Serialized Form (cdk 2.5 API)

Package org.openscience.cdk
- Class org.openscience.cdk.AminoAcid extends Monomer implements Serializable
  
  serialVersionUID:
  
  -5032283549467862509L
  - Serialized Fields
    - nTerminus
```
IAtom nTerminus
```
      The atom that constitutes the N-terminus.
    - cTerminus
```
IAtom cTerminus
```
      The atom that constitutes the C-terminus.
- Class org.openscience.cdk.Association extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  -9138919895942850167L
  - Serialized Fields
    - electronCount
```
int electronCount
```
      Number of electrons in the association.
    - atoms
```
IAtom[] atoms
```
      The atoms which take part in the association.
    - atomCount
```
int atomCount
```
- Class org.openscience.cdk.Atom extends AtomType implements Serializable
  
  serialVersionUID:
  
  -3137373012494608794L
  - Serialized Fields
    - point2d
```
javax.vecmath.Point2d point2d
```
      A 2D point specifying the location of this atom in a 2D coordinate space.
    - point3d
```
javax.vecmath.Point3d point3d
```
      A 3 point specifying the location of this atom in a 3D coordinate space.
    - fractionalPoint3d
```
javax.vecmath.Point3d fractionalPoint3d
```
      A 3 point specifying the location of this atom in a crystal unit cell.
    - hydrogenCount
```
Integer hydrogenCount
```
      The number of implicitly bound hydrogen atoms for this atom.
    - stereoParity
```
Integer stereoParity
```
      A stereo parity descriptor for the stereochemistry of this atom.
    - charge
```
Double charge
```
      The partial charge of the atom. The default value is CDKConstants.UNSET and serves to provide a check whether the charge has been set or not
- Class org.openscience.cdk.AtomContainer extends ChemObject implements Serializable
  
  serialVersionUID:
  
  5678100348445919254L
  - Serialized Fields
    - atomCount
```
int atomCount
```
      Number of atoms contained by this object.
    - bondCount
```
int bondCount
```
      Number of bonds contained by this object.
    - lonePairCount
```
int lonePairCount
```
      Number of lone pairs contained by this object.
    - singleElectronCount
```
int singleElectronCount
```
      Number of single electrons contained by this object.
    - growArraySize
```
int growArraySize
```
      Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
    - atoms
```
IAtom[] atoms
```
      Internal array of atoms.
    - bonds
```
IBond[] bonds
```
      Internal array of bonds.
    - lonePairs
```
ILonePair[] lonePairs
```
      Internal array of lone pairs.
    - singleElectrons
```
ISingleElectron[] singleElectrons
```
      Internal array of single electrons.
    - stereoElements
```
Set<E> stereoElements
```
      Internal list of atom parities.
- Class org.openscience.cdk.AtomContainerSet extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -521290255592768395L
  - Serialized Fields
    - atomContainers
```
IAtomContainer[] atomContainers
```
      Array of AtomContainers.
    - atomContainerCount
```
int atomContainerCount
```
      Number of AtomContainers contained by this container.
    - multipliers
```
Double[] multipliers
```
      Defines the number of instances of a certain molecule in the set. It is 1 by default.
    - growArraySize
```
int growArraySize
```
      Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.AtomType extends Isotope implements Serializable
  
  serialVersionUID:
  
  -7950397716808229972L
  - Serialized Fields
    - maxBondOrder
```
IBond.Order maxBondOrder
```
      The maximum bond order allowed for this atom type.
    - bondOrderSum
```
Double bondOrderSum
```
      The maximum sum of all bond orders allowed for this atom type.
    - covalentRadius
```
Double covalentRadius
```
      The covalent radius of this atom type.
    - formalCharge
```
Integer formalCharge
```
      The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0
    - hybridization
```
IAtomType.Hybridization hybridization
```
      The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
    - electronValency
```
Integer electronValency
```
      The electron Valency of this atom with CDKConstants.UNSET as default.
    - formalNeighbourCount
```
Integer formalNeighbourCount
```
      The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitly connected atoms, including implicit hydrogens.
    - identifier
```
String identifier
```
      String representing the identifier for this atom type with null as default.
- Class org.openscience.cdk.BioPolymer extends Polymer implements Serializable
  
  serialVersionUID:
  
  -5001873073769634393L
  - Serialized Fields
    - strands
```
Map<K,V> strands
```
- Class org.openscience.cdk.Bond extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  7057060562283387384L
  - Serialized Fields
    - order
```
IBond.Order order
```
      The bond order of this bond.
    - atomCount
```
int atomCount
```
      Number of atoms contained by this object.
    - atoms
```
IAtom[] atoms
```
      A list of atoms participating in this bond.
    - stereo
```
IBond.Stereo stereo
```
      A descriptor the stereochemical orientation of this bond.
    - display
```
IBond.Display display
```
- Class org.openscience.cdk.ChemFile extends ChemObject implements Serializable
  
  serialVersionUID:
  
  1926781734333430132L
  - Serialized Fields
    - chemSequences
```
IChemSequence[] chemSequences
```
      Array of ChemSquences.
    - chemSequenceCount
```
int chemSequenceCount
```
      Number of ChemSequences contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.ChemModel extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -5213425310451366185L
  - Serialized Fields
    - setOfMolecules
```
IAtomContainerSet setOfMolecules
```
      A MoleculeSet.
    - setOfReactions
```
IReactionSet setOfReactions
```
      A ReactionSet.
    - ringSet
```
IRingSet ringSet
```
      A RingSet.
    - crystal
```
ICrystal crystal
```
      A Crystal.
- Class org.openscience.cdk.ChemObject extends Object implements Serializable
  
  serialVersionUID:
  
  2798134548764323328L
  - Serialized Fields
    - chemObjectListeners
```
List<E> chemObjectListeners
```
      List for listener administration.
    - properties
```
Map<K,V> properties
```
      A hashtable for the storage of any kind of properties of this IChemObject.
    - flags
```
short flags
```
      You will frequently have to use some flags on a IChemObject. For example, if you want to draw a molecule and see if you've already drawn an atom, or in a ring search to check whether a vertex has been visited in a graph traversal. Use these flags while addressing particular positions in the flag array with self-defined constants (flags[VISITED] = true). 100 flags per object should be more than enough.
    - identifier
```
String identifier
```
      The ID is null by default.
    - doNotification
```
boolean doNotification
```
- Class org.openscience.cdk.ChemSequence extends ChemObject implements Serializable
  
  serialVersionUID:
  
