Serialized Form

Package org.openscience.cdk

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

serialVersionUID:

-9138919895942850167L

Serialized Fields

atomCount

int atomCount

atoms

IAtom[] atoms

The atoms which take part in the association.

electronCount

int electronCount

Number of electrons in the association.

Class org.openscience.cdk.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 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

Set<IStereoElement> stereoElements

Internal list of atom parities.

Class org.openscience.cdk.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 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 extends Polymer implements Serializable

serialVersionUID:

-5001873073769634393L

Serialized Fields

strands

Map<String,IStrand> strands

Class org.openscience.cdk.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.

stereo

IBond.Stereo stereo

A descriptor the stereochemical orientation of this bond.

Class org.openscience.cdk.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 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 extends Object implements Serializable

serialVersionUID:

2798134548764323328L

Serialized Fields

chemObjectListeners

List<IChemObjectListener> chemObjectListeners

List for listener administration.

doNotification

boolean doNotification

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.

properties

Map<Object,Object> properties

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

Class org.openscience.cdk.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 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 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.

massNumber

Integer massNumber

The mass number for this isotope.

naturalAbundance

Double naturalAbundance

Natural abundance of this isotope.

Class org.openscience.cdk.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 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<String,IMonomer> monomers

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

serialVersionUID:

1L

Serialized Fields

attachPoint

int attachPoint

label

String label

Class org.openscience.cdk.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 extends ReactionSet implements Serializable

serialVersionUID:

-3676327644698347260L

Serialized Fields

reactionScheme

List<IReactionScheme> reactionScheme

A List of reaction schemes

Class org.openscience.cdk.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 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

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 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 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

reference

String reference

type

String type

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.NoSuchBondException extends RuntimeException implements Serializable

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

behaveAsBitFingerprint

boolean behaveAsBitFingerprint

hitHashes

int[] hitHashes

numOfHits

int[] numOfHits

Class org.openscience.cdk.fingerprint.IntArrayFingerprint extends Object implements Serializable

serialVersionUID:

5175105019921245323L

Serialized Fields

trueBits

int[] trueBits

Class org.openscience.cdk.fingerprint.ShortestPathFingerprinter extends AbstractFingerprinter implements Serializable

serialVersionUID:

7867864332244557861L

Serialized Fields

fingerprintLength

int fingerprintLength

The default length of created fingerprints.

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

base

IAtomContainer base

baseTable

long[] baseTable

compare

IAtomContainer compare

compareTable

long[] compareTable

sortedBaseTable

long[] sortedBaseTable

sortedCompareTable

long[] sortedCompareTable

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 following 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.

Class org.openscience.cdk.iupac.parser.Token extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

beginColumn

int beginColumn

The column number of the first character of this Token.

beginLine

int beginLine

The line number of the first character of this Token.

endColumn

int endColumn

The column number of the last character of this Token.

endLine

int endLine

The line number of the last character of this Token.

image

String image

The string image of the token.

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.

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

chargeGroups

List<ChargeGroup> chargeGroups

residues

List<Residue> residues

Class org.openscience.cdk.libio.md.Residue extends AtomContainer implements Serializable

serialVersionUID:

6548353601272976798L

Serialized Fields

name

String name

number

int number

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

matchingAtoms

int[] matchingAtoms

smarts

String smarts

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

lower

double lower

upper

double upper

Class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom extends Atom implements Serializable

Serialized Fields

compiledSmarts

SmartsPattern[] compiledSmarts

smarts

String smarts

symbol

String symbol

Class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond extends Bond implements Serializable

Serialized Fields

lower

double lower

upper

double upper

Package org.openscience.cdk.protein.data

Class org.openscience.cdk.protein.data.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 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 extends BioPolymer implements Serializable

serialVersionUID:

4173552834313952358L

Serialized Fields

secondaryStructures

List<IPDBStructure> secondaryStructures

sequentialListOfMonomers

List<String> sequentialListOfMonomers

Class org.openscience.cdk.protein.data.PDBStrand extends Strand implements Serializable

serialVersionUID:

8278569309787734236L

Serialized Fields

sequentialListOfMonomers

List<String> sequentialListOfMonomers

Class org.openscience.cdk.protein.data.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

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

implementationIdentifier

String implementationIdentifier

implementationTitle

String implementationTitle

implementationVendor

String implementationVendor

specificationReference

String specificationReference

Class org.openscience.cdk.qsar.DescriptorValue extends Object implements Serializable

serialVersionUID:

-5672896059814842972L

Serialized Fields

descriptorNames

String[] descriptorNames

exception

Exception exception

parameterNames

String[] parameterNames

parameterSettings

Object[] parameterSettings

specification

DescriptorSpecification specification

value

IDescriptorResult value

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<Double> 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<Integer> 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<IReaction,Integer> hashMapChain

Package org.openscience.cdk.renderer

Class org.openscience.cdk.renderer.RendererModel extends Object implements Serializable

serialVersionUID:

-4420308906715213445L

Serialized Fields

clipboardContent

IAtomContainer clipboardContent

colorHash

IGeneratorParameter<Map<IChemObject,Color>> colorHash

externalHighlightColor

IGeneratorParameter<Color> externalHighlightColor

externalSelectedPart

IAtomContainer externalSelectedPart

highlightedAtom

IAtom highlightedAtom

highlightedBond

IBond highlightedBond

merge

Map<IAtom,IAtom> merge

notification

boolean notification

renderingParameters

Map<String,IGeneratorParameter<?>> renderingParameters

A map of IGeneratorParameter class names to instances.

selection

IChemObjectSelection selection

toolTipTextMap

Map<IAtom,String> toolTipTextMap

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

cTerminus

IAtom cTerminus

The atom that constitutes the C-terminus.

nTerminus

IAtom nTerminus

The atom that constitutes the N-terminus.

