A B C D E F G H I K L M N O P R S T U V W X Y Z

A

Ac - Static variable in class starfish.chemistry.AtomProperty

activate(Flags) - Method in class starfish.chemistry.Noe

active - Variable in class starfish.chemistry.DistanceConstraint

add(Constraint) - Method in class starfish.chemistry.AngleConstraintSet

add(String, String, int) - Method in class starfish.chemistry.Atom

add(Constraint) - Method in interface starfish.chemistry.ConstraintSet

add(Constraint) - Method in class starfish.chemistry.NoeSet

add(SpatialSet) - Method in class starfish.chemistry.SpatialSetGroup

addAtom(Atom) - Method in class starfish.chemistry.Compound

addAtom(Atom) - Method in class starfish.chemistry.Residue

addBond(Bond) - Method in class starfish.chemistry.Atom

addBond(Atom, Atom, int) - Static method in class starfish.chemistry.Atom

addBond(Atom, Atom, int, int) - Static method in class starfish.chemistry.Atom

addCommonName(String, String) - Method in class starfish.chemistry.Entity

addComponents(Interp, Saveframe, ArrayList, ArrayList, ArrayList, ArrayList, Compound) - Method in class starfish.chemistry.Entity

addCoordSet(String, CoordSet) - Method in class starfish.chemistry.Entity

addCoordSet(String, Entity) - Method in class starfish.chemistry.Molecule

addEdge(int, int) - Method in class starfish.chemistry.search.MTree

addEntity(Entity) - Method in class starfish.chemistry.CoordSet

addEntity(Entity) - Method in class starfish.chemistry.Molecule

addEntity(Entity, String) - Method in class starfish.chemistry.Molecule

addMoleculeModel(Interp) - Static method in class starfish.chemistry.Molecule

addNode(MNode) - Method in class starfish.chemistry.search.MNode

addNode() - Method in class starfish.chemistry.search.MTree

addNode(double, double, double, double, double, double) - Method in class starfish.chemistry.Tube

addPseudoAtoms(String, ArrayList<String>) - Method in class starfish.chemistry.Residue

addResidue(Interp, String, Residue, String) - Method in class starfish.chemistry.io.PDB

addResidue(Residue) - Method in class starfish.chemistry.Polymer

addResidueOld(Residue) - Method in class starfish.chemistry.Polymer

addSet(String) - Static method in class starfish.chemistry.AngleConstraintSet

addSet(String) - Static method in class starfish.chemistry.NoeSet

addToSTARString(StringBuilder) - Method in class starfish.chemistry.SpatialSet

addToSTARString(StringBuilder, boolean) - Method in class starfish.chemistry.SpatialSet

addToSTARString(StringBuilder) - Method in class starfish.chemistry.SpatialSetGroup

addTranslation(int, String, String, String) - Static method in class starfish.chemistry.AtomParser

addXYZtoSTAR(StringBuilder, int) - Method in class starfish.chemistry.SpatialSet

Ag - Static variable in class starfish.chemistry.AtomProperty

Al - Static variable in class starfish.chemistry.AtomProperty

altPos - Variable in class starfish.chemistry.SpatialSet

Am - Static variable in class starfish.chemistry.AtomProperty

angle - Variable in class starfish.chemistry.AngleConstraint

AngleConstraint - Class in starfish.chemistry

AngleConstraint(SpatialSet[]) - Constructor for class starfish.chemistry.AngleConstraint

AngleConstraint(String, SpatialSet[]) - Constructor for class starfish.chemistry.AngleConstraint

AngleConstraintCmd - Class in starfish.chemistry

AngleConstraintCmd() - Constructor for class starfish.chemistry.AngleConstraintCmd

AngleConstraintColumns - Enum in starfish.chemistry

AngleConstraintSet - Class in starfish.chemistry

AngleConstraintSet(String) - Constructor for class starfish.chemistry.AngleConstraintSet

AngleConstraintTable - Class in starfish.chemistry

AngleConstraintTable() - Constructor for class starfish.chemistry.AngleConstraintTable

aNum - Variable in class starfish.chemistry.Atom

Ar - Static variable in class starfish.chemistry.AtomProperty

ARIARestraintReader - Class in starfish.chemistry.io

ARIARestraintReader(Interp, String, String) - Constructor for class starfish.chemistry.io.ARIARestraintReader

As - Static variable in class starfish.chemistry.AtomProperty

assemblyID - Variable in class starfish.chemistry.Entity

At - Static variable in class starfish.chemistry.AtomProperty

Atom - Class in starfish.chemistry

Atom(AtomParser) - Constructor for class starfish.chemistry.Atom

Atom(AtomParser, String) - Constructor for class starfish.chemistry.Atom

Atom(String, String) - Constructor for class starfish.chemistry.Atom

Atom(String) - Constructor for class starfish.chemistry.Atom

Atom(String, String, String) - Constructor for class starfish.chemistry.Atom

atom - Variable in class starfish.chemistry.SpatialSet

atom1 - Variable in class starfish.chemistry.DistanceConstraint

atom2 - Variable in class starfish.chemistry.DistanceConstraint

AtomCmd - Class in starfish.chemistry

AtomCmd() - Constructor for class starfish.chemistry.AtomCmd

AtomColors - Class in starfish.chemistry

AtomColors() - Constructor for class starfish.chemistry.AtomColors

Creates a new instance of AtomColors

atomColors - Static variable in class starfish.chemistry.AtomColors

AtomEquivalency - Class in starfish.chemistry

AtomEquivalency() - Constructor for class starfish.chemistry.AtomEquivalency

Creates a new instance of AtomEquivalency

atomList - Static variable in class starfish.chemistry.Molecule

atomName - Variable in class starfish.chemistry.AtomParser

atomNames - Variable in class starfish.chemistry.MolFilter

AtomParser - Class in starfish.chemistry

AtomParser(String) - Constructor for class starfish.chemistry.AtomParser

AtomParser(String, boolean) - Constructor for class starfish.chemistry.AtomParser

AtomProperty - Class in starfish.chemistry

atoms - Variable in class starfish.chemistry.Compound

atoms - Variable in class starfish.chemistry.MoleculePrimitives

atomScale - Variable in class starfish.chemistry.Noe

AtomUtil - Class in starfish.chemistry

AtomUtil() - Constructor for class starfish.chemistry.AtomUtil

Au - Static variable in class starfish.chemistry.AtomProperty

avgAtom(Vector) - Static method in class starfish.chemistry.Atom

avgAtom(Vector, int) - Static method in class starfish.chemistry.Atom

avgCoords(Interp, MolFilter) - Static method in class starfish.chemistry.Molecule

avgDistance(ArrayList<Double>, double, int) - Static method in class starfish.chemistry.Noe

B

B - Static variable in class starfish.chemistry.AtomProperty

Ba - Static variable in class starfish.chemistry.AtomProperty

Be - Static variable in class starfish.chemistry.AtomProperty

begin - Variable in class starfish.chemistry.Bond

bfactor - Variable in class starfish.chemistry.AtomParser

bfactor - Variable in class starfish.chemistry.SpatialSet

Bi - Static variable in class starfish.chemistry.AtomProperty

BioPPMScoreCmd - Class in starfish.chemistry

BioPPMScoreCmd() - Constructor for class starfish.chemistry.BioPPMScoreCmd

Bk - Static variable in class starfish.chemistry.AtomProperty

blue - Variable in class starfish.chemistry.Bond

blue - Variable in class starfish.chemistry.SpatialSet

Bond - Class in starfish.chemistry

Bond(Atom, Atom) - Constructor for class starfish.chemistry.Bond

bondLength - Variable in class starfish.chemistry.Atom

bonds - Variable in class starfish.chemistry.Atom

Br - Static variable in class starfish.chemistry.AtomProperty

broad_path(int) - Method in class starfish.chemistry.search.MTree

broad_path2(int) - Method in class starfish.chemistry.search.MTree

Does a bread-first search through a tree starting at element iStart Returns an array of node indices describing the path through the tree.

BroadSearch - Class in starfish.chemistry.search

BroadSearch(int) - Constructor for class starfish.chemistry.search.BroadSearch

bselected - Static variable in class starfish.chemistry.Molecule

bSides - Variable in class starfish.chemistry.Tube

buildTree(Interp, Molecule, Atom, Vector, MTree) - Static method in class starfish.chemistry.Molecule

