descriptor storage.
 - propsOrNull
```
Map<K,V> propsOrNull
```
 Additional properties.
Package com.chemaxon.overlap.cli.util.pipeline
- Class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl.DeserializerImpl extends Object implements Serializable
 - Serialized Fields
 - deserializedType
```
Class<T> deserializedType
```
 - progressiveDeserializer
```
ProgressiveDeserializer<T> progressiveDeserializer
```
Package com.chemaxon.overlap.cli.util.prop
- Class com.chemaxon.overlap.cli.util.prop.CliParam extends Object implements Serializable
 - Serialized Fields
 - name
```
String name
```
 Name of property to extract.
 - valueType
```
String valueType
```
 Extracted property value type.
 - calcType
```
String calcType
```
 Extractor type.
 - calcSpec
```
String calcSpec
```
 Parameter for extractor.
- Class com.chemaxon.overlap.cli.util.prop.MolProp extends Object implements Serializable
 - Serialized Fields
 - storage
```
MasterStorage<T> storage
```
 Property storage.
 - extractor
```
PropertyExtractor<T> extractor
```
 Associated extractor.
Package com.chemaxon.overlap.cli.util.prop.impl
- Class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor extends Object implements Serializable
 - Serialization Methods
 - readResolve
```
Object readResolve()
```
 Part of Java serialization mechanism. This is a work around to recreate ChemTermPropertyExtractor.threadLocalChemJep on deserialization.
 
 See Also:
 
