Serialized Form

Class org.xmlcml.cml.AbstractAngleImpl implements Serializable

Serialized Fields

angleUnits

AngleUnits angleUnits

Class org.xmlcml.cml.AbstractAtomImpl implements Serializable

Serialized Fields

count

double count

Class org.xmlcml.cml.AbstractAtomRefImpl implements Serializable

Serialized Fields

atomVector

java.util.Vector atomVector

Class org.xmlcml.cml.AbstractBondImpl implements Serializable

Serialized Fields

atomRefVector

java.util.Vector atomRefVector

Class org.xmlcml.cml.AbstractBuiltinContainerImpl implements Serializable

Serialized Fields

builtinValues

StringVal[] builtinValues

nonBuiltinTable

java.util.Hashtable nonBuiltinTable

Class uk.co.demon.ursus.dom.AbstractDocumentImpl implements Serializable

Serialized Fields

docElement

PMRElement docElement

DOM_PARSER

org.apache.xerces.parsers.DOMParser DOM_PARSER

nvparser

NonValidatingDOMParser nvparser

tempDocument

org.w3c.dom.Document tempDocument

Class uk.co.demon.ursus.dom.AbstractElementImpl implements Serializable

Class org.xmlcml.cml.AbstractStringValImpl implements Serializable

Serialized Fields

builtin

java.lang.String builtin

dataType

int dataType

stringValue

java.lang.String stringValue

Class org.xmlcml.cml.AngleImpl implements Serializable

Class jumbo.euclid.ArrayTooSmallException implements Serializable

Class org.xmlcml.cml.AtomArrayImpl implements Serializable

Serialized Fields

builtinFloatArrays

FloatArray[] builtinFloatArrays

builtinIntegerArrays

IntegerArray[] builtinIntegerArrays

builtinStringArrays

StringArray[] builtinStringArrays

nonBuiltinTable

java.util.Hashtable nonBuiltinTable

theSize

int theSize

Class org.xmlcml.cml.AtomImpl implements Serializable

Serialized Fields

atomParity

double atomParity

atomRefVector

java.util.Vector atomRefVector

Vector of Objects than refer to this Atom

elementType

java.lang.String elementType

formalCharge

int formalCharge

hybridization

int hybridization

hydrogenCount

int hydrogenCount

isotope

double isotope

ligandVector

java.util.Vector ligandVector

molecule

Molecule molecule

Atom know which molecule it belongs to. This MUST correspond to the parent element. The programmer must maintain this