C

C - Static variable in class starfish.chemistry.AtomProperty

Ca - Static variable in class starfish.chemistry.AtomProperty

cal_super(double[][], double[][], int) - Method in class starfish.chemistry.SuperMol

calcAllBonds(Interp) - Static method in class starfish.chemistry.Molecule

calcAngle(Point3, Point3, Point3) - Static method in class starfish.chemistry.Atom

calcAngle(Interp, MolFilter, MolFilter, MolFilter) - Static method in class starfish.chemistry.Molecule

calcBond(Atom, Atom, int) - Static method in class starfish.chemistry.Atom

calcBond(Atom, Atom, int, int) - Static method in class starfish.chemistry.Atom

calcBonds() - Method in class starfish.chemistry.Molecule

calcCenter(Interp, int) - Method in class starfish.chemistry.Molecule

calcDihedral(Point3, Point3, Point3, Point3) - Static method in class starfish.chemistry.Atom

calcDihedral(Interp, MolFilter, MolFilter, MolFilter, MolFilter) - Static method in class starfish.chemistry.Molecule

calcDistance(Point3, Point3) - Static method in class starfish.chemistry.Atom

calcDistance(Interp, MolFilter, MolFilter) - Static method in class starfish.chemistry.Molecule

calcDistanceRange(SpatialSetGroup, SpatialSetGroup, int) - Static method in class starfish.chemistry.DistanceRange

calcDistanceRange(SpatialSet, SpatialSet, int) - Static method in class starfish.chemistry.DistanceRange

calcMedian(String, PeakList) - Static method in class starfish.chemistry.Noe

calcMinDistance1(SpatialSet[], int) - Static method in class starfish.chemistry.DistanceRange

calcMinDistance2(SpatialSet[], int) - Static method in class starfish.chemistry.DistanceRange

calcRMSD() - Method in class starfish.chemistry.Molecule

calculateContributions(boolean) - Static method in class starfish.chemistry.Noe

calcWeightedDistance(SpatialSetGroup, SpatialSetGroup, int, double) - Static method in class starfish.chemistry.Atom

calibrateExp(PeakList) - Static method in class starfish.chemistry.Noe

canonValue - Variable in class starfish.chemistry.Atom

capPolymer(Polymer) - Static method in class starfish.chemistry.io.PDB

Cd - Static variable in class starfish.chemistry.AtomProperty

Ce - Static variable in class starfish.chemistry.AtomProperty

center(int) - Method in class starfish.chemistry.Molecule

Cf - Static variable in class starfish.chemistry.AtomProperty

chainID - Variable in class starfish.chemistry.AtomParser

charge - Variable in class starfish.chemistry.Atom

charge - Variable in class starfish.chemistry.AtomParser

checkPattern(Interp, Atom[], String[], String[]) - Static method in class starfish.chemistry.AtomUtil

checkPDBType(Interp, String) - Method in class starfish.chemistry.io.PDB

checkType() - Method in class starfish.chemistry.Molecule

chemCompAtomLoopStrings - Static variable in class starfish.chemistry.Compound

chemCompBondLoopStrings - Static variable in class starfish.chemistry.Compound

chemCompEntityIndexLoopStrings - Static variable in class starfish.chemistry.Compound

chemicalExchangeState - Variable in class starfish.chemistry.Entity

ChemistryExt - Class in starfish.chemistry

ChemistryExt() - Constructor for class starfish.chemistry.ChemistryExt

Cl - Static variable in class starfish.chemistry.AtomProperty

clear() - Method in class starfish.chemistry.AngleConstraintSet

clear() - Method in interface starfish.chemistry.ConstraintSet

clear() - Method in class starfish.chemistry.NoeSet

clearLimitToAssigned() - Static method in class starfish.chemistry.Noe

clearScaleMap() - Static method in class starfish.chemistry.Noe

clearScaleMap() - Method in class starfish.chemistry.NoeSet

Cm - Static variable in class starfish.chemistry.AtomProperty

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.AngleConstraintCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.AtomCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.BioPPMScoreCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.DisConCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.IdPeakCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.io.MMcifCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.io.PDBCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.io.StructureWriteCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.MoleculeCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.NoeCmd

cmdProc(Interp, TclObject[]) - Method in class starfish.chemistry.ResidueCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.AngleConstraintCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.AtomCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.BioPPMScoreCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.DisConCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.IdPeakCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.io.MMcifCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.io.PDBCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.io.StructureWriteCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.MoleculeCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.NoeCmd

cmdProc2(Interp, TclObject[]) - Method in class starfish.chemistry.ResidueCmd

Co - Static variable in class starfish.chemistry.AtomProperty

color - Variable in class starfish.chemistry.Molecule

colorAtoms(Interp, float, float, float) - Static method in class starfish.chemistry.Molecule

colorAtomsByType(Interp) - Static method in class starfish.chemistry.Molecule

colorBonds(Interp, float, float, float) - Static method in class starfish.chemistry.Molecule

colorType - Variable in class starfish.chemistry.Molecule

colorTypes - Static variable in class starfish.chemistry.Molecule

comment - Variable in class starfish.chemistry.Molecule

compare(SpatialSetGroup) - Method in class starfish.chemistry.SpatialSetGroup

compareTo(Object) - Method in class starfish.chemistry.search.MNode

Compound - Class in starfish.chemistry

Compound() - Constructor for class starfish.chemistry.Compound

Compound(String, String) - Constructor for class starfish.chemistry.Compound

Compound(String, String, String) - Constructor for class starfish.chemistry.Compound

compoundMap - Static variable in class starfish.chemistry.Molecule

conditions - Static variable in class starfish.chemistry.Molecule

conformationalIsomer - Variable in class starfish.chemistry.Entity

Constraint - Interface in starfish.chemistry

Constraint.GenTypes - Enum in starfish.chemistry

ConstraintColumns - Interface in starfish.chemistry

constraints - Static variable in class starfish.chemistry.DistanceConstraint

ConstraintSet - Interface in starfish.chemistry

ConstraintSTARWriter - Class in starfish.chemistry.io

ConstraintSTARWriter() - Constructor for class starfish.chemistry.io.ConstraintSTARWriter

ConstraintTable - Interface in starfish.chemistry

contribution - Variable in class starfish.chemistry.Noe

CoordinateSTARWriter - Class in starfish.chemistry.io

CoordinateSTARWriter() - Constructor for class starfish.chemistry.io.CoordinateSTARWriter

coords - Variable in class starfish.chemistry.SpatialSet

CoordSet - Class in starfish.chemistry

CoordSet(String, Entity) - Constructor for class starfish.chemistry.CoordSet

CoordSet - Class in starfish.chemistry.search

CoordSet() - Constructor for class starfish.chemistry.search.CoordSet

Creates a new instance of CoordSet

coordSetExists(String) - Method in class starfish.chemistry.Molecule

coordSets - Variable in class starfish.chemistry.Entity

coordSets - Variable in class starfish.chemistry.Molecule

Cr - Static variable in class starfish.chemistry.AtomProperty

createLabelArray(int, float[], int) - Method in class starfish.chemistry.Molecule

createLineArray(int, float[], int, float[]) - Method in class starfish.chemistry.Molecule

createSelectionArray(int, float[], int[]) - Method in class starfish.chemistry.Molecule

createSphereArray(int, float[], int, float[], float[]) - Method in class starfish.chemistry.Molecule

createTriangleArray(double[], int, float[], float[]) - Method in class starfish.chemistry.Tube

crystal - Variable in class starfish.chemistry.Molecule

Cs - Static variable in class starfish.chemistry.AtomProperty

Cu - Static variable in class starfish.chemistry.AtomProperty

currentToIUPAC(String, String) - Static method in class starfish.chemistry.AtomParser

D

dcClass - Variable in class starfish.chemistry.DistanceConstraint

dcClass - Variable in class starfish.chemistry.Noe

defaultCal(PeakList) - Static method in class starfish.chemistry.Noe

defaultMol - Static variable in class starfish.chemistry.Molecule

defaultSpatialSet - Variable in class starfish.chemistry.Atom

deleted - Variable in class starfish.chemistry.Molecule

depthFirstPath(int) - Method in class starfish.chemistry.search.MTree

depthFirstPath(MNode, ArrayList) - Method in class starfish.chemistry.search.MTree

details - Variable in class starfish.chemistry.Entity

dihedralAngle - Variable in class starfish.chemistry.Atom

DisConCmd - Class in starfish.chemistry

DisConCmd() - Constructor for class starfish.chemistry.DisConCmd

disContrib - Variable in class starfish.chemistry.Noe

DISPLAY - Static variable in class starfish.chemistry.Atom

DISPLAY - Static variable in class starfish.chemistry.Bond

display - Variable in class starfish.chemistry.Molecule

displayStatus - Variable in class starfish.chemistry.SpatialSet

displayTypes - Static variable in class starfish.chemistry.Molecule

disStat - Variable in class starfish.chemistry.AngleConstraint

disStat - Variable in class starfish.chemistry.Noe

disStatAvg - Variable in class starfish.chemistry.Noe

distance - Variable in class starfish.chemistry.DistanceConstraint

DistanceConstraint - Class in starfish.chemistry

DistanceConstraint(Peak, Atom, Atom, double) - Constructor for class starfish.chemistry.DistanceConstraint

DistanceRange - Class in starfish.chemistry

DistanceRange.Status - Enum in starfish.chemistry

DistanceStat - Class in starfish.chemistry

doSuper(int, int, boolean) - Method in class starfish.chemistry.SuperMol

dRange - Variable in class starfish.chemistry.Noe

drawNodes(Graphics, double, double, double, Dimension) - Method in class starfish.chemistry.Tube

dumpCoords(Interp) - Method in class starfish.chemistry.Atom

Dy - Static variable in class starfish.chemistry.AtomProperty

E

elemName - Variable in class starfish.chemistry.AtomParser

elemProc(Interp, TclObject[]) - Method in class starfish.chemistry.AtomCmd

end - Variable in class starfish.chemistry.Bond

ENERGY - Static variable in class starfish.chemistry.Molecule

energyType - Variable in class starfish.chemistry.Molecule

entities - Variable in class starfish.chemistry.CoordSet

entities - Variable in class starfish.chemistry.Molecule

entity - Variable in class starfish.chemistry.Atom

Entity - Class in starfish.chemistry

Entity() - Constructor for class starfish.chemistry.Entity

entityAssemblyLoopStrings - Static variable in class starfish.chemistry.Entity

entityCommonNameLoopStrings - Static variable in class starfish.chemistry.Entity

entityCompIndexLoopStrings - Static variable in class starfish.chemistry.Entity

entityCompIndexLoopStrings - Static variable in class starfish.chemistry.Polymer

entityID - Variable in class starfish.chemistry.Entity

entityLabels - Variable in class starfish.chemistry.Molecule

entityPolySeqLoopStrings - Static variable in class starfish.chemistry.Entity

entityPolySeqLoopStrings - Static variable in class starfish.chemistry.Polymer

entityStrings - Static variable in class starfish.chemistry.Entity

equivAtoms - Variable in class starfish.chemistry.Atom

Er - Static variable in class starfish.chemistry.AtomProperty

error - Variable in class starfish.chemistry.PPMv

Es - Static variable in class starfish.chemistry.AtomProperty

Eu - Static variable in class starfish.chemistry.AtomProperty

extractNoePeaks(Interp, PeakList, int) - Static method in class starfish.chemistry.NoeCmd

extractNoePeaks2(Interp, PeakList, int, boolean) - Static method in class starfish.chemistry.NoeCmd

extractNoePeaksSlow(Interp, PeakList, int) - Static method in class starfish.chemistry.NoeCmd