  2199218627455492000L
  - Serialized Fields
    - chemModels
```
IChemModel[] chemModels
```
      Array of ChemModels.
    - chemModelCount
```
int chemModelCount
```
      Number of ChemModels contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.Crystal extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  5919649450390509278L
  - Serialized Fields
    - aAxis
```
javax.vecmath.Vector3d aAxis
```
      The a axis.
    - bAxis
```
javax.vecmath.Vector3d bAxis
```
      The b axis.
    - cAxis
```
javax.vecmath.Vector3d cAxis
```
      The c axis.
    - zValue
```
Integer zValue
```
      Number of symmetry related atoms.
    - spaceGroup
```
String spaceGroup
```
      Number of symmetry related atoms.
- Class org.openscience.cdk.ElectronContainer extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -2207894536767670743L
  - Serialized Fields
    - electronCount
```
Integer electronCount
```
      Number of electrons in the ElectronContainer.
- Class org.openscience.cdk.Element extends ChemObject implements Serializable
  
  serialVersionUID:
  
  3062529834691231436L
  - Serialized Fields
    - atomicNumber
```
Integer atomicNumber
```
      The atomic number for this element giving their position in the periodic table.
- Class org.openscience.cdk.EnzymeResidueLocator extends PseudoAtom implements Serializable
  
  serialVersionUID:
  
  -4267555433142927412L
- Class org.openscience.cdk.FragmentAtom extends PseudoAtom implements Serializable
  
  serialVersionUID:
  
  -6144605920605752463L
  - Serialized Fields
    - fragment
```
IAtomContainer fragment
```
    - isExpanded
```
boolean isExpanded
```
- Class org.openscience.cdk.Isotope extends Element implements Serializable
  
  serialVersionUID:
  
  6389365978927575858L
  - Serialized Fields
    - exactMass
```
Double exactMass
```
      Exact mass of this isotope.
    - naturalAbundance
```
Double naturalAbundance
```
      Natural abundance of this isotope.
    - massNumber
```
Integer massNumber
```
      The mass number for this isotope.
- Class org.openscience.cdk.LonePair extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  51311422004885329L
  - Serialized Fields
    - electronCount
```
int electronCount
```
      Number of electrons in the lone pair.
    - atom
```
IAtom atom
```
      The atom with which this lone pair is associated.
- Class org.openscience.cdk.Mapping extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -6541914644492043503L
  - Serialized Fields
    - relation
```
IChemObject[] relation
```
- Class org.openscience.cdk.Monomer extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  -6084164963937650703L
  - Serialized Fields
    - monomerName
```
String monomerName
```
      The name of this monomer (e.g. Trp42).
    - monomerType
```
String monomerType
```
      The type of this monomer (e.g. TRP).
- Class org.openscience.cdk.Polymer extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  -2596790658835319339L
  - Serialized Fields
    - monomers
```
Map<K,V> monomers
```
- Class org.openscience.cdk.PseudoAtom extends Atom implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - label
```
String label
```
    - attachPoint
```
int attachPoint
```
- Class org.openscience.cdk.Reaction extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -554752558363533678L
  - Serialized Fields
    - growArraySize
```
int growArraySize
```
    - reactants
```
IAtomContainerSet reactants
```
    - products
```
IAtomContainerSet products
```
    - agents
```
IAtomContainerSet agents
```
      These are the used solvent, catalysts etc that normally appear above the reaction arrow
    - map
```
IMapping[] map
```
    - mappingCount
```
int mappingCount
```
    - reactionDirection
```
IReaction.Direction reactionDirection
```
- Class org.openscience.cdk.ReactionScheme extends ReactionSet implements Serializable
  
  serialVersionUID:
  
  -3676327644698347260L
  - Serialized Fields
    - reactionScheme
```
List<E> reactionScheme
```
      A List of reaction schemes
- Class org.openscience.cdk.ReactionSet extends ChemObject implements Serializable
  
  serialVersionUID:
  
  1555749911904585204L
  - Serialized Fields
    - reactions
```
IReaction[] reactions
```
      Array of Reactions.
    - reactionCount
```
int reactionCount
```
      Number of Reactions contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the Reactions array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.Ring extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  6604894792331865990L
- Class org.openscience.cdk.RingSet extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  7168431521057961434L
- Class org.openscience.cdk.SingleElectron extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  7796574734668490940L
  - Serialized Fields
    - electronCount
```
int electronCount
```
      Number of electron for this class is defined as one.
    - atom
```
IAtom atom
```
      The atom with which this single electron is associated.
- Class org.openscience.cdk.Strand extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  4200943086350928356L
  - Serialized Fields
    - monomers
```
Map<K,V> monomers
```
      The list of all Monomers in the Strand.
    - strandName
```
String strandName
```
      The name of this strand (e.g. A, B).
    - strandType
```
String strandType
```
      The type of this strand (e.g. PEPTIDE, DNA, RNA).
- Class org.openscience.cdk.Substance extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  -4819492883237421487L
Package org.openscience.cdk.debug
- Class org.openscience.cdk.debug.DebugAminoAcid extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  4092864536013855890L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugAtom extends Atom implements Serializable
  
  serialVersionUID:
  
  188945429187084868L
- Class org.openscience.cdk.debug.DebugAtomContainer extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  7584711255625778345L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugAtomContainerSet extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  -8358480615782437454L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugAtomType extends AtomType implements Serializable
  
  serialVersionUID:
  
  1427549696666679540L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugBioPolymer extends BioPolymer implements Serializable
  
  serialVersionUID:
  
  5349870327516864575L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugBond extends Bond implements Serializable
  
  serialVersionUID:
  
  -2330398179697796261L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugChemFile extends ChemFile implements Serializable
  
  serialVersionUID:
  
  -5575043161897814279L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugChemModel extends ChemModel implements Serializable
  
  serialVersionUID:
  
  -920209300005079592L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugChemObject extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -8547443535884526365L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugChemSequence extends ChemSequence implements Serializable
  
  serialVersionUID:
  
  -628120469241907704L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugCrystal extends Crystal implements Serializable
  
  serialVersionUID:
  
  -1749989529794094087L
- Class org.openscience.cdk.debug.DebugElectronContainer extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  5309193617982266230L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugElement extends Element implements Serializable
  
  serialVersionUID:
  
  -8520499563841667066L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugFragmentAtom extends FragmentAtom implements Serializable
  
  serialVersionUID:
  
  0L
- Class org.openscience.cdk.debug.DebugIsotope extends Isotope implements Serializable
  
  serialVersionUID:
  
  -2659188100080921299L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugLonePair extends LonePair implements Serializable
  
  serialVersionUID:
  