nonHydrogenCount

int nonHydrogenCount

occupancy

double occupancy

residueID

java.lang.String residueID

residueType

java.lang.String residueType

xy2

Real2 xy2

xyz3

Point3 xyz3

xyzFract

Point3 xyzFract

Class org.xmlcml.tools.AtomSetImpl implements Serializable

Serialized Fields

atomCountTable

java.util.HashMap atomCountTable

coordinate2Map

java.util.HashMap coordinate2Map

Class jumbo.euclid.BadArgumentException implements Serializable

Class jumbo.euclid.BadSubscriptException implements Serializable

Class org.xmlcml.cml.BondArrayImpl implements Serializable

Serialized Fields

builtinFloatArrays

FloatArray[] builtinFloatArrays

builtinIntegerArrays

IntegerArray[] builtinIntegerArrays

builtinStringArrays

StringArray[] builtinStringArrays

nonBuiltinTable

java.util.Hashtable nonBuiltinTable

theSize

int theSize

Class org.xmlcml.cml.BondImpl implements Serializable

Serialized Fields

atomRefs

Atom[] atomRefs

length

double length

molecule

Molecule molecule

order

java.lang.String order

stereo

java.lang.String stereo

Class org.xmlcml.tools.BondSetImpl implements Serializable

Serialized Fields

atomSet

AtomSet atomSet

Class org.xmlcml.tools.ChainSetImpl implements Serializable

Serialized Fields

acyclicBondSet

BondSet acyclicBondSet

bondSet

BondSet bondSet

molecule

Molecule molecule

ringAtomSet

AtomSet ringAtomSet

spanningTree

SpanningTree spanningTree

usedAtomSet

AtomSet usedAtomSet

Class org.xmlcml.cml.CMLBaseImpl implements Serializable

Serialized Fields

conventionName

java.lang.String conventionName

dictRef

java.lang.String dictRef

id

java.lang.String id

title

java.lang.String title

validity

CMLValidity validity

Class org.xmlcml.cml.CMLDocumentImpl implements Serializable

Class org.xmlcml.cml.CMLException implements Serializable

Class org.xmlcml.cml.CMLImpl implements Serializable

Class org.xmlcml.cml.CMLValidityImpl implements Serializable

Serialized Fields

warningVector

java.util.Vector warningVector

Class org.xmlcml.cml.CrystalImpl implements Serializable

Class jumbo.xml.util.CyclicVector implements Serializable

Class org.xmlcml.cml.ElectronImpl implements Serializable

Serialized Fields

count

double count

Class jumbo.euclid.EuclidVector implements Serializable

Serialized Fields

status

boolean status

Class org.xmlcml.cml.ExecuteImpl implements Serializable

Class org.xmlcml.cml.FeatureImpl implements Serializable

Class org.xmlcml.cml.FloatArrayImpl implements Serializable

Serialized Fields

delimiter

java.lang.String delimiter

realArray

RealArray realArray

stringVector

java.util.Vector stringVector

Class org.xmlcml.cml.FloatMatrixImpl implements Serializable

Serialized Fields

columns

int columns

data

double[][] data

rows

int rows

units

Units units

Class org.xmlcml.cml.FloatValImpl implements Serializable

Serialized Fields

maximum

double maximum

minimum

double minimum

realValue

double realValue

Class org.xmlcml.cml.FormulaImpl implements Serializable

Serialized Fields

count

double count

Class jumbo.euclid.HashedVector implements Serializable

Serialized Fields

count

java.lang.Integer count

stringSet

StringSet stringSet

Class jumbo.euclid.IllCondMatrixException implements Serializable

Class jumbo.euclid.Int2RangeHashtable implements Serializable

Class jumbo.euclid.Int2Vector implements Serializable

Serialized Fields

x

int[] x

xyarray

int[][] xyarray

hold all coordinates as 2D array

xyDone

boolean xyDone

y

int[] y

Class org.xmlcml.cml.IntegerArrayImpl implements Serializable

Serialized Fields

delimiter

java.lang.String delimiter

intArray

IntArray intArray

stringVector

java.util.Vector stringVector

Class org.xmlcml.cml.IntegerValImpl implements Serializable

Serialized Fields

intValue

int intValue

maximum

int maximum

minimum

int minimum

Class jumbo.euclid.IntRangeVector implements Serializable

Class org.xmlcml.noncml.JMEImpl implements Serializable

Serialized Fields

serialTable

java.util.Hashtable serialTable

Class org.xmlcml.cml.LinkImpl implements Serializable

Serialized Fields

href

java.lang.String href

Class org.xmlcml.cml.ListImpl implements Serializable

Class jumbo.euclid.MatrixShapeException implements Serializable

Class org.xmlcml.noncml.MDLMolImpl implements Serializable

Serialized Fields

atomArray

Atom[] atomArray

chirflag

int chirflag

natomlists

int natomlists

nprops

int nprops

serialTable

java.util.Hashtable serialTable

threedim

boolean threedim

Class org.xmlcml.cml.MoleculeImpl implements Serializable

Serialized Fields

angleVector

java.util.Vector angleVector

atomArray

AtomArray atomArray

atomIdTable

java.util.Hashtable atomIdTable

atomVector

java.util.Vector atomVector

bondArray

BondArray bondArray

bondHashTable

java.util.Hashtable bondHashTable

bondIdTable

java.util.Hashtable bondIdTable

bondVector

java.util.Vector bondVector

count

double count

crystal

Crystal crystal

electronVector

java.util.Vector electronVector

featureVector

java.util.Vector featureVector

moleculeVector

java.util.Vector moleculeVector

sequenceVector

java.util.Vector sequenceVector

torsionVector

java.util.Vector torsionVector