 http://docs.oracle.com/javase/6/docs/platform/serialization/spec/input.html#5903
 - Serialized Fields
 - extractedType
```
Class<T> extractedType
```
 Extracted type.
 - cast
```
Function<F,T> cast
```
 Cast to the desired type.
 - expression
```
String expression
```
 Expression source.
 - allowFailed
```
boolean allowFailed
```
 Allow failed.
- Class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractor extends Object implements Serializable
 - Serialized Fields
 - allowMissing
```
boolean allowMissing
```
 Allow missing properties.
- Class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor extends Object implements Serializable
 - Serialized Fields
 - extractedType
```
Class<T> extractedType
```
 Extracted type.
 - parse
```
Function<F,T> parse
```
 Parser.
 - propname
```
String propname
```
 Property name.
 - allowMissing
```
boolean allowMissing
```
 Allow missing properties.
Package com.chemaxon.overlap.context
- Class com.chemaxon.overlap.context.OverlapAnalysisContext extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - standardizer
```
StandardizerWrapper standardizer
```
 Represented Standardizer which can not be null.
 - generator
```
DescriptorGenerator generator
```
 Represented descriptor generator which can not be null.
 - comparator
```
DescriptorComparator<D extends Descriptor> comparator
```
 Represented descriptor comparator which can not be null.
 - pagesize
```
int pagesize
```
 Represented page size.
 - queryPagesize
```
int queryPagesize
```
 Represented query page size.
 - unguardedFormExtractor
```
UnguardedExtractor<D extends Descriptor,T extends Serializable> unguardedFormExtractor
```
 Extractor function which can not be null.
 - unguardedDissimCalc
```
UnguardedDissimilarityCalculator<T> unguardedDissimCalc
```
 Unguarded dissimilarity calculation used for searches which can not be null.
Package com.chemaxon.overlap.io
- Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage extends Object implements Serializable
  - Serialized Fields
    - size
```
int size
```
      Virtual size; all absent.
- Class com.chemaxon.overlap.io.CompactStringStorage extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - pagesize
```
int pagesize
```
      Number of master entities stored on one page.
      All but the last page is expected to contain the given entity count.
    - absentCount
```
int absentCount
```
      Total number of absent master entities, including skippeds.
    - size
```
int size
```
      Total number of covered master entities, including absents (and skippeds).
    - skips
```
int skips
```
      Number of initial skips.
      The given number of master entities are all absent, they are not stored.
    - starts
```
int[][] starts
```
      Index of the first byte of the i * pagesize + j-th non-skipped structure.
    - storage
```
byte[][] storage
```
      Storage array.
- Class com.chemaxon.overlap.io.MasterMoleculeStorageImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - importOptsOrNull
```
String importOptsOrNull
```
      Options to pass MolImporter.importMol(java.lang.String, java.lang.String).
    - sources
```
CompactStringStorage sources
```
      Structure sources which can be imported with MolImporter.
      Since ImmutableList does not permit null elements missing structures are represented as a special String literal stored in
Package com.chemaxon.overlap.persistence.serialization
- Class com.chemaxon.overlap.persistence.serialization.AbstractSerialization extends Object implements Serializable
 - Serialized Fields
 - cl
```
Class<T> cl
```
 Class to expose as AbstractSerialization.getDeserializedType().
- Class com.chemaxon.overlap.persistence.serialization.DelegatingDeserializer extends Object implements Serializable
 - Serialized Fields
 - cl
```
Class<T> cl
```
 Deserialized class type.
 - wu
```
long wu
```
 Work units to be reported.
Package com.chemaxon.overlap.persistence.storage
- Class com.chemaxon.overlap.persistence.storage.CompactStringStorageSerialization extends AbstractSerialization<CompactStringStorage,MasterStringStorage> implements Serializable
- Class com.chemaxon.overlap.persistence.storage.DescriptorContainer extends Object implements Serializable
 - Serialized Fields
 - context
```
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> context
```
 Underlying context.
 - indexProjector
```
IndexProjector indexProjector
```
 Index projector between descriptors and master.
 - descriptors
```
UnguardedPagedOverlap<T extends Serializable> descriptors
```
 Descriptor storage.
- Class com.chemaxon.overlap.persistence.storage.MasterMoleculeStorageSerialization extends AbstractSerialization<MasterMoleculeStorageImpl,MasterMoleculeStorage> implements Serializable
Package com.chemaxon.overlap.result
Package com.chemaxon.overlap.result.impl
- Class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - k
```
int k
```
      Number of nearest neighbor IDs stored.
    - queryCount
```
int queryCount
```
      Number of queries.
    - targets
```
int[] targets
```
      Concatenated kNN lists.
      First item is the nearest neighbor of the first query (having index [0]; Item n+1 (having index n]) is the nearest neighbor of the second query (having index [1])
    - dissimilarities
```
double[] dissimilarities
```
      Array of dissimilarities.
      Items are associate to the contents of FixedKnnResultsImpl.targets array.
    - minDissim
```
double minDissim
```
      Minimum of dissimilarities.
    - maxDissim
```
double maxDissim
```
      Maximum of dissimilarities.
    - minTargetIndex
```
int minTargetIndex
```
      Minimum of target indexes.
    - maxTargetIndex
```
int maxTargetIndex
```
      Maximum of target indexes.
    - missingDissimilarity
```
double missingDissimilarity
```
      Value representing missing items.
- Class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - minNeighborCount
```
int minNeighborCount
```
      Minimal number of nearest neighbor IDs stored.
    - maxNeighborCount
```
int maxNeighborCount
```
      Maximal number of nearest neighbor IDs stored.
    - allNeighborCount
```
int allNeighborCount
```
      All neighbor count.
    - queryCount
```
int queryCount
```
      Number of queries.
    - index
```
int[] index
```
      Index of queries in the IndexedKnnResultsImpl.targets and dissimilarities arrays. Note that this array contains IndexedKnnResultsImpl.queryCount+1 elements.
    - targets
```
int[] targets
```
      Concatenated kNN lists.
      First item is the nearest neighbor of the first query (having index [0]; Item n+1 (having index n]) is the nearest neighbor of the second query (having index [1])
    - dissimilarities
```
double[] dissimilarities
```
      Array of dissimilarities.
      Items are associate to the contents of IndexedKnnResultsImpl.targets array.
    - minDissim
```
double minDissim
```
      Minimum of dissimilarities.
    - maxDissim
```
double maxDissim
```
      Maximum of dissimilarities.
    - minTargetIndex
```
int minTargetIndex
```
      Minimum of target indexes.
    - maxTargetIndex
```
int maxTargetIndex
```
      Maximum of target indexes.
    - missingDissimilarity
```
double missingDissimilarity
```
      Value representing missing items.
- Class com.chemaxon.overlap.result.impl.SimilarityResultImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - targetIndex
```
int targetIndex
```
      Represented target index.
    - dissimilarity
```
double dissimilarity
```
      Represented dissimilarity.
- Class com.chemaxon.overlap.result.impl.SimilarityResultsImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - queries
```
int[] queries
```
      Array of queries.
    - targets
```
int[] targets
```
      Array of targets.
    - dissimilarities
```
double[] dissimilarities
```
      Array of dissimilarities.
Package com.chemaxon.overlap.service.async
- Class com.chemaxon.overlap.service.async.AsyncCallService.AsyncCallIdNotFoundException extends RuntimeException implements Serializable
Package com.chemaxon.overlap.service.task
- Class com.chemaxon.overlap.service.task.TaskService.TaskNotDeletableException extends RuntimeException implements Serializable
- Class com.chemaxon.overlap.service.task.TaskService.TaskNotFoundException extends RuntimeException implements Serializable
Package com.chemaxon.overlap.servlets
- Class com.chemaxon.overlap.servlets.KnnServlet extends HttpServlet implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - log
```
org.apache.commons.logging.Log log
```
      Logger to use.
- Class com.chemaxon.overlap.servlets.MetaServlet extends HttpServlet implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - log
```
org.apache.commons.logging.Log log
```
      Deprecated.
      