  5683399496728893341L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugMapping extends Mapping implements Serializable
  
  serialVersionUID:
  
  -3785399530153469835L
- Class org.openscience.cdk.debug.DebugMonomer extends Monomer implements Serializable
  
  serialVersionUID:
  
  -7312839949399572435L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugPDBAtom extends PDBAtom implements Serializable
  
  serialVersionUID:
  
  -2432127382224382452L
- Class org.openscience.cdk.debug.DebugPDBMonomer extends PDBMonomer implements Serializable
  
  serialVersionUID:
  
  -5156111560946745699L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugPDBPolymer extends PDBPolymer implements Serializable
  
  serialVersionUID:
  
  -8485559594520919850L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugPDBStructure extends PDBStructure implements Serializable
  
  serialVersionUID:
  
  1934748703085969097L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugPolymer extends Polymer implements Serializable
  
  serialVersionUID:
  
  -1459933635059023539L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugPseudoAtom extends PseudoAtom implements Serializable
  
  serialVersionUID:
  
  -5935090219383862070L
- Class org.openscience.cdk.debug.DebugReaction extends Reaction implements Serializable
  
  serialVersionUID:
  
  -8958358842308217875L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugReactionScheme extends ReactionScheme implements Serializable
  
  serialVersionUID:
  
  705803374163613819L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugReactionSet extends ReactionSet implements Serializable
  
  serialVersionUID:
  
  1620489912540131959L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugRing extends Ring implements Serializable
  
  serialVersionUID:
  
  -6420813246421544803L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugRingSet extends RingSet implements Serializable
  
  serialVersionUID:
  
  -4144201128508373352L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugSingleElectron extends SingleElectron implements Serializable
  
  serialVersionUID:
  
  -2895377834940311825L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugStrand extends Strand implements Serializable
  
  serialVersionUID:
  
  1794588804926192427L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
- Class org.openscience.cdk.debug.DebugSubstance extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  7729610512495602788L
  - Serialized Fields
    - logger
```
ILoggingTool logger
```
Package org.openscience.cdk.dict
- Class org.openscience.cdk.dict.DictRef extends Object implements Serializable
  
  serialVersionUID:
  
  -3691244168587563625L
  - Serialized Fields
    - type
```
String type
```
    - reference
```
String reference
```
Package org.openscience.cdk.event
- Class org.openscience.cdk.event.ChemObjectChangeEvent extends EventObject implements Serializable
  
  serialVersionUID:
  
  5418604788783986725L
Package org.openscience.cdk.exception
- Class org.openscience.cdk.exception.CDKException extends Exception implements Serializable
  
  serialVersionUID:
  
  8371328769230823678L
- Class org.openscience.cdk.exception.IncorrectUseOfCDKCoreClassError extends Error implements Serializable
  
  serialVersionUID:
  
  5307727155023470782L
- Class org.openscience.cdk.exception.Intractable extends CDKException implements Serializable
- Class org.openscience.cdk.exception.InvalidSmilesException extends CDKException implements Serializable
  
  serialVersionUID:
  
  1932255464874201495L
- Class org.openscience.cdk.exception.NoSuchAtomException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -6367051798808824272L
- Class org.openscience.cdk.exception.NoSuchAtomTypeException extends CDKException implements Serializable
  
  serialVersionUID:
  
  2689048410917221667L
- Class org.openscience.cdk.exception.UnsupportedChemObjectException extends CDKException implements Serializable
  
  serialVersionUID:
  
  -5348883360384907383L
Package org.openscience.cdk.fingerprint
- Class org.openscience.cdk.fingerprint.BitSetFingerprint extends Object implements Serializable
  
  serialVersionUID:
  
  9034774011095165227L
  - Serialized Fields
    - bitset
```
BitSet bitset
```
- Class org.openscience.cdk.fingerprint.IntArrayCountFingerprint extends Object implements Serializable
  
  serialVersionUID:
  
  8656072054328822795L
  - Serialized Fields
    - hitHashes
```
int[] hitHashes
```
    - numOfHits
```
int[] numOfHits
```
    - behaveAsBitFingerprint
```
boolean behaveAsBitFingerprint
```
- Class org.openscience.cdk.fingerprint.IntArrayFingerprint extends Object implements Serializable
  
  serialVersionUID:
  
  5175105019921245323L
  - Serialized Fields
    - trueBits
```
int[] trueBits
```
- Class org.openscience.cdk.fingerprint.RandomNumber extends Object implements Serializable
  
  serialVersionUID:
  
  23345464573453571L
- Class org.openscience.cdk.fingerprint.ShortestPathFingerprinter extends AbstractFingerprinter implements Serializable
  
  serialVersionUID:
  
  7867864332244557861L
  - Serialized Fields
    - fingerprintLength
```
int fingerprintLength
```
      The default length of created fingerprints.
    - rand
```
RandomNumber rand
```
- Class org.openscience.cdk.fingerprint.SimpleAtomComparator extends Object implements Serializable
  
  serialVersionUID:
  
  2345252069991872083L
Package org.openscience.cdk.graph.invariant.exception
- Class org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException extends Exception implements Serializable
  
  serialVersionUID:
  
  -4592379323522144603L
- Class org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException extends Exception implements Serializable
  
  serialVersionUID:
  
  -1781128244202287777L
- Class org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException extends Exception implements Serializable
  
  serialVersionUID:
  
  8597172558566661068L
Package org.openscience.cdk.io
- Class org.openscience.cdk.io.ReaderEvent extends EventObject implements Serializable
  
  serialVersionUID:
  
  660541244342274716L
Package org.openscience.cdk.isomorphism
- Class org.openscience.cdk.isomorphism.IsomorphismTester extends Object implements Serializable
  
  serialVersionUID:
  
  2499779110996693974L
  - Serialized Fields
    - baseTable
```
long[] baseTable
```
    - sortedBaseTable
```
long[] sortedBaseTable
```
    - compareTable
```
long[] compareTable
```
    - sortedCompareTable
```
long[] sortedCompareTable
```
    - base
```
IAtomContainer base
```
    - compare
```
IAtomContainer compare
```
Package org.openscience.cdk.isomorphism.matchers
- Class org.openscience.cdk.isomorphism.matchers.RGroupQuery extends QueryChemObject implements Serializable
  
  serialVersionUID:
  