Class org.xmlcml.noncml.NonCMLDocumentImpl implements Serializable

Serialized Fields

atomList

org.w3c.dom.NodeList atomList

general tools for input and output

atomParent

CMLBase atomParent

bondList

org.w3c.dom.NodeList bondList

bondParent

CMLBase bondParent

bReader

java.io.BufferedReader bReader

most input requires a BufferedReader

inputCML

CML inputCML

the CML object created from the input legacy

inputCMLMolecule

Molecule inputCMLMolecule

the molecule created from the input legacy

line

java.lang.String line

and uses a line as the container

natoms

int natoms

nbonds

int nbonds

outputCML

CML outputCML

a CML object to be output as legacy

outputCMLMolecule

Molecule outputCMLMolecule

a CML Molecule to be output as legacy

Class jumbo.euclid.NonRectMatrixException implements Serializable

Class jumbo.euclid.NonSquareException implements Serializable

Class jumbo.euclid.NPDMatrixException implements Serializable

Class org.xmlcml.cml.NumericValImpl implements Serializable

Serialized Fields

units

Units units

Class uk.co.demon.ursus.dom.PMRDocumentImpl implements Serializable

Class uk.co.demon.ursus.dom.PMRElementImpl implements Serializable

Serialized Fields

processFlag

boolean processFlag

Class jumbo.euclid.Point3Vector implements Serializable

Serialized Fields

x

double[] x

xyzarray

double[][] xyzarray

hold all coordinates as 2D array

xyzDone

boolean xyzDone

y

double[] y

z

double[] z

Class org.xmlcml.cml.ReactionImpl implements Serializable

Serialized Fields

productVector

java.util.Vector productVector

reactantVector

java.util.Vector reactantVector

Class jumbo.euclid.Real2RangeHashtable implements Serializable

Class jumbo.euclid.Real2Vector implements Serializable

Serialized Fields

x

double[] x

xyarray

double[][] xyarray

hold all coordinates as 2D array

xyDone

boolean xyDone

y

double[] y

Class jumbo.euclid.RealRangeVector implements Serializable

Class org.xmlcml.tools.RingImpl implements Serializable

Serialized Fields

centroid

Real2 centroid

points of coordinates

cyclicAtomVector

CyclicVector cyclicAtomVector

ordered list of atoms - each element is an Atom as we traverse the Ring cyclicly.

cyclicBondVector

CyclicVector cyclicBondVector

ordered list of bonds - each element is a Bond and links to the next bond in the ring cyclicly

id

java.lang.String id

each ring has a unique ID

molecule

Molecule molecule

ringOverlapVector

java.util.Vector ringOverlapVector

what rings does this overlap with (FUSED or BRIDGED)? Vector stores RingOverlaps

Class org.xmlcml.tools.RingNucleusImpl implements Serializable

Serialized Fields

chainVector

java.util.Vector chainVector

vector of chains (substituents)

count

int count

ringOverlapVector

java.util.Vector ringOverlapVector

what RingOverlaps are there between these rings?

ringVector

java.util.Vector ringVector

what Rings are there in this nucleus?

spanningTree

SpanningTree spanningTree

Class org.xmlcml.noncml.SDFImpl implements Serializable

Serialized Fields

id

java.lang.String id

mdlMol

MDLMol mdlMol

Class org.xmlcml.cml.SequenceImpl implements Serializable

Class jumbo.euclid.SingMatrixException implements Serializable

Class org.xmlcml.noncml.SMILESImpl implements Serializable

Serialized Fields

linkVector

java.util.Vector linkVector

order

java.lang.String order

serialTable

java.util.Hashtable serialTable

smilesString

java.lang.String smilesString

spanningTree

SpanningTree spanningTree

Class org.xmlcml.tools.SpanningTreeImpl implements Serializable

Serialized Fields

acyclicBondSet

BondSet acyclicBondSet

atomElementTable

java.util.Hashtable atomElementTable

bondSet

BondSet bondSet

chainCount

int chainCount

chainVector

java.util.Vector chainVector

cyclicBondSet

BondSet cyclicBondSet

cyclicBondVector

java.util.Vector cyclicBondVector

linkTable

java.util.Hashtable linkTable

linkVector

java.util.Vector linkVector

molecule

Molecule molecule

ringCount

int ringCount

ringNucleusVector

java.util.Vector ringNucleusVector

ringVector

java.util.Vector ringVector

Class org.xmlcml.tools.STElementImpl implements Serializable

Serialized Fields

atom

Atom atom

Class org.xmlcml.cml.StringArrayImpl implements Serializable

Serialized Fields

delimiter

java.lang.String delimiter

stringVector

java.util.Vector stringVector

Class jumbo.euclid.StringSetException implements Serializable

Class org.xmlcml.cml.StringValImpl implements Serializable

Class org.xmlcml.tools.ToolHashSetImpl implements Serializable

Class org.xmlcml.cml.TorsionImpl implements Serializable

Class jumbo.euclid.UnequalArraysException implements Serializable

Class jumbo.euclid.UnequalMatricesException implements Serializable

Class jumbo.euclid.UnimplementedException implements Serializable

Class jumbo.euclid.UninitialisedException implements Serializable

Class uk.co.demon.ursus.dom.ValidityImpl implements Serializable

Class jumbo.xml.util.XHashtableImpl implements Serializable

Class org.xmlcml.noncml.XYZImpl implements Serializable

Serialized Fields

serialTable

java.util.Hashtable serialTable

Class jumbo.euclid.ZeroVectorException implements Serializable