F

F - Static variable in class starfish.chemistry.AtomProperty

fcharge - Variable in class starfish.chemistry.Atom

Fe - Static variable in class starfish.chemistry.AtomProperty

FFDReader - Class in starfish.chemistry.io

FFDReader() - Constructor for class starfish.chemistry.io.FFDReader

Creates a new instance of FFDReader

FFDWriter - Class in starfish.chemistry.io

FFDWriter() - Constructor for class starfish.chemistry.io.FFDWriter

Creates a new instance of FFDWriter

findEquivalentAtoms(Interp, String) - Static method in class starfish.chemistry.Molecule

findEquivalentAtoms(Entity) - Static method in class starfish.chemistry.Molecule

findNetworks(boolean) - Static method in class starfish.chemistry.Noe

findRedundant() - Static method in class starfish.chemistry.Noe

findRes(String) - Method in class starfish.chemistry.MoleculeTableModel

findResLast(String) - Method in class starfish.chemistry.MoleculeTableModel

findSymmetrical() - Static method in class starfish.chemistry.Noe

finishSaveFrameProcessing(Interp, Saveframe, Compound, String) - Method in class starfish.chemistry.Entity

finishSaveFrameProcessing(Interp, Saveframe, String) - Method in class starfish.chemistry.Polymer

firstAtom - Variable in class starfish.chemistry.Entity

firstBond - Variable in class starfish.chemistry.Entity

firstRes - Variable in class starfish.chemistry.MolFilter

firstResidue - Variable in class starfish.chemistry.Polymer

firstResType - Variable in class starfish.chemistry.MolFilter

Fm - Static variable in class starfish.chemistry.AtomProperty

forceFieldCode - Variable in class starfish.chemistry.Atom

Fr - Static variable in class starfish.chemistry.AtomProperty

fromFile(String) - Method in class starfish.chemistry.io.MMcifReader

G

Ga - Static variable in class starfish.chemistry.AtomProperty

Gd - Static variable in class starfish.chemistry.AtomProperty

Ge - Static variable in class starfish.chemistry.AtomProperty

genCoords(Interp, boolean) - Method in class starfish.chemistry.Molecule

get() - Method in class starfish.chemistry.AngleConstraintSet

get(int) - Method in class starfish.chemistry.AngleConstraintSet

get(String) - Static method in class starfish.chemistry.AtomProperty

get(int) - Static method in class starfish.chemistry.AtomProperty

get(int) - Method in interface starfish.chemistry.ConstraintSet

get(int) - Static method in class starfish.chemistry.DistanceConstraint

get(String) - Static method in class starfish.chemistry.Molecule

get(int) - Static method in class starfish.chemistry.Noe

get() - Method in class starfish.chemistry.NoeSet

get(int) - Method in class starfish.chemistry.NoeSet

getActive() - Method in class starfish.chemistry.AngleConstraint

getActive() - Method in class starfish.chemistry.Noe

getActiveSet() - Static method in class starfish.chemistry.AngleConstraint

getActiveSet() - Static method in class starfish.chemistry.Noe

getActiveStructures() - Method in class starfish.chemistry.Molecule

getActivityFlags() - Method in class starfish.chemistry.Noe

getAmbigCode() - Method in class starfish.chemistry.PPMv

getAnAtom() - Method in class starfish.chemistry.SpatialSetGroup

getAtom(String) - Method in class starfish.chemistry.Compound

getAtom(Interp, MolFilter) - Static method in class starfish.chemistry.Molecule

getAtom(String) - Method in class starfish.chemistry.Residue

getAtomByName(Interp, String) - Static method in class starfish.chemistry.Molecule

getAtomColor(int) - Static method in class starfish.chemistry.AtomColors

getAtomicNumber() - Method in class starfish.chemistry.Atom

getAtoms(String) - Method in class starfish.chemistry.Compound

getAtoms(int, Atom[]) - Method in class starfish.chemistry.Molecule

getAtoms() - Method in class starfish.chemistry.Molecule

getAtoms(Interp, Peak) - Static method in class starfish.chemistry.NoeCmd

getAtomsByProp(int) - Method in class starfish.chemistry.Molecule

getAtomTypes(Molecule) - Static method in class starfish.chemistry.Molecule

getAttachedHydrogens(Atom) - Method in class starfish.chemistry.Molecule

getBFactor() - Method in class starfish.chemistry.Atom

getBFactor() - Method in class starfish.chemistry.SpatialSet

getBlue() - Method in class starfish.chemistry.Atom

getBlue() - Method in class starfish.chemistry.AtomProperty

getBMRBAmbiguity() - Method in class starfish.chemistry.Atom

getBonds() - Method in class starfish.chemistry.Molecule

getCalibration(PeakList) - Method in class starfish.chemistry.NoeSet

getCategory() - Method in class starfish.chemistry.AngleConstraintSet

getCategory() - Method in interface starfish.chemistry.ConstraintSet

getCategory() - Method in class starfish.chemistry.NoeSet

getChildren() - Method in class starfish.chemistry.Atom

getColorTypes(Interp) - Static method in class starfish.chemistry.Molecule

getColumnClass() - Method in enum starfish.chemistry.AngleConstraintColumns

getColumnClass(int) - Method in class starfish.chemistry.AngleConstraintTable

getColumnClass() - Method in interface starfish.chemistry.ConstraintColumns

getColumnClass(int) - Method in class starfish.chemistry.MoleculeTableModel

getColumnClass() - Method in enum starfish.chemistry.NOEColumns

getColumnClass(int) - Method in class starfish.chemistry.NOEConstraintTable

getColumnCount() - Method in class starfish.chemistry.AngleConstraintTable

getColumnCount() - Method in class starfish.chemistry.MoleculeTableModel

getColumnCount() - Method in class starfish.chemistry.NOEConstraintTable

getColumnName(int) - Method in class starfish.chemistry.AngleConstraintTable

getColumnName(int) - Method in class starfish.chemistry.MoleculeTableModel

getColumnName(int) - Method in class starfish.chemistry.NOEConstraintTable

getConnected() - Method in class starfish.chemistry.Atom

getConstraints(boolean) - Static method in class starfish.chemistry.Noe

getConstraints(String, boolean) - Static method in class starfish.chemistry.Noe

getConstraintsForPeak(Peak) - Method in class starfish.chemistry.NoeSet

getCoordEntity() - Method in class starfish.chemistry.MolFilter

getCoordLoopStrings() - Method in class starfish.chemistry.Molecule

getCoordSetName() - Method in class starfish.chemistry.MolFilter

getCoordSets() - Method in class starfish.chemistry.Entity

getDefaultSpatialSet() - Method in class starfish.chemistry.Atom

getDescription() - Method in enum starfish.chemistry.AngleConstraintColumns

getDescription() - Method in enum starfish.chemistry.Constraint.GenTypes

getDescription() - Method in interface starfish.chemistry.ConstraintColumns

getDescription() - Method in enum starfish.chemistry.DistanceRange.Status

getDescription() - Method in enum starfish.chemistry.NOEColumns

getDisplayTypes(Interp) - Static method in class starfish.chemistry.Molecule

getDistance() - Method in class starfish.chemistry.Noe

getDistances(SpatialSetGroup, SpatialSetGroup, int, ArrayList<Double>) - Static method in class starfish.chemistry.Atom

getElem(Interp, String, TclObject) - Method in class starfish.chemistry.AngleConstraint

getElem(Interp, String, TclObject) - Method in class starfish.chemistry.DistanceConstraint

getElem(Interp, String, TclObject) - Method in class starfish.chemistry.Noe

getElementName(int) - Static method in class starfish.chemistry.Atom

getElementName(int) - Static method in class starfish.chemistry.AtomProperty

getElementNumber() - Method in class starfish.chemistry.Atom

getElementNumber(String) - Static method in class starfish.chemistry.Atom

getElementNumber() - Method in class starfish.chemistry.AtomProperty

getElementNumber(String) - Static method in class starfish.chemistry.AtomProperty