  -1656116487614720605L
  - Serialized Fields
    - rootStructure
```
IAtomContainer rootStructure
```
      The root structure (or scaffold) to which R-groups r attached.
    - rGroupDefinitions
```
Map<K,V> rGroupDefinitions
```
      Rgroup definitions, each a list of possible substitutes for the given R number.
    - rootAttachmentPoints
```
Map<K,V> rootAttachmentPoints
```
      For each Rgroup Atom there may be a map containing (number,bond), being the attachment order (1,2) and the bond to attach to.
Package org.openscience.cdk.iupac.parser
- Class org.openscience.cdk.iupac.parser.ParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentToken
```
Token currentToken
```
      This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
      Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.
    - tokenImage
```
String[] tokenImage
```
      This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.
    - eol
```
String eol
```
      The end of line string for this machine.
- Class org.openscience.cdk.iupac.parser.Token extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kind
```
int kind
```
      An integer that describes the kind of this token. This numbering system is determined by JavaCCParser, and a table of these numbers is stored in the file ...Constants.java.
    - beginLine
```
int beginLine
```
      The line number of the first character of this Token.
    - beginColumn
```
int beginColumn
```
      The column number of the first character of this Token.
    - endLine
```
int endLine
```
      The line number of the last character of this Token.
    - endColumn
```
int endColumn
```
      The column number of the last character of this Token.
    - image
```
String image
```
      The string image of the token.
    - next
```
Token next
```
      A reference to the next regular (non-special) token from the input stream. If this is the last token from the input stream, or if the token manager has not read tokens beyond this one, this field is set to null. This is true only if this token is also a regular token. Otherwise, see below for a description of the contents of this field.
    - specialToken
```
Token specialToken
```
      This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token. If there are no such special tokens, this field is set to null. When there are more than one such special token, this field refers to the last of these special tokens, which in turn refers to the next previous special token through its specialToken field, and so on until the first special token (whose specialToken field is null). The next fields of special tokens refer to other special tokens that immediately follow it (without an intervening regular token). If there is no such token, this field is null.
- Class org.openscience.cdk.iupac.parser.TokenMgrError extends Error implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorCode
```
int errorCode
```
      Indicates the reason why the exception is thrown. It will have one of the above 4 values.
Package org.openscience.cdk.libio.md
- Class org.openscience.cdk.libio.md.ChargeGroup extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  362147331841737028L
  - Serialized Fields
    - number
```
int number
```
    - parentMolecule
```
MDMolecule parentMolecule
```
    - switchingAtom
```
IAtom switchingAtom
```
- Class org.openscience.cdk.libio.md.MDMolecule extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  -3129626782945020908L
  - Serialized Fields
    - residues
```
List<E> residues
```
    - chargeGroups
```
List<E> chargeGroups
```
- Class org.openscience.cdk.libio.md.Residue extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  6548353601272976798L
  - Serialized Fields
    - number
```
int number
```
    - name
```
String name
```
    - parentMolecule
```
MDMolecule parentMolecule
```
Package org.openscience.cdk.math
- Class org.openscience.cdk.math.RandomNumbersTool extends Random implements Serializable
  
  serialVersionUID:
  
  -8238833473383641882L
Package org.openscience.cdk.pharmacophore
- Class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond extends Bond implements Serializable
- Class org.openscience.cdk.pharmacophore.PharmacophoreAtom extends Atom implements Serializable
  - Serialized Fields
    - smarts
```
String smarts
```
    - matchingAtoms
```
int[] matchingAtoms
```
    - symbol
```
String symbol
```
- Class org.openscience.cdk.pharmacophore.PharmacophoreBond extends Bond implements Serializable
- Class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond extends Bond implements Serializable
  - Serialized Fields
    - upper
```
double upper
```
    - lower
```
double lower
```
- Class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom extends Atom implements Serializable
  - Serialized Fields
    - smarts
```
String smarts
```
    - compiledSmarts
```
SmartsPattern[] compiledSmarts
```
    - symbol
```
String symbol
```
- Class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond extends Bond implements Serializable
  - Serialized Fields
    - upper
```
double upper
```
    - lower
```
double lower
```
Package org.openscience.cdk.protein.data
- Class org.openscience.cdk.protein.data.PDBAtom extends Atom implements Serializable
  
  serialVersionUID:
  
  7670650135045832543L
  - Serialized Fields
    - record
```
String record
```
    - tempFactor
```
double tempFactor
```
    - resName
```
String resName
```
    - iCode
```
String iCode
```
    - occupancy
```
double occupancy
```
    - name
```
String name
```
    - chainID
```
String chainID
```
    - altLoc
```
String altLoc
```
    - segID
```
String segID
```
    - serial
```
int serial
```
    - resSeq
```
String resSeq
```
    - oxt
```
boolean oxt
```
    - hetAtom
```
boolean hetAtom
```
- Class org.openscience.cdk.protein.data.PDBMonomer extends Monomer implements Serializable
  
  serialVersionUID:
  
  -7236625816763776733L
  - Serialized Fields
    - iCode
```
String iCode
```
    - chainID
```
String chainID
```
      Denotes which chain in the PDB file this monomer is in.
    - resSeq
```
String resSeq
```
      Denotes which residue sequence in the current chain that this monomer is in.
- Class org.openscience.cdk.protein.data.PDBPolymer extends BioPolymer implements Serializable
  
  serialVersionUID:
  
  4173552834313952358L
  - Serialized Fields
    - sequentialListOfMonomers
```
List<E> sequentialListOfMonomers
```
    - secondaryStructures
```
List<E> secondaryStructures
```
- Class org.openscience.cdk.protein.data.PDBStrand extends Strand implements Serializable
  
  serialVersionUID:
  
  8278569309787734236L
  - Serialized Fields
    - sequentialListOfMonomers
```
List<E> sequentialListOfMonomers
```
- Class org.openscience.cdk.protein.data.PDBStructure extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -1877529009319324448L
  - Serialized Fields
    - structureType
```
String structureType
```
    - startChainID
```
Character startChainID
```
    - startSequenceNumber
```
Integer startSequenceNumber
```
    - startInsertionCode
```
Character startInsertionCode
```
    - endChainID
```
Character endChainID
```
    - endSequenceNumber
```
Integer endSequenceNumber
```
    - endInsertionCode
```
Character endInsertionCode
```
Package org.openscience.cdk.qsar
- Class org.openscience.cdk.qsar.DescriptorException extends CDKException implements Serializable
  
  serialVersionUID:
  
  2564845219649348102L
- Class org.openscience.cdk.qsar.DescriptorSpecification extends Object implements Serializable
  
  serialVersionUID:
  
  7044545275802343828L
  - Serialized Fields
    - specificationReference
```
String specificationReference
```
    - implementationTitle
```
String implementationTitle
```
    - implementationIdentifier
```
String implementationIdentifier
```
    - implementationVendor
```
String implementationVendor
```
- Class org.openscience.cdk.qsar.DescriptorValue extends Object implements Serializable
  
  serialVersionUID:
  