      Logger to use.
- Class com.chemaxon.overlap.servlets.MolsServlet extends HttpServlet implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - log
```
org.apache.commons.logging.Log log
```
      Deprecated.
      
      Logger to use.
- Class com.chemaxon.overlap.servlets.SelfOverlapServlet extends HttpServlet implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - log
```
org.apache.commons.logging.Log log
```
      Logger to use.
Package com.chemaxon.overlap.storage
Package com.chemaxon.overlap.storage.impl
- Class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - pages
```
ImmutableList<E> pages
```
 Page storage.
 All but the last page is expected to have the same size.
 - size
```
int size
```
 Total number of descriptors stored.
 - pagesize
```
int pagesize
```
 Page size for all but the last page.
Package com.chemaxon.overlap.version
- Class com.chemaxon.overlap.version.OverlapVersionInfo extends Object implements Serializable
  - Serialized Fields
    - overlapVersion
```
String overlapVersion
```
      Overlap-examples package main version.
      
      See Also:
      
      OverlapVersion.overlapVersion()
    - overlapBuildTimestamp
```
String overlapBuildTimestamp
```
      Build time stamp, expected format is yyyy-MM-dd HH:mm:ss z.
      
      See Also:
      
      OverlapVersion.overlapBuildTimestamp()
    - cxnInternalVersion
```
String cxnInternalVersion
```
      CXN backend internal version.
      
      See Also:
      
      OverlapVersion.cxnInternalVersion()
    - mjsVersion
```
String mjsVersion
```
      Packaged MarvinJS version.
      
      See Also:
      
      OverlapVersion.mjsVersion()
    - info
```
String info
```
      Human readable String.
      
      See Also:
      