getEntities() - Method in class starfish.chemistry.CoordSet

Creates a new instance of CoordSet

getEntity() - Method in class starfish.chemistry.Atom

getEntity(String) - Method in class starfish.chemistry.Molecule

getEntity(SpatialSetGroup) - Method in class starfish.chemistry.Noe

getEquivalency(Interp) - Method in class starfish.chemistry.Atom

getEquivIndices() - Method in class starfish.chemistry.Atom

getFirstAtom() - Method in class starfish.chemistry.Entity

getFirstSet() - Method in class starfish.chemistry.SpatialSetGroup

getFormalCharge() - Method in class starfish.chemistry.Atom

getFracInBound() - Method in class starfish.chemistry.DistanceStat

getFullName() - Method in class starfish.chemistry.Atom

getFullName() - Method in class starfish.chemistry.SpatialSet

getFullName() - Method in class starfish.chemistry.SpatialSetGroup

getGenType() - Method in class starfish.chemistry.Noe

getGreen() - Method in class starfish.chemistry.Atom

getGreen() - Method in class starfish.chemistry.AtomProperty

getID() - Method in class starfish.chemistry.AngleConstraint

getID() - Method in interface starfish.chemistry.Constraint

getID() - Method in class starfish.chemistry.Noe

getID() - Method in class starfish.chemistry.search.MNode

getIDNum() - Method in class starfish.chemistry.Compound

getIDNum() - Method in class starfish.chemistry.Entity

getIDNum() - Method in class starfish.chemistry.Residue

getLabelCount(int) - Method in class starfish.chemistry.Molecule

getLabelTypes(Interp) - Static method in class starfish.chemistry.Molecule

getLine() - Method in class starfish.chemistry.io.MMcifReader

getLineCount(int) - Method in class starfish.chemistry.Molecule

getListType() - Method in class starfish.chemistry.AngleConstraintSet

getListType() - Method in interface starfish.chemistry.ConstraintSet

getListType() - Method in class starfish.chemistry.NoeSet

getLoopStrings() - Method in class starfish.chemistry.AngleConstraintSet

getLoopStrings() - Method in interface starfish.chemistry.ConstraintSet

getLoopStrings() - Method in class starfish.chemistry.NoeSet

getMax() - Method in class starfish.chemistry.DistanceRange

getMax() - Method in class starfish.chemistry.DistanceStat

getMean() - Method in class starfish.chemistry.DistanceStat

getMin() - Method in class starfish.chemistry.DistanceRange

getMin() - Method in class starfish.chemistry.DistanceStat

getMoleculeBonds() - Method in class starfish.chemistry.Molecule

getName() - Method in class starfish.chemistry.AngleConstraintSet

getName() - Method in class starfish.chemistry.Atom

getName() - Method in class starfish.chemistry.Compound

getName() - Method in interface starfish.chemistry.ConstraintSet

getName() - Method in class starfish.chemistry.CoordSet

getName() - Method in class starfish.chemistry.Entity

getName() - Method in class starfish.chemistry.NoeSet

getName() - Method in class starfish.chemistry.SpatialSet

getName() - Method in class starfish.chemistry.SpatialSetGroup

getNames() - Static method in class starfish.chemistry.AngleConstraintSet

getNames() - Static method in class starfish.chemistry.NoeSet

getNomenclature() - Method in class starfish.chemistry.Polymer

getNStructures() - Static method in class starfish.chemistry.Noe

getNumber() - Method in class starfish.chemistry.Compound

getOccupancy() - Method in class starfish.chemistry.Atom

getOccupancy() - Method in class starfish.chemistry.SpatialSet

getOneLetter() - Method in class starfish.chemistry.Residue

getOneLetterCode() - Method in class starfish.chemistry.Polymer

getParent() - Method in class starfish.chemistry.Atom

getPartners(int, int) - Method in class starfish.chemistry.Atom

getPeakList(Peak) - Static method in class starfish.chemistry.Noe

getPeakListName() - Method in class starfish.chemistry.Noe

getPeakMapEntries() - Method in class starfish.chemistry.NoeSet

getPeakNum() - Method in class starfish.chemistry.Noe

getPoint() - Method in class starfish.chemistry.Atom

getPoint(int) - Method in class starfish.chemistry.Atom

getPoint(String, int) - Method in class starfish.chemistry.Atom

getPoint() - Method in class starfish.chemistry.SpatialSet

getPoint(int) - Method in class starfish.chemistry.SpatialSet

getPointCount() - Method in class starfish.chemistry.SpatialSet

getPointValidity(String, int) - Method in class starfish.chemistry.Atom

getPointValidity(int) - Method in class starfish.chemistry.SpatialSet

getPolymerType() - Method in class starfish.chemistry.Polymer

getPPM(int) - Method in class starfish.chemistry.Atom

getPPM(String, int) - Method in class starfish.chemistry.Atom

getPPM(int) - Method in class starfish.chemistry.SpatialSet

getProperty(String) - Method in class starfish.chemistry.AngleConstraintTable

getProperty(int) - Method in class starfish.chemistry.Atom

getProperty(String, int) - Method in class starfish.chemistry.Atom

getProperty(int) - Method in class starfish.chemistry.Bond

getProperty(String) - Method in class starfish.chemistry.MoleculeTableModel

getProperty(String) - Method in class starfish.chemistry.NOEConstraintTable

getProperty(int) - Method in class starfish.chemistry.SpatialSet

getPseudo(String) - Method in class starfish.chemistry.Residue

getPseudoName(int) - Method in class starfish.chemistry.Atom

getRed() - Method in class starfish.chemistry.Atom

getRed() - Method in class starfish.chemistry.AtomProperty

getRefPPM() - Method in class starfish.chemistry.SpatialSet

getResidue(String) - Method in class starfish.chemistry.Polymer

getResidue(int) - Method in class starfish.chemistry.Polymer

getResidues() - Method in class starfish.chemistry.Polymer

getReslibDir() - Static method in class starfish.chemistry.io.PDB

getResonanceSet() - Method in class starfish.chemistry.Atom

getResults(Vector[], MatchCriteria[]) - Method in class starfish.chemistry.IdPeakCmd

getResults2(Vector[], MatchCriteria[]) - Method in class starfish.chemistry.IdPeakCmd

getRowCount() - Method in class starfish.chemistry.AngleConstraintTable

getRowCount() - Method in class starfish.chemistry.MoleculeTableModel

getRowCount() - Method in class starfish.chemistry.NOEConstraintTable

getScore(int) - Method in class starfish.chemistry.search.BroadSearch

getSelected() - Method in class starfish.chemistry.Atom

getSelected(String) - Method in class starfish.chemistry.Atom

getSelected() - Method in class starfish.chemistry.SpatialSet

getSet(String) - Static method in class starfish.chemistry.AngleConstraintSet

getSet(String) - Static method in class starfish.chemistry.NoeSet

getShapeTypes(Interp) - Static method in class starfish.chemistry.Molecule

getShortDescription() - Method in enum starfish.chemistry.Constraint.GenTypes

getShortName() - Method in class starfish.chemistry.Atom

getSize() - Static method in class starfish.chemistry.AngleConstraint

getSize() - Method in class starfish.chemistry.AngleConstraintSet

getSize() - Method in interface starfish.chemistry.ConstraintSet

getSize() - Static method in class starfish.chemistry.Noe

getSize() - Method in class starfish.chemistry.NoeSet

getSize() - Method in class starfish.chemistry.SpatialSetGroup

getSpatialSet(int) - Method in class starfish.chemistry.AngleConstraint

getSpatialSet(String) - Method in class starfish.chemistry.Atom

getSpatialSet(Interp, MolFilter) - Static method in class starfish.chemistry.Molecule

getSpatialSetIterator() - Method in class starfish.chemistry.Molecule

getSPG(int, boolean, boolean) - Method in class starfish.chemistry.Noe

getSphereCount(int) - Method in class starfish.chemistry.Molecule

getStartAtom(Molecule) - Static method in class starfish.chemistry.Molecule

getStat() - Method in class starfish.chemistry.AngleConstraint

getStat() - Method in interface starfish.chemistry.Constraint

getStat() - Method in class starfish.chemistry.Noe

getStatus() - Method in class starfish.chemistry.DistanceRange

getStdDev() - Method in class starfish.chemistry.DistanceStat

getStereo() - Method in class starfish.chemistry.Atom

getStrandID() - Method in class starfish.chemistry.Polymer

getString() - Method in class starfish.chemistry.MolFilter

getTclToken(Interp) - Method in class starfish.chemistry.io.MMcifReader

getToken(Interp) - Method in class starfish.chemistry.io.MMcifReader

getTotalScore() - Method in class starfish.chemistry.PPMScore

getTranslation(String, String, String) - Static method in class starfish.chemistry.AtomParser

getTranslation(String, int) - Static method in class starfish.chemistry.AtomParser

getType() - Method in class starfish.chemistry.AngleConstraintSet

getType() - Method in class starfish.chemistry.Atom

getType() - Method in interface starfish.chemistry.ConstraintSet

getType() - Method in class starfish.chemistry.NoeSet

getValue() - Method in class starfish.chemistry.AngleConstraint

getValue(ConstraintTable, Constraint) - Method in enum starfish.chemistry.AngleConstraintColumns

getValue() - Method in interface starfish.chemistry.Constraint

getValue(ConstraintTable, Constraint) - Method in interface starfish.chemistry.ConstraintColumns

getValue() - Method in class starfish.chemistry.Noe

getValue(ConstraintTable, Constraint) - Method in enum starfish.chemistry.NOEColumns

getValue() - Method in class starfish.chemistry.search.MNode

getValueAt(int, int) - Method in class starfish.chemistry.AngleConstraintTable

getValueAt(int, int) - Method in class starfish.chemistry.MoleculeTableModel

getValueAt(int, int) - Method in class starfish.chemistry.NOEConstraintTable

getViol(double) - Method in class starfish.chemistry.AngleConstraint

getViolChars(DistanceStat) - Method in class starfish.chemistry.AngleConstraint

getViolChars(DistanceStat) - Method in class starfish.chemistry.Noe

getViolStructures() - Method in class starfish.chemistry.DistanceStat

globalSelected - Static variable in class starfish.chemistry.Molecule

GRADIENT - Static variable in class starfish.chemistry.Molecule

green - Variable in class starfish.chemistry.Bond

green - Variable in class starfish.chemistry.SpatialSet

H

H - Static variable in class starfish.chemistry.AtomProperty

hasEquivalentAtoms() - Method in class starfish.chemistry.Entity

hasNext() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

He - Static variable in class starfish.chemistry.AtomProperty

Hf - Static variable in class starfish.chemistry.AtomProperty

Hg - Static variable in class starfish.chemistry.AtomProperty

Ho - Static variable in class starfish.chemistry.AtomProperty

I

I - Static variable in class starfish.chemistry.AtomProperty

iAtom - Variable in class starfish.chemistry.Atom

ID - Static variable in class starfish.chemistry.AngleConstraintSet

ID - Static variable in class starfish.chemistry.NoeSet

IdPeakCmd - Class in starfish.chemistry

IdPeakCmd() - Constructor for class starfish.chemistry.IdPeakCmd

In - Static variable in class starfish.chemistry.AtomProperty

inactivate(Flags) - Method in class starfish.chemistry.Noe

inactivateDiagonal() - Static method in class starfish.chemistry.Noe

init(Interp) - Method in class starfish.chemistry.ChemistryExt

init(Interp) - Method in class starfish.chemistry.search.MolSearchExtension

intensity - Variable in class starfish.chemistry.DistanceConstraint

intensity - Variable in class starfish.chemistry.Noe

INTER_ENERGY - Static variable in class starfish.chemistry.Molecule

INTRA_ENERGY - Static variable in class starfish.chemistry.Molecule

Ir - Static variable in class starfish.chemistry.AtomProperty

iRes - Variable in class starfish.chemistry.Compound

irpIndex - Variable in class starfish.chemistry.Atom

isActive() - Method in class starfish.chemistry.Noe

isCalibratable() - Static method in class starfish.chemistry.Noe

isCellEditable(int, int) - Method in class starfish.chemistry.AngleConstraintTable

