Serialized Form

Package starfish.chemistry

Class starfish.chemistry.AngleConstraintTable extends starfish.tables.NvTableModel implements Serializable

Serialized Fields

doubleTableRenderer

starfish.chemistry.AngleConstraintTable.DoubleTableCellRenderer doubleTableRenderer

spreadRenderer

starfish.tables.SpreadRenderer spreadRenderer

requireActive

boolean requireActive

dMode

java.lang.String dMode

RendererSet

boolean RendererSet

constraints

java.util.List<E> constraints

displayColumns

ConstraintColumns[] displayColumns

Class starfish.chemistry.Atom extends java.lang.Object implements Serializable

Serialized Fields

iAtom

int iAtom

parent

Atom parent

name

java.lang.String name

type

java.lang.String type

label

java.lang.String label

entity

Entity entity

bonds

java.util.Vector<E> bonds

previous

Atom previous

next

Atom next

mass

double mass

stereo

int stereo

nPiBonds

byte nPiBonds

nonHydrogens

byte nonHydrogens

charge

float charge

fcharge

float fcharge

bondLength

float bondLength

valanceAngle

float valanceAngle

dihedralAngle

float dihedralAngle

stereoStr

java.lang.String stereoStr

radius

float radius

aNum

int aNum

atomProperty

AtomProperty atomProperty

forceFieldCode

java.lang.String forceFieldCode

value

float value

equivAtoms

java.util.ArrayList<E> equivAtoms

defaultSpatialSet

SpatialSet defaultSpatialSet

spatialSets

java.util.Map<K,V> spatialSets

resonanceSet

starfish.datasets.peaks.ResonanceSet resonanceSet

irpIndex

int irpIndex

rotUnit

Atom rotUnit

rotGroup

Atom rotGroup

canonValue

int canonValue

Class starfish.chemistry.Bond extends java.lang.Object implements Serializable

Serialized Fields

properties

boolean[] properties

radius

float radius

red

float red

green

float green

blue

float blue

order

int order

stereo

int stereo

previous

Bond previous

next

Bond next

begin

Atom begin

end

Atom end

Class starfish.chemistry.Compound extends Entity implements Serializable

Serialized Fields

atoms

java.util.HashMap<K,V> atoms

number

java.lang.String number

iRes

int iRes

labelNum

int labelNum

Class starfish.chemistry.DistanceConstraint extends java.lang.Object implements Serializable

Serialized Fields

previous

Atom previous

next

Atom next

atom1

Atom[] atom1

atom2

Atom[] atom2

peak

starfish.datasets.peaks.Peak peak

intensity

double intensity

volume

double volume

scale

double scale

distance

double distance

lower

double lower

upper

double upper

dcClass

int dcClass

active

double active

Class starfish.chemistry.Entity extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

label

java.lang.String label

molecule

Molecule molecule

firstAtom

Atom firstAtom

lastAtom

Atom lastAtom

firstBond

Bond firstBond

lastBond

Bond lastBond

hasEquivalentAtoms

boolean hasEquivalentAtoms

coordSets

java.util.TreeMap<K,V> coordSets

entityID

int entityID

assemblyID

int assemblyID

physicalState

java.lang.String physicalState

conformationalIsomer

java.lang.String conformationalIsomer

chemicalExchangeState

java.lang.String chemicalExchangeState

magneticEquivalenceGroupCode

java.lang.String magneticEquivalenceGroupCode

role

java.lang.String role

details

java.lang.String details

commonNames

java.util.ArrayList<E> commonNames

Class starfish.chemistry.Molecule extends java.lang.Object implements Serializable

Serialized Fields

structures

java.util.Set<E> structures

activeStructures

int[] activeStructures

labelsCurrent

boolean labelsCurrent

nResidues

int nResidues

name

java.lang.String name

originalName

java.lang.String originalName

source

java.lang.String source

comment

java.lang.String comment

display

java.lang.String display

posShapeType

java.lang.String posShapeType

negShapeType

java.lang.String negShapeType

title

java.lang.String title

label

byte label

colorType

java.lang.String colorType

model

float[][] model

view

float[][] view

values

float[] values

color

float[] color

center

double[] center

titlePosition

float[] titlePosition

energyType

java.lang.String energyType

deleted

boolean deleted

bondSpace

float bondSpace

crystal

java.lang.String crystal

entities

java.util.TreeMap<K,V> entities

entityLabels

java.util.LinkedHashMap<K,V> entityLabels

coordSets

java.util.TreeMap<K,V> coordSets

Class starfish.chemistry.MoleculeTableModel extends starfish.tables.NvTableModel implements Serializable

Serialized Fields

selected

java.util.ArrayList<E> selected

doubleTableRenderer

starfish.chemistry.MoleculeTableModel.DoubleTableCellRenderer doubleTableRenderer

filterString

java.lang.String filterString

dMode

java.lang.String dMode

RendererSet

boolean RendererSet

Class starfish.chemistry.Noe extends java.lang.Object implements Serializable

Serialized Fields

idNum

int idNum

spg1

SpatialSetGroup spg1

spg2

SpatialSetGroup spg2

peak

starfish.datasets.peaks.Peak peak

intensity

double intensity

volume

double volume

scale

double scale

atomScale

double atomScale

disStat

DistanceStat disStat

disStatAvg

DistanceStat disStatAvg

lower

double lower

upper

double upper

dcClass

int dcClass

ppmError

double ppmError

active

short active

symmetrical

boolean symmetrical

contribution

double contribution

disContrib

double disContrib

dRange

DistanceRange dRange

nPossible

int nPossible

netWorkValue

double netWorkValue

swapped

boolean swapped

filterSwapped

boolean filterSwapped

resMap

java.util.Map<K,V> resMap

activeFlags

java.util.EnumSet<E extends java.lang.Enum<E>> activeFlags

genType

Constraint.GenTypes genType

Class starfish.chemistry.NOEConstraintTable extends starfish.tables.NvTableModel implements Serializable

Serialized Fields

doubleTableRenderer

starfish.chemistry.NOEConstraintTable.DoubleTableCellRenderer doubleTableRenderer

spreadRenderer

starfish.tables.SpreadRenderer spreadRenderer

filterString

java.lang.String filterString

requireActive

boolean requireActive

dMode

java.lang.String dMode

RendererSet

boolean RendererSet

constraints

java.util.List<E> constraints

displayColumns

ConstraintColumns[] displayColumns

Class starfish.chemistry.Point3 extends java.lang.Object implements Serializable

Serialized Fields

x

double x

y

double y

z

double z

Class starfish.chemistry.Polymer extends Entity implements Serializable

Serialized Fields

residues

java.util.Hashtable<K,V> residues

residueVector

java.util.Vector<E> residueVector

firstResidue

Residue firstResidue

lastResidue

Residue lastResidue

polymerType

java.lang.String polymerType

strandID

java.lang.String strandID

oneLetterCode

java.lang.String oneLetterCode

nomenclature

java.lang.String nomenclature

Class starfish.chemistry.PPMv extends java.lang.Object implements Serializable

Serialized Fields

value

double value

error

double error

ambigCode

short ambigCode

valid

boolean valid

Class starfish.chemistry.Residue extends Compound implements Serializable

Serialized Fields

previous

Residue previous

next

Residue next

polymer

Polymer polymer

standard

boolean standard

pseudoMap

java.util.Map<K,V> pseudoMap

Class starfish.chemistry.Water extends Polymer implements Serializable