Class org.openscience.cdk.silent.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.silent.AtomContainer 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

Set<IStereoElement> stereoElements

Internal list of atom parities.

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

serialVersionUID:

-5001873073769634393L

Serialized Fields

strands

Map<String,IStrand> strands

Class org.openscience.cdk.silent.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.

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

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.silent.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.silent.ChemObject extends Object implements Serializable

serialVersionUID:

2798134548764323328L

Serialized Fields

doNotification

boolean doNotification

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.

properties

Map<Object,Object> properties

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

Class org.openscience.cdk.silent.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.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.

spaceGroup

String spaceGroup

Number of symmetry related atoms.

zValue

Integer zValue

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.

massNumber

Integer massNumber

The mass number for this isotope.

naturalAbundance

Double naturalAbundance

Natural abundance of this isotope.

Class org.openscience.cdk.silent.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.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

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.silent.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.silent.PDBPolymer extends BioPolymer implements Serializable

serialVersionUID:

4173552834313952358L

Serialized Fields

secondaryStructures

List<IPDBStructure> secondaryStructures

sequentialListOfMonomers

List<String> sequentialListOfMonomers

Class org.openscience.cdk.silent.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

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

serialVersionUID:

-2596790658835319339L

Serialized Fields

monomers

Map<String,IMonomer> monomers

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

serialVersionUID:

1L

Serialized Fields

attachPoint

int attachPoint

label

String label

Class org.openscience.cdk.silent.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.silent.ReactionScheme extends ReactionSet implements Serializable

serialVersionUID:

-3676327644698347260L

Serialized Fields

reactionScheme

List<IReactionScheme> reactionScheme

A List of reaction schemes

Class org.openscience.cdk.silent.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.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

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.silent.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.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

atom

IAtom atom

curr

long curr

last

long last

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 following 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.

Class org.openscience.cdk.smiles.smarts.parser.Token extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

beginColumn

int beginColumn

The column number of the first character of this Token.

beginLine

int beginLine

The line number of the first character of this Token.

endColumn

int endColumn

The column number of the last character of this Token.

endLine

int endLine

The line number of the last character of this Token.

image

String image

The string image of the token.

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.

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

algorithmType

Algorithm algorithmType

Deprecated.

allAtomMCS

List<Map<IAtom,IAtom>> allAtomMCS

Deprecated.

allBondMCS

List<Map<IBond,IBond>> allBondMCS

Deprecated.

allMCS

List<Map<Integer,Integer>> allMCS

Deprecated.

bEnergies

List<Double> bEnergies

Deprecated.

bondInSensitiveTimeOut

double bondInSensitiveTimeOut

Deprecated.

bondSensitiveTimeOut

double bondSensitiveTimeOut

Deprecated.

firstAtomMCS

Map<IAtom,IAtom> firstAtomMCS

Deprecated.

firstBondMCS

Map<IBond,IBond> firstBondMCS

Deprecated.

firstSolution

Map<Integer,Integer> firstSolution

Deprecated.

fragmentSize

List<Integer> fragmentSize

Deprecated.

matchBonds

boolean matchBonds

Deprecated.

pAC

IAtomContainer pAC

Deprecated.

pMol

MolHandler pMol

Deprecated.

queryMol

IQueryAtomContainer queryMol

Deprecated.

removeHydrogen

boolean removeHydrogen

Deprecated.

rMol

MolHandler rMol

Deprecated.

stereoScore

List<Double> stereoScore

Deprecated.

subGraph

boolean subGraph

Deprecated.

Package org.openscience.cdk.smsd.algorithm.vflib.builder

Class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties extends Object implements Serializable

Serialized Fields

atoms

Map<IAtom,Integer> atoms

Deprecated.

atomsIndex

Map<Integer,IAtom> atomsIndex

Deprecated.

connectedTargetAtomCountMap

Map<IAtom,Integer> connectedTargetAtomCountMap

Deprecated.

connectedTargetAtomListMap

Map<IAtom,List<IAtom>> connectedTargetAtomListMap

Deprecated.

map

IBond[][] map

Deprecated.

Package org.openscience.cdk.tools

Class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor extends Object implements Serializable

serialVersionUID:

4382025930031432321L

Serialized Fields

ht

Hashtable<String,org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor.HOSECodeShiftRange> ht

Class org.openscience.cdk.tools.HOSECodeGenerator extends Object implements Serializable

serialVersionUID:

-4353471818831864513L

Serialized Fields

acold

IAtomContainer acold

atomContainer

IAtomContainer atomContainer

The molecular structure on which we work

bondSymbols

String[] bondSymbols

The bond symbols used for bond orders "single", "double", "triple" and "aromatic"

centerCode

String centerCode

debug

boolean debug

flags

int flags

HOSECode

StringBuffer HOSECode

The HOSECode string that we assemble

isotopeFac

IsotopeFactory isotopeFac

maxSphere

int maxSphere

How many spheres are we supposed inspect.

nextSphereNodes

List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode> nextSphereNodes

Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".

rootNode

org.openscience.cdk.tools.HOSECodeGenerator.TreeNode rootNode

soar

IRingSet soar

sphere

int sphere

Counter for the sphere in which we currently work.

sphereDelimiters

String[] sphereDelimiters

Delimiters used to separate spheres in the output string. Bremser uses the sequence"(//)" for the first four spheres.

sphereNodes

List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode> sphereNodes

Container for the nodes in a sphere.

sphereNodesWithAtoms

List<IAtom> sphereNodesWithAtoms

spheres

List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode>[] spheres

Here we store the spheres that we assemble, in order to parse them into a code later.

spheresWithAtoms

List<IAtom>[] spheresWithAtoms