isCellEditable(int, int) - Method in class starfish.chemistry.MoleculeTableModel

isCellEditable(int, int) - Method in class starfish.chemistry.NOEConstraintTable

isDirty() - Method in class starfish.chemistry.AngleConstraintSet

isDirty() - Method in interface starfish.chemistry.ConstraintSet

isDirty() - Static method in class starfish.chemistry.Noe

isDirty() - Method in class starfish.chemistry.NoeSet

isEditable() - Method in enum starfish.chemistry.AngleConstraintColumns

isEditable() - Method in interface starfish.chemistry.ConstraintColumns

isEditable() - Method in enum starfish.chemistry.NOEColumns

isIUPACMode() - Static method in class starfish.chemistry.io.PDB

isMethyl() - Method in class starfish.chemistry.Atom

isMethylene() - Method in class starfish.chemistry.Atom

isOK() - Method in class starfish.chemistry.DistanceRange

isStereo() - Method in class starfish.chemistry.SpatialSet

isUserActive() - Method in class starfish.chemistry.AngleConstraint

isUserActive() - Method in interface starfish.chemistry.Constraint

isUserActive() - Method in class starfish.chemistry.Noe

isValid() - Method in class starfish.chemistry.PPMv

iterator() - Method in class starfish.chemistry.AngleConstraintSet

iterator() - Method in interface starfish.chemistry.ConstraintSet

iterator() - Method in class starfish.chemistry.NoeSet

iupacToCurrent(String, String) - Static method in class starfish.chemistry.AtomParser

K

K - Static variable in class starfish.chemistry.AtomProperty

Kr - Static variable in class starfish.chemistry.AtomProperty

L

La - Static variable in class starfish.chemistry.AtomProperty

LABEL - Static variable in class starfish.chemistry.Atom

label - Variable in class starfish.chemistry.Atom

label - Variable in class starfish.chemistry.Entity

label - Variable in class starfish.chemistry.Molecule

LABEL_BOND - Static variable in class starfish.chemistry.Molecule

LABEL_CHARGE - Static variable in class starfish.chemistry.Molecule

LABEL_CUSTOM - Static variable in class starfish.chemistry.Molecule

LABEL_FC - Static variable in class starfish.chemistry.Molecule

LABEL_FFC - Static variable in class starfish.chemistry.Molecule

LABEL_HPPM - Static variable in class starfish.chemistry.Molecule

LABEL_LABEL - Static variable in class starfish.chemistry.Molecule

LABEL_MOLECULE_NAME - Static variable in class starfish.chemistry.Molecule

LABEL_NAME - Static variable in class starfish.chemistry.Molecule

LABEL_NONE - Static variable in class starfish.chemistry.Molecule

LABEL_NUMBER - Static variable in class starfish.chemistry.Molecule

LABEL_PPM - Static variable in class starfish.chemistry.Molecule

LABEL_RESIDUE - Static variable in class starfish.chemistry.Molecule

LABEL_SECONDARY_STRUCTURE - Static variable in class starfish.chemistry.Molecule

LABEL_STRING - Static variable in class starfish.chemistry.Molecule

LABEL_SYMBOL - Static variable in class starfish.chemistry.Molecule

LABEL_SYMBOL_AND_NUMBER - Static variable in class starfish.chemistry.Molecule

LABEL_TITLE - Static variable in class starfish.chemistry.Molecule

LABEL_VALUE - Static variable in class starfish.chemistry.Molecule

labelCoords - Variable in class starfish.chemistry.MoleculePrimitives

labelNum - Variable in class starfish.chemistry.Compound

labels - Variable in class starfish.chemistry.MoleculePrimitives

labelsCurrent - Variable in class starfish.chemistry.Molecule

labelStatus - Variable in class starfish.chemistry.SpatialSet

labelTypes - Static variable in class starfish.chemistry.Molecule

lastAngle - Variable in class starfish.chemistry.Tube

lastAtom - Variable in class starfish.chemistry.Entity

lastBond - Variable in class starfish.chemistry.Entity

lastPeakWritten - Static variable in class starfish.chemistry.NoeSet

lastRes - Variable in class starfish.chemistry.MolFilter

lastResidue - Variable in class starfish.chemistry.Polymer

lastResType - Variable in class starfish.chemistry.MolFilter

Li - Static variable in class starfish.chemistry.AtomProperty

limitToAssigned(Interp) - Static method in class starfish.chemistry.Noe

limitToMaxAmbig(int) - Static method in class starfish.chemistry.Noe

limitToMaxViol(double) - Static method in class starfish.chemistry.Noe

limitToMinContrib(double) - Static method in class starfish.chemistry.Noe

limitToMinPPMError(double) - Static method in class starfish.chemistry.Noe

lineColors - Variable in class starfish.chemistry.MoleculePrimitives

lineCoords - Variable in class starfish.chemistry.MoleculePrimitives

lineReader - Variable in class starfish.chemistry.io.FFDReader

listAtoms(Interp) - Static method in class starfish.chemistry.Molecule

listAtomsWithProperty(Interp, int) - Method in class starfish.chemistry.Molecule

listBonds(Interp) - Method in class starfish.chemistry.Molecule

listStartPoints() - Method in class starfish.chemistry.search.BroadSearch

loc - Variable in class starfish.chemistry.AtomParser

lower - Variable in class starfish.chemistry.AngleConstraint

lower - Variable in class starfish.chemistry.DistanceConstraint

lower - Variable in class starfish.chemistry.Noe

Lr - Static variable in class starfish.chemistry.AtomProperty

Lu - Static variable in class starfish.chemistry.AtomProperty

M

magneticEquivalenceGroupCode - Variable in class starfish.chemistry.Entity

makeAtomList(Interp) - Static method in class starfish.chemistry.Molecule

makeSite(Interp, String) - Static method in class starfish.chemistry.Molecule

mass - Variable in class starfish.chemistry.Atom

matchAtoms(Interp, MolFilter) - Static method in class starfish.chemistry.Molecule

matchAtoms(MolFilter) - Static method in class starfish.chemistry.Molecule

matchAtoms(MolFilter, Molecule) - Static method in class starfish.chemistry.Molecule

matchBonds(Interp) - Static method in class starfish.chemistry.Molecule

matchCoordSetAndEntity(String, String) - Method in class starfish.chemistry.MolFilter

MatchCriteria - Class in starfish.chemistry

matchName(String, String[]) - Method in class starfish.chemistry.IdPeakCmd

MBTree - Class in starfish.chemistry.search

MBTree() - Constructor for class starfish.chemistry.search.MBTree

Md - Static variable in class starfish.chemistry.AtomProperty

memberID - Static variable in class starfish.chemistry.NoeSet

Mg - Static variable in class starfish.chemistry.AtomProperty

MMcifCmd - Class in starfish.chemistry.io

MMcifCmd() - Constructor for class starfish.chemistry.io.MMcifCmd

MMcifReader - Class in starfish.chemistry.io

Mn - Static variable in class starfish.chemistry.AtomProperty

MNode - Class in starfish.chemistry.search

MNode() - Constructor for class starfish.chemistry.search.MNode

MNode(int) - Constructor for class starfish.chemistry.search.MNode

Mo - Static variable in class starfish.chemistry.AtomProperty

model - Variable in class starfish.chemistry.Molecule

modelMethod(String, Object[]) - Method in class starfish.chemistry.AngleConstraintTable

modelMethod(String, Object[]) - Method in class starfish.chemistry.MoleculeTableModel

modelMethod(String, Object[]) - Method in class starfish.chemistry.NOEConstraintTable

molecule - Variable in class starfish.chemistry.Entity

Molecule - Class in starfish.chemistry

Molecule(String) - Constructor for class starfish.chemistry.Molecule

Molecule.SpatialSetIterator - Class in starfish.chemistry

Molecule.SpatialSetIterator(Molecule) - Constructor for class starfish.chemistry.Molecule.SpatialSetIterator

MoleculeCmd - Class in starfish.chemistry

MoleculeCmd() - Constructor for class starfish.chemistry.MoleculeCmd

MoleculePrimitives - Class in starfish.chemistry

MoleculePrimitives() - Constructor for class starfish.chemistry.MoleculePrimitives

Creates a new instance of MoleculePrimitives

molecules - Static variable in class starfish.chemistry.Molecule

MoleculeTableModel - Class in starfish.chemistry

MoleculeTableModel() - Constructor for class starfish.chemistry.MoleculeTableModel

MolFilter - Class in starfish.chemistry

MolFilter(String) - Constructor for class starfish.chemistry.MolFilter

MolSearchExtension - Class in starfish.chemistry.search

MolSearchExtension() - Constructor for class starfish.chemistry.search.MolSearchExtension

