Serialized Form

Package org.openscience.cdk

Class org.openscience.cdk.AminoAcid

class AminoAcid extends Monomer implements Serializable

serialVersionUID:

-5032283549467862509L

Serialized Fields

cTerminus

IAtom cTerminus

The atom that constitutes the C-terminus.

nTerminus

IAtom nTerminus

The atom that constitutes the N-terminus.

Class org.openscience.cdk.Atom

class Atom extends AtomType implements Serializable

serialVersionUID:

-3137373012494608794L

Serialized Fields

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

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.

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.

stereoParity

Integer stereoParity

A stereo parity descriptor for the stereochemistry of this atom.

Class org.openscience.cdk.AtomContainer

class AtomContainer extends ChemObject implements Serializable

Serialized Fields

atoms

org.openscience.cdk.AtomContainer.BaseAtomRef[] atoms

bonds

org.openscience.cdk.AtomContainer.BaseBondRef[] bonds

electrons

ISingleElectron[] electrons

lonepairs

ILonePair[] lonepairs

numAtoms

int numAtoms

numBonds

int numBonds

numLonePairs

int numLonePairs

numSingleElectrons

int numSingleElectrons

stereo

List<IStereoElement> stereo

Class org.openscience.cdk.AtomContainerLegacy

class AtomContainerLegacy extends ChemObject implements Serializable

serialVersionUID:

5678100348445919254L

Serialized Fields

atomCount

int atomCount

Number of atoms contained by this object.

atoms

IAtom[] atoms

Internal array of atoms.

bondCount

int bondCount

Number of bonds contained by this object.

bonds

IBond[] bonds

Internal array of bonds.

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.

lonePairCount

int lonePairCount

Number of lone pairs contained by this object.

lonePairs

ILonePair[] lonePairs

Internal array of lone pairs.

singleElectronCount

int singleElectronCount

Number of single electrons contained by this object.

singleElectrons

ISingleElectron[] singleElectrons

Internal array of single electrons.

stereoElements

List<IStereoElement> stereoElements

Internal list of atom parities.

Class org.openscience.cdk.AtomContainerSet

class AtomContainerSet extends ChemObject implements Serializable

serialVersionUID:

-521290255592768395L

Serialized Fields

atomContainerCount

int atomContainerCount

Number of AtomContainers contained by this container.

atomContainers

IAtomContainer[] atomContainers

Array of AtomContainers.

growArraySize

int growArraySize

Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.

multipliers

Double[] multipliers

Defines the number of instances of a certain molecule in the set. It is 1 by default.

Class org.openscience.cdk.AtomType

class AtomType extends Isotope implements Serializable

serialVersionUID:

-7950397716808229972L

Serialized Fields

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.

electronValency

Integer electronValency

The electron Valency of this atom with CDKConstants.UNSET as default.

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

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.

hybridization

IAtomType.Hybridization hybridization

The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.

identifier

String identifier

String representing the identifier for this atom type with null as default.

maxBondOrder

IBond.Order maxBondOrder

The maximum bond order allowed for this atom type.

Class org.openscience.cdk.BioPolymer

class BioPolymer extends Polymer implements Serializable

serialVersionUID:

-5001873073769634393L

Serialized Fields

strands

Map<String,IStrand> strands

Class org.openscience.cdk.Bond

class Bond extends ElectronContainer implements Serializable

serialVersionUID:

7057060562283387384L

Serialized Fields

atomCount

int atomCount

Number of atoms contained by this object.

atoms

IAtom[] atoms

A list of atoms participating in this bond.

display

IBond.Display display

order

IBond.Order order

The bond order of this bond.

Class org.openscience.cdk.ChemFile

class ChemFile extends ChemObject implements Serializable

serialVersionUID:

1926781734333430132L

Serialized Fields

chemSequenceCount

int chemSequenceCount

Number of ChemSequences contained by this container.

chemSequences

IChemSequence[] chemSequences

Array of ChemSquences.

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

class ChemModel extends ChemObject implements Serializable

serialVersionUID:

-5213425310451366185L

Serialized Fields

crystal

ICrystal crystal

A Crystal.

ringSet

IRingSet ringSet

A RingSet.

setOfMolecules

IAtomContainerSet setOfMolecules

A MoleculeSet.

setOfReactions

IReactionSet setOfReactions

A ReactionSet.

Class org.openscience.cdk.ChemObject

class ChemObject extends Object implements Serializable

serialVersionUID:

2798134548764323328L

Serialized Fields

chemObjectListeners

List<IChemObjectListener> chemObjectListeners

List for listener administration.

doNotification

boolean doNotification

flags

int 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.

properties

Map<Object,Object> properties

A hashtable for the storage of any kind of properties of this IChemObject.

Class org.openscience.cdk.ChemSequence

class ChemSequence extends ChemObject implements Serializable

serialVersionUID:

2199218627455492000L

Serialized Fields

chemModelCount

int chemModelCount

Number of ChemModels contained by this container.

chemModels

IChemModel[] chemModels

Array of ChemModels.

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

class 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.

spaceGroup

String spaceGroup

Number of symmetry related atoms.

zValue

Integer zValue

Number of symmetry related atoms.

Class org.openscience.cdk.ElectronContainer

class ElectronContainer extends ChemObject implements Serializable

serialVersionUID:

-2207894536767670743L

Serialized Fields

electronCount

Integer electronCount

Number of electrons in the ElectronContainer.