  -5672896059814842972L
  - Serialized Fields
    - specification
```
DescriptorSpecification specification
```
    - parameterNames
```
String[] parameterNames
```
    - parameterSettings
```
Object[] parameterSettings
```
    - value
```
IDescriptorResult value
```
    - descriptorNames
```
String[] descriptorNames
```
    - exception
```
Exception exception
```
Package org.openscience.cdk.qsar.result
- Class org.openscience.cdk.qsar.result.BooleanResult extends BooleanResultType implements Serializable
  
  serialVersionUID:
  
  3746767816253035856L
  - Serialized Fields
    - value
```
boolean value
```
- Class org.openscience.cdk.qsar.result.BooleanResultType extends Object implements Serializable
  
  serialVersionUID:
  
  143647705094158395L
- Class org.openscience.cdk.qsar.result.DoubleArrayResult extends DoubleArrayResultType implements Serializable
  
  serialVersionUID:
  
  2345607580017306612L
  - Serialized Fields
    - array
```
List<E> array
```
- Class org.openscience.cdk.qsar.result.DoubleArrayResultType extends Object implements Serializable
  
  serialVersionUID:
  
  -8255004284721233969L
  - Serialized Fields
    - size
```
int size
```
- Class org.openscience.cdk.qsar.result.DoubleResult extends Object implements Serializable
  
  serialVersionUID:
  
  7711619468523616757L
  - Serialized Fields
    - value
```
double value
```
- Class org.openscience.cdk.qsar.result.DoubleResultType extends Object implements Serializable
  
  serialVersionUID:
  
  -6641147506132424322L
- Class org.openscience.cdk.qsar.result.IntegerArrayResult extends IntegerArrayResultType implements Serializable
  
  serialVersionUID:
  
  4077762427385735922L
  - Serialized Fields
    - array
```
List<E> array
```
- Class org.openscience.cdk.qsar.result.IntegerArrayResultType extends Object implements Serializable
  
  serialVersionUID:
  
  1492674654677531635L
  - Serialized Fields
    - size
```
int size
```
- Class org.openscience.cdk.qsar.result.IntegerResult extends Object implements Serializable
  
  serialVersionUID:
  
  -8066984646119839996L
  - Serialized Fields
    - value
```
int value
```
- Class org.openscience.cdk.qsar.result.IntegerResultType extends Object implements Serializable
  
  serialVersionUID:
  
  -6643953534920216664L
Package org.openscience.cdk.reaction
- Class org.openscience.cdk.reaction.ReactionChain extends ReactionSet implements Serializable
  
  serialVersionUID:
  
  5006986269373043994L
  - Serialized Fields
    - hashMapChain
```
HashMap<K,V> hashMapChain
```
Package org.openscience.cdk.renderer
- Class org.openscience.cdk.renderer.RendererModel extends Object implements Serializable
  
  serialVersionUID:
  
  -4420308906715213445L
  - Serialized Fields
    - notification
```
boolean notification
```
    - toolTipTextMap
```
Map<K,V> toolTipTextMap
```
    - highlightedAtom
```
IAtom highlightedAtom
```
    - highlightedBond
```
IBond highlightedBond
```
    - externalSelectedPart
```
IAtomContainer externalSelectedPart
```
    - clipboardContent
```
IAtomContainer clipboardContent
```
    - selection
```
IChemObjectSelection selection
```
    - merge
```
Map<K,V> merge
```
    - externalHighlightColor
```
IGeneratorParameter<T> externalHighlightColor
```
    - colorHash
```
IGeneratorParameter<T> colorHash
```
    - renderingParameters
```
Map<K,V> renderingParameters
```
      A map of IGeneratorParameter class names to instances.
Package org.openscience.cdk.renderer.color
- Class org.openscience.cdk.renderer.color.CDK2DAtomColors extends Object implements Serializable
  
  serialVersionUID:
  
  6712994043820219426L
- Class org.openscience.cdk.renderer.color.CPKAtomColors extends Object implements Serializable
  
  serialVersionUID:
  
  -3205785984391537452L
- Class org.openscience.cdk.renderer.color.RasmolColors extends Object implements Serializable
  
  serialVersionUID:
  
  2588969984094169759L
Package org.openscience.cdk.ringsearch
- Class org.openscience.cdk.ringsearch.Queue extends Vector implements Serializable
  
  serialVersionUID:
  
  1008167867733841614L
Package org.openscience.cdk.ringsearch.cyclebasis
- Class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle extends org._3pq.jgrapht.graph.UndirectedSubgraph implements Serializable
  
  serialVersionUID:
  
  -3330742084804445688L
Package org.openscience.cdk.silent
- Class org.openscience.cdk.silent.AminoAcid extends Monomer implements Serializable
  
  serialVersionUID:
  
  -5032283549467862509L
  - Serialized Fields
    - nTerminus
```
IAtom nTerminus
```
      The atom that constitutes the N-terminus.
    - cTerminus
```
IAtom cTerminus
```
      The atom that constitutes the C-terminus.
- Class org.openscience.cdk.silent.Atom extends AtomType implements Serializable
  
  serialVersionUID:
  
  -3137373012494608794L
  - Serialized Fields
    - point2d
```
javax.vecmath.Point2d point2d
```
      A 2D point specifying the location of this atom in a 2D coordinate space.
    - point3d
```
javax.vecmath.Point3d point3d
```
      A 3 point specifying the location of this atom in a 3D coordinate space.
    - fractionalPoint3d
```
javax.vecmath.Point3d fractionalPoint3d
```
      A 3 point specifying the location of this atom in a crystal unit cell.
    - hydrogenCount
```
Integer hydrogenCount
```
      The number of implicitly bound hydrogen atoms for this atom.
    - stereoParity
```
Integer stereoParity
```
      A stereo parity descriptor for the stereochemistry of this atom.
    - charge
```
Double charge
```
      The partial charge of the atom. The default value is CDKConstants.UNSET and serves to provide a check whether the charge has been set or not
- Class org.openscience.cdk.silent.AtomContainer extends ChemObject implements Serializable
  
  serialVersionUID:
  