MTree - Class in starfish.chemistry.search

MTree() - Constructor for class starfish.chemistry.search.MTree

N

N - Static variable in class starfish.chemistry.AtomProperty

Na - Static variable in class starfish.chemistry.AtomProperty

name - Variable in class starfish.chemistry.AngleConstraint

name - Variable in class starfish.chemistry.Atom

name - Variable in class starfish.chemistry.Entity

name - Variable in class starfish.chemistry.Molecule

Nb - Static variable in class starfish.chemistry.AtomProperty

nChords - Variable in class starfish.chemistry.Tube

Nd - Static variable in class starfish.chemistry.AtomProperty

Ne - Static variable in class starfish.chemistry.AtomProperty

negShapeType - Variable in class starfish.chemistry.Molecule

netWorkValue - Variable in class starfish.chemistry.Noe

next - Variable in class starfish.chemistry.Atom

next - Variable in class starfish.chemistry.Bond

next - Variable in class starfish.chemistry.DistanceConstraint

next() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

next - Variable in class starfish.chemistry.Residue

nextAtom() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

nextCompound() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

nextCoordSet() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

nextEntity() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

Ni - Static variable in class starfish.chemistry.AtomProperty

nLabels - Variable in class starfish.chemistry.MoleculePrimitives

nLines - Variable in class starfish.chemistry.MoleculePrimitives

No - Static variable in class starfish.chemistry.AtomProperty

nodes - Variable in class starfish.chemistry.Tube

Noe - Class in starfish.chemistry

Noe(Peak, SpatialSet, SpatialSet, double) - Constructor for class starfish.chemistry.Noe

Noe(Peak, SpatialSetGroup, SpatialSetGroup, double) - Constructor for class starfish.chemistry.Noe

NoeCalibration - Class in starfish.chemistry

NoeCmd - Class in starfish.chemistry

NoeCmd() - Constructor for class starfish.chemistry.NoeCmd

NOEColumns - Enum in starfish.chemistry

NOEConstraintTable - Class in starfish.chemistry

NOEConstraintTable() - Constructor for class starfish.chemistry.NOEConstraintTable

NoeSet - Class in starfish.chemistry

NoeSet(String) - Constructor for class starfish.chemistry.NoeSet

nonHydrogens - Variable in class starfish.chemistry.Atom

Np - Static variable in class starfish.chemistry.AtomProperty

nPiBonds - Variable in class starfish.chemistry.Atom

nPossible - Variable in class starfish.chemistry.Noe

nResidues - Variable in class starfish.chemistry.Molecule

nSelected - Variable in class starfish.chemistry.MoleculePrimitives

nSpheres - Variable in class starfish.chemistry.MoleculePrimitives

NULL_PPM - Static variable in class starfish.chemistry.Atom

nullCoords(Interp) - Method in class starfish.chemistry.Molecule

number - Variable in class starfish.chemistry.Compound

Nv_ReadPSF(Interp, String) - Method in class starfish.chemistry.io.PDB

O

O - Static variable in class starfish.chemistry.AtomProperty

occupancy - Variable in class starfish.chemistry.AtomParser

occupancy - Variable in class starfish.chemistry.SpatialSet

ok() - Method in class starfish.chemistry.PPMScore

order - Variable in class starfish.chemistry.Bond

OrderSVD - Class in starfish.chemistry

OrderSVD(ArrayList<Vector3D>, ArrayList<Double>, ArrayList<Double>, ArrayList<Double>) - Constructor for class starfish.chemistry.OrderSVD

originalName - Variable in class starfish.chemistry.Molecule

Os - Static variable in class starfish.chemistry.AtomProperty

P

P - Static variable in class starfish.chemistry.AtomProperty

Pa - Static variable in class starfish.chemistry.AtomProperty

parent - Variable in class starfish.chemistry.Atom

Pb - Static variable in class starfish.chemistry.AtomProperty

Pd - Static variable in class starfish.chemistry.AtomProperty

PDB - Class in starfish.chemistry.io

PDB() - Constructor for class starfish.chemistry.io.PDB

PDBCmd - Class in starfish.chemistry.io

PDBCmd() - Constructor for class starfish.chemistry.io.PDBCmd

pdbResToPRFName(String, char) - Static method in class starfish.chemistry.AtomParser

peak - Variable in class starfish.chemistry.DistanceConstraint

peak - Variable in class starfish.chemistry.Noe

physicalState - Variable in class starfish.chemistry.Entity

Pm - Static variable in class starfish.chemistry.AtomProperty

Po - Static variable in class starfish.chemistry.AtomProperty

Point3 - Class in starfish.chemistry

Point3(double, double, double) - Constructor for class starfish.chemistry.Point3

pointCount() - Method in class starfish.chemistry.SpatialSet

points - Variable in class starfish.chemistry.SpatialSet

Polymer - Class in starfish.chemistry

Polymer(String) - Constructor for class starfish.chemistry.Polymer

Polymer(String, String) - Constructor for class starfish.chemistry.Polymer

polymer - Variable in class starfish.chemistry.Residue

posShapeType - Variable in class starfish.chemistry.Molecule

ppmError - Variable in class starfish.chemistry.Noe

ppms - Variable in class starfish.chemistry.SpatialSet

PPMScore - Class in starfish.chemistry

PPMScore(String[]) - Constructor for class starfish.chemistry.PPMScore

PPMScore(AtomShiftData[]) - Constructor for class starfish.chemistry.PPMScore

ppmToString(Interp, int, int) - Method in class starfish.chemistry.Atom

ppmToString(Interp, String, int, int) - Method in class starfish.chemistry.Atom

ppmToString(Interp, SpatialSet, int, int) - Method in class starfish.chemistry.Atom

ppmToXMLString(Interp, int, int) - Method in class starfish.chemistry.Atom

ppmToXMLString(Interp, String, int, int) - Method in class starfish.chemistry.Atom

ppmToXMLString(Interp, SpatialSet, int, int) - Method in class starfish.chemistry.Atom

PPMv - Class in starfish.chemistry

PPMv(double) - Constructor for class starfish.chemistry.PPMv

Pr - Static variable in class starfish.chemistry.AtomProperty

previous - Variable in class starfish.chemistry.Atom

previous - Variable in class starfish.chemistry.Bond

previous - Variable in class starfish.chemistry.DistanceConstraint

previous - Variable in class starfish.chemistry.Residue

processEnd() - Method in class starfish.chemistry.io.ARIARestraintReader

processLoop(STAR3, List) - Static method in class starfish.chemistry.Entity

processStart() - Method in class starfish.chemistry.io.ARIARestraintReader

properties - Variable in class starfish.chemistry.SpatialSet

Pt - Static variable in class starfish.chemistry.AtomProperty

Pu - Static variable in class starfish.chemistry.AtomProperty

R

R_FACTOR - Static variable in class starfish.chemistry.Molecule

Ra - Static variable in class starfish.chemistry.AtomProperty

radius - Variable in class starfish.chemistry.Atom

radius - Variable in class starfish.chemistry.Bond

radiusAtoms(Interp, float) - Static method in class starfish.chemistry.Molecule

radiusBonds(Interp, float) - Static method in class starfish.chemistry.Molecule

Rb - Static variable in class starfish.chemistry.AtomProperty

Re - Static variable in class starfish.chemistry.AtomProperty

read() - Method in class starfish.chemistry.io.ARIARestraintReader

read(Interp, String, String) - Method in class starfish.chemistry.io.FFDReader

read(Interp, String, String, boolean) - Method in class starfish.chemistry.io.FFDReader

readBTree(String) - Static method in class starfish.chemistry.search.MBTree

readMMcifAtomSite(Interp, int[], int) - Method in class starfish.chemistry.io.MMcifReader

readMMcifCompAtoms(Interp, int[], Compound, String, int) - Method in class starfish.chemistry.io.MMcifReader

readMMcifCompBonds(Interp, int[], Compound) - Method in class starfish.chemistry.io.MMcifReader

readMolecule(Interp, String, String) - Method in class starfish.chemistry.io.FFDReader

readPDB(Interp, String, boolean) - Method in class starfish.chemistry.io.PDB

readPDBSeq(Interp, String) - Method in class starfish.chemistry.io.PDB

readPDBXYZ(Interp, String, int) - Method in class starfish.chemistry.io.PDB

readSD(Interp, String, String) - Method in class starfish.chemistry.io.PDB

readSDResidue(Interp, String, String, Molecule, String) - Method in class starfish.chemistry.io.PDB

readSeq(Interp, String, TclObject, boolean) - Method in class starfish.chemistry.io.PDB

red - Variable in class starfish.chemistry.Bond

red - Variable in class starfish.chemistry.SpatialSet

refPPMV - Variable in class starfish.chemistry.SpatialSet

remove() - Method in class starfish.chemistry.Atom

remove(Interp) - Method in class starfish.chemistry.Molecule

remove() - Method in class starfish.chemistry.Molecule.SpatialSetIterator

removeAll(Interp) - Static method in class starfish.chemistry.Molecule

removeBonds() - Method in class starfish.chemistry.Atom

removeBondTo(Atom) - Method in class starfish.chemistry.Atom

removeResidue(Residue) - Method in class starfish.chemistry.Polymer

reName(Molecule, Compound, String, String) - Method in class starfish.chemistry.Molecule