      OverlapVersion.detailedVersionInfo()
    - git
```
String git
```
      Git revision.
    - gitAbbrev
```
String gitAbbrev
```
      Git abbreviated revision.
    - gitClean
```
boolean gitClean
```
      Git clean.
    - overlapDevelVersion
```
String overlapDevelVersion
```
      Development version info. in the format (overlapVersion)-(gitAbbrev)[-M]
Package com.chemaxon.overlap.wui
- Class com.chemaxon.overlap.wui.SlowlyDeserializingMms extends Object implements Serializable
- Class com.chemaxon.overlap.wui.SlowUnguardedComparator extends Object implements Serializable
 - Serialized Fields
 - base
```
UnguardedDissimilarityCalculator<T> base
```
 - delay
```
long delay
```
Package com.chemaxon.overlap.wui.resources.exceptions
- Class com.chemaxon.overlap.wui.resources.exceptions.WuiBadRequestException extends WuiException implements Serializable
- Class com.chemaxon.overlap.wui.resources.exceptions.WuiException extends RuntimeException implements Serializable
- Class com.chemaxon.overlap.wui.resources.exceptions.WuiForbiddenException extends WuiException implements Serializable
- Class com.chemaxon.overlap.wui.resources.exceptions.WuiInternalServerErrorException extends WuiException implements Serializable
- Class com.chemaxon.overlap.wui.resources.exceptions.WuiNotFoundException extends WuiException implements Serializable
Package com.chemaxon.virtuallib.sc.model.sdf
- Class com.chemaxon.virtuallib.sc.model.sdf.Attachment extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - attachmentAtomIndex
```
int attachmentAtomIndex
```
 Index of pseudo atom representing the attachment point.
 - attachedAtomIndex
```
int attachedAtomIndex
```
 Index of the attached atom. Two special cases TBD:
 
 Zx-Zy like bond only fragment attachment(s); currently not supported
 
 Zx-H hydrogen substitution with implicit Hs; special value or explicit H?
 - attachmentIndex
```
int attachmentIndex
```
 Attachment index, eg n from Rn or Zn.
 - bondOrder
```
int bondOrder
```
 Bond order of the attachment.
- Class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - attachmentAtoms
```
com.chemaxon.calculations.sc.util.IntListSet attachmentAtoms
```
 Indices of pseuodo atoms represented.
 - attachedAtoms
```
com.chemaxon.calculations.sc.util.IntListSet attachedAtoms
```
 Indices of atoms having at least one represented attachment neighbor.
 - attachmentByAtom
```
ImmutableMap<K,V> attachmentByAtom
```
 Mapping of attachments.
- Class com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroupImpl extends AttachmentGroupImpl implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - attachmentIndices
```
com.chemaxon.calculations.sc.util.IntListSet attachmentIndices
```
 Indices of attachments
 - attachmentByIndex
```
ImmutableMap<K,V> attachmentByIndex
```
 Mapping of attachments.
- Class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - attachmentIndices
```
com.chemaxon.calculations.sc.util.IntListSet attachmentIndices
```
 R/Zn indices represented by this group.
 - fragments
```
List<E> fragments
```
 Fragments.
 - scaffold
```
Scaffold scaffold
```
 Scaffold.
 - totalRealAtomCount
```
int totalRealAtomCount
```
 Total real atom count in all fragments.
- Class com.chemaxon.virtuallib.sc.model.sdf.RgFrag extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - log
```
org.apache.commons.logging.Log log
```
 Logger to use.
 - reactantId
```
String reactantId
```
 Reactant ID.
 - mol
```
Molecule mol
```
 Represented molecule.
 - connectivity
```
com.chemaxon.calculations.sc.graph.Connectivity connectivity
```
 Connetivity of the represented molecule.
 - realAtoms
```
com.chemaxon.calculations.sc.util.IntListSet realAtoms
```
 Real, non-attachment atoms.
 - zAttachments
```
IndexedAttachmentGroup zAttachments
```
 Z attachments.
- Class com.chemaxon.virtuallib.sc.model.sdf.Scaffold extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - libraryId
```
String libraryId
```
 Library ID.
 - rxnId
```
Optional<T> rxnId
```
 Optional RXN ID.
 - comment
```
Optional<T> comment
```
 Optional comment.
 - rAttachments
```
IndexedAttachmentGroup rAttachments
```
 R attachments.
- Class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - extension
```
Molecule extension
```
 Structure associated to the extension. Semantics is similar to the RgFrag/Scaffold semantics; using R/Z aliased atoms.
 - connectivity
```
com.chemaxon.calculations.sc.graph.Connectivity connectivity
```
 - zattachments
```
IndexedAttachmentGroup zattachments
```
 Z attachments. Attachments to the original scaffold.
 - rattachments
```
IndexedAttachmentGroup rattachments
```
 R attachments. Attachment points for the remaining R definitions.
 - cxSmiles
```
String cxSmiles
```
 Structure in canonical cxsmiles format.
 - smiles
```
String smiles
```
 Structure in canonical smiles format.
- Class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder extends Object implements Serializable
 
 serialVersionUID:
 