  5678100348445919254L
  - Serialized Fields
    - atomCount
```
int atomCount
```
      Number of atoms contained by this object.
    - bondCount
```
int bondCount
```
      Number of bonds contained by this object.
    - lonePairCount
```
int lonePairCount
```
      Number of lone pairs contained by this object.
    - singleElectronCount
```
int singleElectronCount
```
      Number of single electrons contained by this object.
    - growArraySize
```
int growArraySize
```
      Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
    - atoms
```
IAtom[] atoms
```
      Internal array of atoms.
    - bonds
```
IBond[] bonds
```
      Internal array of bonds.
    - lonePairs
```
ILonePair[] lonePairs
```
      Internal array of lone pairs.
    - singleElectrons
```
ISingleElectron[] singleElectrons
```
      Internal array of single electrons.
    - stereoElements
```
Set<E> stereoElements
```
      Internal list of atom parities.
- Class org.openscience.cdk.silent.AtomContainerSet extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -521290255592768395L
  - Serialized Fields
    - atomContainers
```
IAtomContainer[] atomContainers
```
      Array of AtomContainers.
    - atomContainerCount
```
int atomContainerCount
```
      Number of AtomContainers contained by this container.
    - multipliers
```
Double[] multipliers
```
      Defines the number of instances of a certain molecule in the set. It is 1 by default.
    - growArraySize
```
int growArraySize
```
      Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.silent.AtomType extends Isotope implements Serializable
  
  serialVersionUID:
  
  -7950397716808229972L
  - Serialized Fields
    - maxBondOrder
```
IBond.Order maxBondOrder
```
      The maximum bond order allowed for this atom type.
    - bondOrderSum
```
Double bondOrderSum
```
      The maximum sum of all bond orders allowed for this atom type.
    - covalentRadius
```
Double covalentRadius
```
      The covalent radius of this atom type.
    - formalCharge
```
Integer formalCharge
```
      The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0
    - hybridization
```
IAtomType.Hybridization hybridization
```
      The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
    - electronValency
```
Integer electronValency
```
      The electron Valency of this atom with CDKConstants.UNSET as default.
    - formalNeighbourCount
```
Integer formalNeighbourCount
```
      The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitely connected atoms, including implicit hydrogens.
    - identifier
```
String identifier
```
      String representing the identifier for this atom type with null as default.
- Class org.openscience.cdk.silent.BioPolymer extends Polymer implements Serializable
  
  serialVersionUID:
  
  -5001873073769634393L
  - Serialized Fields
    - strands
```
Map<K,V> strands
```
- Class org.openscience.cdk.silent.Bond extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  7057060562283387384L
  - Serialized Fields
    - order
```
IBond.Order order
```
      The bond order of this bond.
    - atomCount
```
int atomCount
```
      Number of atoms contained by this object.
    - atoms
```
IAtom[] atoms
```
      A list of atoms participating in this bond.
    - stereo
```
IBond.Stereo stereo
```
      A descriptor the stereochemical orientation of this bond.
    - display
```
IBond.Display display
```
- Class org.openscience.cdk.silent.ChemFile extends ChemObject implements Serializable
  
  serialVersionUID:
  
  1926781734333430132L
  - Serialized Fields
    - chemSequences
```
IChemSequence[] chemSequences
```
      Array of ChemSquences.
    - chemSequenceCount
```
int chemSequenceCount
```
      Number of ChemSequences contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.silent.ChemModel extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -5213425310451366185L
  - Serialized Fields
    - setOfMolecules
```
IAtomContainerSet setOfMolecules
```
      A MoleculeSet.
    - setOfReactions
```
IReactionSet setOfReactions
```
      A ReactionSet.
    - ringSet
```
IRingSet ringSet
```
      A RingSet.
    - crystal
```
ICrystal crystal
```
      A Crystal.
- Class org.openscience.cdk.silent.ChemObject extends Object implements Serializable
  
  serialVersionUID:
  
  2798134548764323328L
  - Serialized Fields
    - properties
```
Map<K,V> properties
```
      A hashtable for the storage of any kind of properties of this IChemObject.
    - flags
```
short flags
```
      You will frequently have to use some flags on a IChemObject. For example, if you want to draw a molecule and see if you've already drawn an atom, or in a ring search to check whether a vertex has been visited in a graph traversal. Use these flags while addressing particular positions in the flag array with self-defined constants (flags[VISITED] = true). 100 flags per object should be more than enough.
    - identifier
```
String identifier
```
      The ID is null by default.
    - doNotification
```
boolean doNotification
```
- Class org.openscience.cdk.silent.ChemSequence extends ChemObject implements Serializable
  
  serialVersionUID:
  
  2199218627455492000L
  - Serialized Fields
    - chemModels
```
IChemModel[] chemModels
```
      Array of ChemModels.
    - chemModelCount
```
int chemModelCount
```
      Number of ChemModels contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.silent.Crystal extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  5919649450390509278L
  - Serialized Fields
    - aAxis
```
javax.vecmath.Vector3d aAxis
```
      The a axis.
    - bAxis
```
javax.vecmath.Vector3d bAxis
```
      The b axis.
    - cAxis
```
javax.vecmath.Vector3d cAxis
```
      The c axis.
    - zValue
```
Integer zValue
```
      Number of symmetry related atoms.
    - spaceGroup
```
String spaceGroup
```
      Number of symmetry related atoms.
- Class org.openscience.cdk.silent.ElectronContainer extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -2207894536767670743L
  - Serialized Fields
    - electronCount
```
Integer electronCount
```
      Number of electrons in the ElectronContainer.
- Class org.openscience.cdk.silent.Element extends ChemObject implements Serializable
  
  serialVersionUID:
  
  3062529834691231436L
  - Serialized Fields
    - atomicNumber
```
Integer atomicNumber
```
      The atomic number for this element giving their position in the periodic table.
- Class org.openscience.cdk.silent.FragmentAtom extends PseudoAtom implements Serializable
  
  serialVersionUID:
  
  -6144605920605752463L
  - Serialized Fields
    - fragment
```
IAtomContainer fragment
```
    - isExpanded
```
boolean isExpanded
```
- Class org.openscience.cdk.silent.Isotope extends Element implements Serializable
  
  serialVersionUID:
  
  6389365978927575858L
  - Serialized Fields
    - exactMass
```
Double exactMass
```
      Exact mass of this isotope.
    - naturalAbundance
```
Double naturalAbundance
```
      Natural abundance of this isotope.
    - massNumber
```
Integer massNumber
```
      The mass number for this isotope.
- Class org.openscience.cdk.silent.LonePair extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  51311422004885329L
  - Serialized Fields
    - electronCount
```
int electronCount
```
      Number of electrons in the lone pair.
    - atom
```
IAtom atom
```
      The atom with which this lone pair is associated.
- Class org.openscience.cdk.silent.Mapping extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -6541914644492043503L
  - Serialized Fields
    - relation
```
IChemObject[] relation
```
- Class org.openscience.cdk.silent.Monomer extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  -6084164963937650703L
  - Serialized Fields
    - monomerName
```
String monomerName
```
      The name of this monomer (e.g. Trp42).
    - monomerType
```
String monomerType
```
      The type of this monomer (e.g. TRP).
- Class org.openscience.cdk.silent.PDBAtom extends Atom implements Serializable
  
  serialVersionUID:
  