renameAtom(String, String) - Method in class starfish.chemistry.Compound

renumberResidue(String, String) - Method in class starfish.chemistry.Polymer

reset() - Static method in class starfish.chemistry.AngleConstraintSet

reset() - Static method in class starfish.chemistry.NoeSet

resetActiveStructures() - Method in class starfish.chemistry.Molecule

resetConstraints() - Static method in class starfish.chemistry.AngleConstraint

resetConstraints() - Static method in class starfish.chemistry.Noe

resetLastAtom() - Static method in class starfish.chemistry.Atom

resetWriting() - Method in class starfish.chemistry.AngleConstraintSet

resetWriting() - Method in interface starfish.chemistry.ConstraintSet

resetWriting() - Method in class starfish.chemistry.NoeSet

Residue - Class in starfish.chemistry

Residue(String, String) - Constructor for class starfish.chemistry.Residue

ResidueCmd - Class in starfish.chemistry

ResidueCmd() - Constructor for class starfish.chemistry.ResidueCmd

residueMap - Static variable in class starfish.chemistry.BioPPMScoreCmd

residues - Variable in class starfish.chemistry.Polymer

residueVector - Variable in class starfish.chemistry.Polymer

resMap - Variable in class starfish.chemistry.Noe

resName - Variable in class starfish.chemistry.AtomParser

resNum - Variable in class starfish.chemistry.AtomParser

Rh - Static variable in class starfish.chemistry.AtomProperty

rmsAtom() - Method in class starfish.chemistry.Atom

rmsAtom(String) - Method in class starfish.chemistry.Atom

rmsAtom(SpatialSet) - Method in class starfish.chemistry.Atom

Rn - Static variable in class starfish.chemistry.AtomProperty

role - Variable in class starfish.chemistry.Entity

rotGroup - Variable in class starfish.chemistry.Atom

rotUnit - Variable in class starfish.chemistry.Atom

Ru - Static variable in class starfish.chemistry.AtomProperty

S

S - Static variable in class starfish.chemistry.AtomProperty

Sb - Static variable in class starfish.chemistry.AtomProperty

Sc - Static variable in class starfish.chemistry.AtomProperty

scale - Variable in class starfish.chemistry.DistanceConstraint

scale - Variable in class starfish.chemistry.Noe

scan(MatchCriteria[]) - Method in class starfish.chemistry.IdPeakCmd

scan3(MatchCriteria[]) - Method in class starfish.chemistry.IdPeakCmd

score(int, int[]) - Method in class starfish.chemistry.search.BroadSearch

scoreAtomPPM(double, Residue, AtomShiftData[]) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(double, String, String[], double[]) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(double, String, double) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(double, String[], double[]) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(double, String[], double[], boolean) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(String, String, double) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreAtomPPM(Residue, String, double) - Static method in class starfish.chemistry.BioPPMScoreCmd

scoreFragment(Interp, TclObject[]) - Static method in class starfish.chemistry.BioPPMScoreCmd

scores - Variable in class starfish.chemistry.search.BroadSearch

Se - Static variable in class starfish.chemistry.AtomProperty

segment - Variable in class starfish.chemistry.AtomParser

selCycleCount - Static variable in class starfish.chemistry.Molecule

SELECT - Static variable in class starfish.chemistry.Atom

SELECT - Static variable in class starfish.chemistry.Bond

selectAtoms(Interp, MolFilter, boolean, boolean) - Static method in class starfish.chemistry.Molecule

selectBonds(Interp, String) - Static method in class starfish.chemistry.Molecule

selected - Variable in class starfish.chemistry.SpatialSet

selectionCoords - Variable in class starfish.chemistry.MoleculePrimitives

selectionLevels - Variable in class starfish.chemistry.MoleculePrimitives

selectResidues(Interp) - Static method in class starfish.chemistry.Molecule

selectSite(Interp, String) - Static method in class starfish.chemistry.Molecule

set(int, int, byte[]) - Method in class starfish.chemistry.search.BroadSearch

setActive(AngleConstraintSet) - Static method in class starfish.chemistry.AngleConstraint

setActive(int) - Method in class starfish.chemistry.AngleConstraint

setActive(NoeSet) - Static method in class starfish.chemistry.Noe

setActive(int) - Method in class starfish.chemistry.Noe

setActiveStructures(TreeSet) - Method in class starfish.chemistry.Molecule

setAmbigCode(short) - Method in class starfish.chemistry.PPMv

setAtomicNumber(int) - Method in class starfish.chemistry.Atom

setAtomicNumber(String) - Method in class starfish.chemistry.Atom

setAtomProperty(int, boolean) - Static method in class starfish.chemistry.Molecule

setBFactor(float) - Method in class starfish.chemistry.Atom

setBFactor(String, float) - Method in class starfish.chemistry.Atom

setBFactor(float) - Method in class starfish.chemistry.SpatialSet

setBlue(float) - Method in class starfish.chemistry.Atom

setBondProperty(int, boolean) - Method in class starfish.chemistry.Molecule

setCalibratable(boolean) - Static method in class starfish.chemistry.Noe

setColor(float, float, float) - Method in class starfish.chemistry.Atom

setColor(float, float, float) - Method in class starfish.chemistry.SpatialSet

setColor(int, float, float, float) - Method in class starfish.chemistry.Tube

setColorByType() - Method in class starfish.chemistry.Atom

setDefaultSpatialSet(String) - Method in class starfish.chemistry.Atom

setDictionary(int, byte[]) - Method in class starfish.chemistry.search.BroadSearch

setDirty() - Method in class starfish.chemistry.AngleConstraintSet

setDirty() - Method in interface starfish.chemistry.ConstraintSet

setDirty() - Static method in class starfish.chemistry.Noe

setDirty() - Method in class starfish.chemistry.NoeSet

setDisplayStatus(int) - Method in class starfish.chemistry.Atom

setDisplayStatus(int) - Method in class starfish.chemistry.SpatialSet

setFilter(String) - Method in class starfish.chemistry.MoleculeTableModel

setFilter(String) - Method in class starfish.chemistry.NOEConstraintTable

setFormalCharge(float) - Method in class starfish.chemistry.Atom

setGenType(Constraint.GenTypes) - Method in class starfish.chemistry.Noe

setGreen(float) - Method in class starfish.chemistry.Atom

setHasEquivalentAtoms(boolean) - Method in class starfish.chemistry.Entity

setIDNum(int) - Method in class starfish.chemistry.Entity

setLabelStatus(int) - Method in class starfish.chemistry.Atom

setLabelStatus(int) - Method in class starfish.chemistry.SpatialSet

setName(String) - Method in class starfish.chemistry.Atom

setNChords(int) - Method in class starfish.chemistry.Tube

setNomenclature(String) - Method in class starfish.chemistry.Polymer

setNSides(int) - Method in class starfish.chemistry.Tube

setOccupancy(float) - Method in class starfish.chemistry.Atom

setOccupancy(String, float) - Method in class starfish.chemistry.Atom

setOccupancy(float) - Method in class starfish.chemistry.SpatialSet

setOK(boolean) - Method in class starfish.chemistry.PPMScore

setPointValidity(int, boolean) - Method in class starfish.chemistry.Atom

setPointValidity(String, int, boolean) - Method in class starfish.chemistry.Atom

setPointValidity(int, boolean) - Method in class starfish.chemistry.SpatialSet

setPolymerType(String) - Method in class starfish.chemistry.Polymer

setPPM(double) - Method in class starfish.chemistry.MatchCriteria

setPPMValidity(int, boolean) - Method in class starfish.chemistry.Atom

setPPMValidity(String, int, boolean) - Method in class starfish.chemistry.Atom

setPPMValidity(int, boolean) - Method in class starfish.chemistry.SpatialSet

setProperty(String, String) - Method in class starfish.chemistry.AngleConstraintTable

setProperty(int) - Method in class starfish.chemistry.Atom

setProperty(String, int) - Method in class starfish.chemistry.Atom

setProperty(int) - Method in class starfish.chemistry.Bond

setProperty(String, String) - Method in class starfish.chemistry.MoleculeTableModel

setProperty(String, String) - Method in class starfish.chemistry.NOEConstraintTable

setProperty(int) - Method in class starfish.chemistry.SpatialSet

setRadius(int, double, double, double) - Method in class starfish.chemistry.Tube

setRed(float) - Method in class starfish.chemistry.Atom

setRefPPMValidity(boolean) - Method in class starfish.chemistry.SpatialSet

setResonanceSet(ResonanceSet) - Method in class starfish.chemistry.Atom

setScale(PeakList, NoeCalibration) - Static method in class starfish.chemistry.Noe

setScale(PeakList, NoeCalibration) - Method in class starfish.chemistry.NoeSet

setScore(int, double) - Method in class starfish.chemistry.PPMScore

setSelected(int) - Method in class starfish.chemistry.Atom

setSelected(Interp, Vector, boolean, boolean) - Static method in class starfish.chemistry.Molecule

setSelected(int) - Method in class starfish.chemistry.SpatialSet

setStereo(int) - Method in class starfish.chemistry.Atom

setStrandID(String) - Method in class starfish.chemistry.Polymer

setType(String) - Method in class starfish.chemistry.Atom

setup(Interp, Molecule, TclObject[]) - Method in class starfish.chemistry.IdPeakCmd

setupRotGroups() - Method in class starfish.chemistry.Molecule

setValid(boolean, Atom) - Method in class starfish.chemistry.PPMv

setValue(int) - Method in class starfish.chemistry.search.MNode

setValueAt(Object, int, int) - Method in class starfish.chemistry.AngleConstraintTable

setValueAt(Object, int, int) - Method in class starfish.chemistry.MoleculeTableModel

setValueAt(Object, int, int) - Method in class starfish.chemistry.NOEConstraintTable

shapeTypes - Static variable in class starfish.chemistry.Molecule

Si - Static variable in class starfish.chemistry.AtomProperty

sites - Static variable in class starfish.chemistry.Molecule

Sm - Static variable in class starfish.chemistry.AtomProperty

Sn - Static variable in class starfish.chemistry.AtomProperty

sortNodes() - Method in class starfish.chemistry.search.MNode

sortNodes() - Method in class starfish.chemistry.search.MTree

source - Variable in class starfish.chemistry.Molecule

SpatialSet - Class in starfish.chemistry

SpatialSet(String, Atom) - Constructor for class starfish.chemistry.SpatialSet

SpatialSet(float, float, float) - Constructor for class starfish.chemistry.SpatialSet