Class org.openscience.cdk.Element

class 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.FragmentAtom

class FragmentAtom extends PseudoAtom implements Serializable

serialVersionUID:

-6144605920605752463L

Serialized Fields

fragment

IAtomContainer fragment

isExpanded

boolean isExpanded

Class org.openscience.cdk.Isotope

class Isotope extends Element implements Serializable

serialVersionUID:

6389365978927575858L

Serialized Fields

exactMass

Double exactMass

Exact mass of this isotope.

massNumber

Integer massNumber

The mass number for this isotope.

naturalAbundance

Double naturalAbundance

Natural abundance of this isotope.

Class org.openscience.cdk.LonePair

class LonePair extends ElectronContainer implements Serializable

serialVersionUID:

51311422004885329L

Serialized Fields

atom

IAtom atom

The atom with which this lone pair is associated.

electronCount

int electronCount

Number of electrons in the lone pair.

Class org.openscience.cdk.Mapping

class Mapping extends ChemObject implements Serializable

serialVersionUID:

-6541914644492043503L

Serialized Fields

relation

IChemObject[] relation

Class org.openscience.cdk.Monomer

class 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

class Polymer extends AtomContainer implements Serializable

serialVersionUID:

-2596790658835319339L

Serialized Fields

monomers

Map<String,IMonomer> monomers

Class org.openscience.cdk.PseudoAtom

class PseudoAtom extends Atom implements Serializable

serialVersionUID:

1L

Serialized Fields

attachPoint

int attachPoint

label

String label

Class org.openscience.cdk.Reaction

class Reaction extends ChemObject implements Serializable

serialVersionUID:

-554752558363533678L

Serialized Fields

agents

IAtomContainerSet agents

These are the used solvent, catalysts etc that normally appear above the reaction arrow

growArraySize

int growArraySize

map

IMapping[] map

mappingCount

int mappingCount

products

IAtomContainerSet products

reactants

IAtomContainerSet reactants

reactionDirection

IReaction.Direction reactionDirection

Class org.openscience.cdk.ReactionScheme

class ReactionScheme extends ReactionSet implements Serializable

serialVersionUID:

-3676327644698347260L

Serialized Fields

reactionScheme

List<IReactionScheme> reactionScheme

A List of reaction schemes

Class org.openscience.cdk.ReactionSet

class ReactionSet extends ChemObject implements Serializable

serialVersionUID:

1555749911904585204L

Serialized Fields

growArraySize

int growArraySize

Amount by which the Reactions array grows when elements are added and the array is not large enough for that.

reactionCount

int reactionCount

Number of Reactions contained by this container.

reactions

IReaction[] reactions

Array of Reactions.

Class org.openscience.cdk.Ring

class Ring extends AtomContainer implements Serializable

serialVersionUID:

6604894792331865990L

Class org.openscience.cdk.RingSet

class RingSet extends AtomContainerSet implements Serializable

serialVersionUID:

7168431521057961434L

Class org.openscience.cdk.SingleElectron

class SingleElectron extends ElectronContainer implements Serializable

serialVersionUID:

7796574734668490940L

Serialized Fields

atom

IAtom atom

The atom with which this single electron is associated.

electronCount

int electronCount

Number of electron for this class is defined as one.

Class org.openscience.cdk.Strand

class Strand extends AtomContainer implements Serializable

serialVersionUID:

4200943086350928356L

Serialized Fields

monomers

Map<String,IMonomer> 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

class Substance extends AtomContainerSet implements Serializable

serialVersionUID:

-4819492883237421487L

Package org.openscience.cdk.event

Class org.openscience.cdk.event.ChemObjectChangeEvent

class ChemObjectChangeEvent extends EventObject implements Serializable

serialVersionUID:

5418604788783986725L

Package org.openscience.cdk.protein.data

Class org.openscience.cdk.protein.data.PDBAtom

class PDBAtom extends Atom implements Serializable

serialVersionUID:

7670650135045832543L

Serialized Fields

altLoc

String altLoc

chainID

String chainID

hetAtom

boolean hetAtom

iCode

String iCode

name

String name

occupancy

double occupancy

oxt

boolean oxt

record

String record

resName

String resName

resSeq

String resSeq

segID

String segID

serial

int serial

tempFactor

double tempFactor

Class org.openscience.cdk.protein.data.PDBMonomer

class PDBMonomer extends Monomer implements Serializable

serialVersionUID:

-7236625816763776733L

Serialized Fields

chainID

String chainID

Denotes which chain in the PDB file this monomer is in.

iCode

String iCode

resSeq

String resSeq

Denotes which residue sequence in the current chain that this monomer is in.

Class org.openscience.cdk.protein.data.PDBPolymer

class PDBPolymer extends BioPolymer implements Serializable

serialVersionUID:

4173552834313952358L

Serialized Fields

secondaryStructures

List<IPDBStructure> secondaryStructures

sequentialListOfMonomers

List<String> sequentialListOfMonomers

Class org.openscience.cdk.protein.data.PDBStructure

class PDBStructure extends ChemObject implements Serializable

serialVersionUID:

-1877529009319324448L

Serialized Fields

endChainID

Character endChainID

endInsertionCode

Character endInsertionCode

endSequenceNumber

Integer endSequenceNumber

startChainID

Character startChainID

startInsertionCode

Character startInsertionCode

startSequenceNumber

Integer startSequenceNumber

structureType

String structureType