  7670650135045832543L
  - Serialized Fields
    - record
```
String record
```
    - tempFactor
```
double tempFactor
```
    - resName
```
String resName
```
    - iCode
```
String iCode
```
    - occupancy
```
double occupancy
```
    - name
```
String name
```
    - chainID
```
String chainID
```
    - altLoc
```
String altLoc
```
    - segID
```
String segID
```
    - serial
```
int serial
```
    - resSeq
```
String resSeq
```
    - oxt
```
boolean oxt
```
    - hetAtom
```
boolean hetAtom
```
- Class org.openscience.cdk.silent.PDBMonomer extends Monomer implements Serializable
  
  serialVersionUID:
  
  -7236625816763776733L
  - Serialized Fields
    - iCode
```
String iCode
```
    - chainID
```
String chainID
```
      Denotes which chain in the PDB file this monomer is in.
    - resSeq
```
String resSeq
```
      Denotes which residue sequence in the current chain that this monomer is in.
- Class org.openscience.cdk.silent.PDBPolymer extends BioPolymer implements Serializable
  
  serialVersionUID:
  
  4173552834313952358L
  - Serialized Fields
    - sequentialListOfMonomers
```
List<E> sequentialListOfMonomers
```
    - secondaryStructures
```
List<E> secondaryStructures
```
- Class org.openscience.cdk.silent.PDBStructure extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -1877529009319324448L
  - Serialized Fields
    - structureType
```
String structureType
```
    - startChainID
```
Character startChainID
```
    - startSequenceNumber
```
Integer startSequenceNumber
```
    - startInsertionCode
```
Character startInsertionCode
```
    - endChainID
```
Character endChainID
```
    - endSequenceNumber
```
Integer endSequenceNumber
```
    - endInsertionCode
```
Character endInsertionCode
```
- Class org.openscience.cdk.silent.Polymer extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  -2596790658835319339L
  - Serialized Fields
    - monomers
```
Map<K,V> monomers
```
- Class org.openscience.cdk.silent.PseudoAtom extends Atom implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - label
```
String label
```
    - attachPoint
```
int attachPoint
```
- Class org.openscience.cdk.silent.Reaction extends ChemObject implements Serializable
  
  serialVersionUID:
  
  -554752558363533678L
  - Serialized Fields
    - growArraySize
```
int growArraySize
```
    - reactants
```
IAtomContainerSet reactants
```
    - products
```
IAtomContainerSet products
```
    - agents
```
IAtomContainerSet agents
```
      These are the used solvent, catalysts etc that normally appear above the reaction arrow
    - map
```
IMapping[] map
```
    - mappingCount
```
int mappingCount
```
    - reactionDirection
```
IReaction.Direction reactionDirection
```
- Class org.openscience.cdk.silent.ReactionScheme extends ReactionSet implements Serializable
  
  serialVersionUID:
  
  -3676327644698347260L
  - Serialized Fields
    - reactionScheme
```
List<E> reactionScheme
```
      A List of reaction schemes
- Class org.openscience.cdk.silent.ReactionSet extends ChemObject implements Serializable
  
  serialVersionUID:
  
  1555749911904585204L
  - Serialized Fields
    - reactions
```
IReaction[] reactions
```
      Array of Reactions.
    - reactionCount
```
int reactionCount
```
      Number of Reactions contained by this container.
    - growArraySize
```
int growArraySize
```
      Amount by which the Reactions array grows when elements are added and the array is not large enough for that.
- Class org.openscience.cdk.silent.Ring extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  6604894792331865990L
- Class org.openscience.cdk.silent.RingSet extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  7168431521057961434L
- Class org.openscience.cdk.silent.SingleElectron extends ElectronContainer implements Serializable
  
  serialVersionUID:
  
  7796574734668490940L
  - Serialized Fields
    - electronCount
```
int electronCount
```
      Number of electron for this class is defined as one.
    - atom
```
IAtom atom
```
      The atom with which this single electron is associated.
- Class org.openscience.cdk.silent.Strand extends AtomContainer implements Serializable
  
  serialVersionUID:
  
  4200943086350928356L
  - Serialized Fields
    - monomers
```
Map<K,V> monomers
```
      The list of all Monomers in the Strand.
    - strandName
```
String strandName
```
      The name of this strand (e.g. A, B).
    - strandType
```
String strandType
```
      The type of this strand (e.g. PEPTIDE, DNA, RNA).
- Class org.openscience.cdk.silent.Substance extends AtomContainerSet implements Serializable
  
  serialVersionUID:
  
  -4819492883237421487L
Package org.openscience.cdk.smiles
- Class org.openscience.cdk.smiles.InvPair extends Object implements Serializable
  
  serialVersionUID:
  
  -1397634098919863122L
  - Serialized Fields
    - last
```
long last
```
    - curr
```
long curr
```
    - atom
```
IAtom atom
```
    - prime
```
int prime
```
Package org.openscience.cdk.smiles.smarts.parser
- Class org.openscience.cdk.smiles.smarts.parser.ParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentToken
```
Token currentToken
```
      This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
      Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.
    - tokenImage
```
String[] tokenImage
```
      This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.
    - eol
```
String eol
```
      The end of line string for this machine.
- Class org.openscience.cdk.smiles.smarts.parser.Token extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kind
```
int kind
```
      An integer that describes the kind of this token. This numbering system is determined by JavaCCParser, and a table of these numbers is stored in the file ...Constants.java.
    - beginLine
```
int beginLine
```
      The line number of the first character of this Token.
    - beginColumn
```
int beginColumn
```
      The column number of the first character of this Token.
    - endLine
```
int endLine
```
      The line number of the last character of this Token.
    - endColumn
```
int endColumn
```
      The column number of the last character of this Token.
    - image
```
String image
```
      The string image of the token.
    - next
```
Token next
```
      A reference to the next regular (non-special) token from the input stream. If this is the last token from the input stream, or if the token manager has not read tokens beyond this one, this field is set to null. This is true only if this token is also a regular token. Otherwise, see below for a description of the contents of this field.
    - specialToken
```
Token specialToken
```
      This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token. If there are no such special tokens, this field is set to null. When there are more than one such special token, this field refers to the last of these special tokens, which in turn refers to the next previous special token through its specialToken field, and so on until the first special token (whose specialToken field is null). The next fields of special tokens refer to other special tokens that immediately follow it (without an intervening regular token). If there is no such token, this field is null.
- Class org.openscience.cdk.smiles.smarts.parser.TokenMgrError extends Error implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorCode
```
int errorCode
```
      Indicates the reason why the exception is thrown. It will have one of the above 4 values.
Package org.openscience.cdk.smsd
- Class org.openscience.cdk.smsd.Isomorphism extends AbstractMCS implements Serializable
  
  serialVersionUID:
  
