Serialized Form (cdk-silent 2.1.1 API)

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.AtomType(String) and AtomType.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.
- 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
    - symbol
```
String symbol
```
      The element symbol for this element as listed in the periodic table.
    - 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

Serialized Form

Package org.openscience.cdk.silent

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

Serialized Fields

nTerminus

cTerminus

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

Serialized Fields

point2d

point3d

fractionalPoint3d

hydrogenCount

stereoParity

charge

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

Serialized Fields

atomCount

bondCount

lonePairCount

singleElectronCount

growArraySize

atoms

bonds

lonePairs

singleElectrons

stereoElements

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

Serialized Fields

atomContainers

atomContainerCount

multipliers

growArraySize

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

Serialized Fields

maxBondOrder

bondOrderSum

covalentRadius

formalCharge

hybridization

electronValency

formalNeighbourCount

identifier

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

Serialized Fields

strands

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

Serialized Fields

order

atomCount

atoms

stereo

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

Serialized Fields

chemSequences

chemSequenceCount

growArraySize

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

Serialized Fields

setOfMolecules

setOfReactions

ringSet

crystal

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

Serialized Fields

properties

flags

identifier

doNotification

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

Serialized Fields

chemModels

chemModelCount

growArraySize

Class org.openscience.cdk.silent.Crystal extends AtomContainer implements Serializable

Serialized Fields

aAxis

bAxis

cAxis

zValue

spaceGroup