 0L
 - Serialized Fields
 - log
```
org.apache.commons.logging.Log log
```
 Logger to use.
 - frag
```
RgFrag frag
```
 Underlying RGroup fragment.
 - atomsToKeep
```
com.chemaxon.calculations.sc.util.IntListSetBuilder atomsToKeep
```
 Selected atoms to keep. Z atoms should not be selected.

Serialized Form

Package com.chemaxon.apidiscovery.linenote

Package com.chemaxon.calculations.io

Class com.chemaxon.calculations.io.OrderedInputProcessingException extends IllegalArgumentException implements Serializable

Serialized Fields

inputIndex

Package com.chemaxon.calculations.util

Class com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus extends RuntimeException implements Serializable

Class com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus extends RuntimeException implements Serializable

Package com.chemaxon.clustering.framework

Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk extends Object implements Serializable

Class com.chemaxon.clustering.framework.RemoveSidechainsSc extends Object implements Serializable

Serialized Fields

keepUnsaturatedConnections

Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation extends Object implements Serializable

Serialized Fields

indexToFramework

Package com.chemaxon.descriptors.alignment

Class com.chemaxon.descriptors.alignment.AbstractShapeComparator extends Object implements Serializable

Serialized Fields

generator

Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator extends Object implements Serializable

Serialized Fields

parameters

Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter extends Object implements Serializable

Serialized Fields

atomTyping

Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter extends Object implements Serializable

Serialized Fields

flexibilityMode

shapeFunction

tryCount

Class com.chemaxon.descriptors.alignment.ShapeComparatorException extends RuntimeException implements Serializable

Class com.chemaxon.descriptors.alignment.ShapeGeneratorException extends RuntimeException implements Serializable

Package com.chemaxon.descriptors.alignment.drshape

Class com.chemaxon.descriptors.alignment.drshape.DRShape extends Object implements Serializable

Serialized Fields

shapeData

generator

Class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter extends BaseShapeComparatorParameter implements Serializable

Serialized Fields

metrics

Class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator extends Object implements Serializable

Serialized Fields

parameters

Class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter extends AbstractShapeGeneratorParameter implements Serializable

Class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable

Serialized Fields

comparatorParameter

Class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable

Serialized Fields

comparatorParameter

Class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator extends AbstractShapeComparator<DRShapeDescriptor> implements Serializable

Serialized Fields

comparatorParameter

Package com.chemaxon.descriptors.alignment.shape

Class com.chemaxon.descriptors.alignment.shape.Shape extends Object implements Serializable

Serialized Fields

shapeData

generator

Class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter extends BaseShapeComparatorParameter implements Serializable

Serialized Fields

metrics

Class com.chemaxon.descriptors.alignment.shape.ShapeGenerator extends AbstractShapeGenerator<ShapeDescriptor,ShapeGeneratorParameter> implements Serializable

Class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter extends AbstractShapeGeneratorParameter implements Serializable

Class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator extends AbstractShapeComparator<ShapeDescriptor> implements Serializable

Serialized Fields

comparatorParameter

Class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator extends AbstractShapeComparator<ShapeDescriptor> implements Serializable

Serialized Fields

comparatorParameter

Package com.chemaxon.descriptors.common

Package com.chemaxon.descriptors.common.binary

Class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator extends Object implements Serializable

Serialized Fields

comparator

descriptorSerializer

unguardedContext

lowerb

upperb