  10278639972837495L
  - Serialized Fields
    - allMCS
```
List<E> allMCS
```
      Deprecated.
    - firstSolution
```
Map<K,V> firstSolution
```
      Deprecated.
    - allAtomMCS
```
List<E> allAtomMCS
```
      Deprecated.
    - firstAtomMCS
```
Map<K,V> firstAtomMCS
```
      Deprecated.
    - allBondMCS
```
List<E> allBondMCS
```
      Deprecated.
    - firstBondMCS
```
Map<K,V> firstBondMCS
```
      Deprecated.
    - rMol
```
MolHandler rMol
```
      Deprecated.
    - queryMol
```
IQueryAtomContainer queryMol
```
      Deprecated.
    - pMol
```
MolHandler pMol
```
      Deprecated.
    - pAC
```
IAtomContainer pAC
```
      Deprecated.
    - stereoScore
```
List<E> stereoScore
```
      Deprecated.
    - fragmentSize
```
List<E> fragmentSize
```
      Deprecated.
    - bEnergies
```
List<E> bEnergies
```
      Deprecated.
    - algorithmType
```
Algorithm algorithmType
```
      Deprecated.
    - removeHydrogen
```
boolean removeHydrogen
```
      Deprecated.
    - bondSensitiveTimeOut
```
double bondSensitiveTimeOut
```
      Deprecated.
    - bondInSensitiveTimeOut
```
double bondInSensitiveTimeOut
```
      Deprecated.
    - subGraph
```
boolean subGraph
```
      Deprecated.
    - matchBonds
```
boolean matchBonds
```
      Deprecated.
Package org.openscience.cdk.smsd.algorithm.vflib.builder
- Class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties extends Object implements Serializable
  - Serialized Fields
    - connectedTargetAtomCountMap
```
Map<K,V> connectedTargetAtomCountMap
```
      Deprecated.
    - connectedTargetAtomListMap
```
Map<K,V> connectedTargetAtomListMap
```
      Deprecated.
    - map
```
IBond[][] map
```
      Deprecated.
    - atoms
```
Map<K,V> atoms
```
      Deprecated.
    - atomsIndex
```
Map<K,V> atomsIndex
```
      Deprecated.
Package org.openscience.cdk.tools
- Class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor extends Object implements Serializable
  
  serialVersionUID:
  
  4382025930031432321L
  - Serialized Fields
    - ht
```
Hashtable<K,V> ht
```
- Class org.openscience.cdk.tools.HOSECodeGenerator extends Object implements Serializable
  
  serialVersionUID:
  
  -4353471818831864513L
  - Serialized Fields
    - sphereNodes
```
List<E> sphereNodes
```
      Container for the nodes in a sphere.
    - sphereNodesWithAtoms
```
List<E> sphereNodesWithAtoms
```
    - nextSphereNodes
```
List<E> nextSphereNodes
```
      Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".
    - sphere
```
int sphere
```
      Counter for the sphere in which we currently work.
    - maxSphere
```
int maxSphere
```
      How many spheres are we supposed inspect.
    - spheres
```
List<E>[] spheres
```
      Here we store the spheres that we assemble, in order to parse them into a code later.
    - spheresWithAtoms
```
List<E>[] spheresWithAtoms
```
    - HOSECode
```
StringBuffer HOSECode
```
      The HOSECode string that we assemble
    - atomContainer
```
IAtomContainer atomContainer
```
      The molecular structure on which we work
    - sphereDelimiters
```
String[] sphereDelimiters
```
      Delimiters used to separate spheres in the output string. Bremser uses the sequence"(//)" for the first four spheres.
    - bondSymbols
```
String[] bondSymbols
```
      The bond symbols used for bond orders "single", "double", "triple" and "aromatic"
    - centerCode
```
String centerCode
```
    - rootNode
```
org.openscience.cdk.tools.HOSECodeGenerator.TreeNode rootNode
```
    - debug
```
boolean debug
```
    - acold
```
IAtomContainer acold
```
    - soar
```
IRingSet soar
```
    - isotopeFac
```
IsotopeFactory isotopeFac
```

Serialized Form

Package org.openscience.cdk

Class org.openscience.cdk.AminoAcid extends Monomer implements Serializable

Serialized Fields

nTerminus

cTerminus

Class org.openscience.cdk.Association extends ElectronContainer implements Serializable

Serialized Fields

electronCount

atoms

atomCount

Class org.openscience.cdk.Atom extends AtomType implements Serializable

Serialized Fields

point2d

point3d

fractionalPoint3d

hydrogenCount

stereoParity

charge

Class org.openscience.cdk.AtomContainer extends ChemObject implements Serializable

Serialized Fields

atomCount

bondCount

lonePairCount

singleElectronCount

growArraySize

atoms

bonds

lonePairs

singleElectrons

stereoElements

Class org.openscience.cdk.AtomContainerSet extends ChemObject implements Serializable

Serialized Fields

atomContainers

atomContainerCount

multipliers

growArraySize

Class org.openscience.cdk.AtomType extends Isotope implements Serializable

Serialized Fields

maxBondOrder

bondOrderSum

covalentRadius

formalCharge

hybridization

electronValency

formalNeighbourCount

identifier

Class org.openscience.cdk.BioPolymer extends Polymer implements Serializable

Serialized Fields

strands

Class org.openscience.cdk.Bond extends ElectronContainer implements Serializable

Serialized Fields

order

atomCount

atoms

stereo

display

Class org.openscience.cdk.ChemFile extends ChemObject implements Serializable

Serialized Fields

chemSequences

chemSequenceCount

growArraySize

Class org.openscience.cdk.ChemModel extends ChemObject implements Serializable

Serialized Fields

setOfMolecules

setOfReactions

ringSet

crystal

Class org.openscience.cdk.ChemObject extends Object implements Serializable

Serialized Fields

chemObjectListeners

properties

flags

identifier

doNotification

Class org.openscience.cdk.ChemSequence extends ChemObject implements Serializable

Serialized Fields

chemModels

chemModelCount

growArraySize