SpatialSet(double) - Constructor for class starfish.chemistry.SpatialSet

SpatialSetGroup - Class in starfish.chemistry

SpatialSetGroup(String) - Constructor for class starfish.chemistry.SpatialSetGroup

SpatialSetGroup(SpatialSet) - Constructor for class starfish.chemistry.SpatialSetGroup

SpatialSetGroup(Atom[]) - Constructor for class starfish.chemistry.SpatialSetGroup

spg1 - Variable in class starfish.chemistry.Noe

spg2 - Variable in class starfish.chemistry.Noe

sphereColors - Variable in class starfish.chemistry.MoleculePrimitives

sphereCoords - Variable in class starfish.chemistry.MoleculePrimitives

sphereValues - Variable in class starfish.chemistry.MoleculePrimitives

spSets - Variable in class starfish.chemistry.AngleConstraint

SQ_SCORE - Static variable in class starfish.chemistry.Molecule

Sr - Static variable in class starfish.chemistry.AtomProperty

starfish.chemistry - package starfish.chemistry

starfish.chemistry.io - package starfish.chemistry.io

starfish.chemistry.search - package starfish.chemistry.search

stereo - Variable in class starfish.chemistry.Bond

STEREO_BOND_DOWN - Static variable in class starfish.chemistry.Bond

STEREO_BOND_EITHER - Static variable in class starfish.chemistry.Bond

STEREO_BOND_UP - Static variable in class starfish.chemistry.Bond

stereoStr - Variable in class starfish.chemistry.Atom

structureNum - Variable in class starfish.chemistry.MolFilter

structures - Variable in class starfish.chemistry.Molecule

StructureWriteCmd - Class in starfish.chemistry.io

StructureWriteCmd() - Constructor for class starfish.chemistry.io.StructureWriteCmd

SUPER - Static variable in class starfish.chemistry.Atom

SuperMol - Class in starfish.chemistry

SuperMol(String) - Constructor for class starfish.chemistry.SuperMol

symmetrical - Variable in class starfish.chemistry.Noe

T

Ta - Static variable in class starfish.chemistry.AtomProperty

Tb - Static variable in class starfish.chemistry.AtomProperty

Tc - Static variable in class starfish.chemistry.AtomProperty

Te - Static variable in class starfish.chemistry.AtomProperty

Th - Static variable in class starfish.chemistry.AtomProperty

Ti - Static variable in class starfish.chemistry.AtomProperty

title - Variable in class starfish.chemistry.Molecule

titlePosition - Variable in class starfish.chemistry.Molecule

Tl - Static variable in class starfish.chemistry.AtomProperty

Tm - Static variable in class starfish.chemistry.AtomProperty

toSTARString() - Method in class starfish.chemistry.AngleConstraint

toSTARString() - Method in interface starfish.chemistry.Constraint

toSTARString() - Method in class starfish.chemistry.Noe

toString() - Method in class starfish.chemistry.AtomProperty

toString() - Method in class starfish.chemistry.Point3

triangles - Variable in class starfish.chemistry.Tube

Tube - Class in starfish.chemistry

Tube() - Constructor for class starfish.chemistry.Tube

type - Variable in class starfish.chemistry.Atom

U

U - Static variable in class starfish.chemistry.AtomProperty

uncompressCodes(byte[], int) - Method in class starfish.chemistry.search.BroadSearch

unCompXYZToArray(byte[], int) - Method in class starfish.chemistry.MoleculePrimitives

unSelectLastAtom(Interp) - Static method in class starfish.chemistry.Molecule

unsetProperty(int) - Method in class starfish.chemistry.Atom

unsetProperty(String, int) - Method in class starfish.chemistry.Atom

unsetProperty(int) - Method in class starfish.chemistry.Bond

unsetProperty(int) - Method in class starfish.chemistry.SpatialSet

update() - Method in class starfish.chemistry.AngleConstraintTable

update() - Method in class starfish.chemistry.NOEConstraintTable

updateAngleData() - Method in class starfish.chemistry.AngleConstraintSet

updateContributions(boolean) - Static method in class starfish.chemistry.Noe

updateDistanceContribs() - Static method in class starfish.chemistry.Noe

updateDistances() - Static method in class starfish.chemistry.Noe

updateDistancesIndividual() - Static method in class starfish.chemistry.Noe

updateFromSTAR3ChemComp(Interp, Saveframe) - Method in class starfish.chemistry.Compound

updateGenType(Interp, Map<String, NoeCmd.NoeMatch>, MatchCriteria[]) - Method in class starfish.chemistry.Noe

updateGenTypes(Interp) - Static method in class starfish.chemistry.Noe

updateLabels() - Method in class starfish.chemistry.Molecule

updateNames() - Method in class starfish.chemistry.Compound

updateNames() - Method in class starfish.chemistry.Molecule

updateNPossible(PeakList) - Static method in class starfish.chemistry.Noe

updatePPMError(Interp, MatchCriteria[]) - Method in class starfish.chemistry.Noe

updatePPMErrors(Interp) - Static method in class starfish.chemistry.Noe

updateSpatialSets() - Method in class starfish.chemistry.Molecule

upper - Variable in class starfish.chemistry.AngleConstraint

upper - Variable in class starfish.chemistry.DistanceConstraint

upper - Variable in class starfish.chemistry.Noe

V

V - Static variable in class starfish.chemistry.AtomProperty

valanceAngle - Variable in class starfish.chemistry.Atom

value - Variable in class starfish.chemistry.Atom

value - Variable in class starfish.chemistry.PPMv

valueOf(String) - Static method in enum starfish.chemistry.AngleConstraintColumns

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum starfish.chemistry.Constraint.GenTypes

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum starfish.chemistry.DistanceRange.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum starfish.chemistry.NOEColumns

Returns the enum constant of this type with the specified name.

values() - Static method in enum starfish.chemistry.AngleConstraintColumns

Returns an array containing the constants of this enum type, in the order they are declared.

VALUES - Static variable in class starfish.chemistry.AtomProperty

values() - Static method in enum starfish.chemistry.Constraint.GenTypes

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum starfish.chemistry.DistanceRange.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class starfish.chemistry.Molecule

values() - Static method in enum starfish.chemistry.NOEColumns

Returns an array containing the constants of this enum type, in the order they are declared.

view - Variable in class starfish.chemistry.Molecule

violCharArray - Static variable in class starfish.chemistry.AngleConstraintSet

volume(Vector3D, Vector3D, Vector3D, Vector3D) - Static method in class starfish.chemistry.Atom

volume - Variable in class starfish.chemistry.DistanceConstraint

volume - Variable in class starfish.chemistry.Noe

W

W - Static variable in class starfish.chemistry.AtomProperty

Water - Class in starfish.chemistry

Water(String) - Constructor for class starfish.chemistry.Water

withinSite(Interp, String, float) - Static method in class starfish.chemistry.Molecule

worst() - Method in class starfish.chemistry.PPMScore

writeAssignmentsSTAR3(Interp, String) - Method in class starfish.chemistry.Molecule

writeCompoundToSTAR3(Interp, String, int) - Method in class starfish.chemistry.Compound

writeConstraintsSTAR3(Interp, String, ConstraintSet, int) - Static method in class starfish.chemistry.io.ConstraintSTARWriter

writeEntityCommonNamesSTAR3(Interp, String, int) - Method in class starfish.chemistry.Entity

writeEntityHeaderSTAR3(Interp, String, int) - Method in class starfish.chemistry.Compound

writeEntityHeaderSTAR3(Interp, String, int) - Method in class starfish.chemistry.Entity

writeEntitySeqSTAR3(Interp, String, int) - Method in class starfish.chemistry.Polymer

writeFFD(Interp, String, int) - Method in class starfish.chemistry.io.FFDWriter

writeMoleculeSTAR3(Interp, String, int) - Method in class starfish.chemistry.Molecule

writePPM(Interp, String, int) - Static method in class starfish.chemistry.Molecule

writePPMToXML(Interp, String, int) - Static method in class starfish.chemistry.Molecule

writeToken(String) - Method in class starfish.chemistry.io.MMcifReader

writeToSTAR3(Interp, String, Molecule, int) - Static method in class starfish.chemistry.io.CoordinateSTARWriter

writeXYZ(Interp, String, int) - Static method in class starfish.chemistry.Molecule

writeXYZToXML(Interp, String, int) - Static method in class starfish.chemistry.Molecule

X

x - Variable in class starfish.chemistry.AtomParser

X - Static variable in class starfish.chemistry.AtomProperty

x - Variable in class starfish.chemistry.Point3

Xe - Static variable in class starfish.chemistry.AtomProperty

xyzToFFDString(Interp, SpatialSet, int, int, String) - Method in class starfish.chemistry.Atom

xyzToString(Interp, int, int) - Method in class starfish.chemistry.Atom

xyzToString(Interp, String, int, int) - Method in class starfish.chemistry.Atom

xyzToString(Interp, SpatialSet, int, int) - Method in class starfish.chemistry.Atom

xyzToXMLString(Interp, int, int) - Method in class starfish.chemistry.Atom

xyzToXMLString(Interp, String, int, int) - Method in class starfish.chemistry.Atom

xyzToXMLString(Interp, SpatialSet, int, int) - Method in class starfish.chemistry.Atom

Y

y - Variable in class starfish.chemistry.AtomParser

Y - Static variable in class starfish.chemistry.AtomProperty

y - Variable in class starfish.chemistry.Point3

Yb - Static variable in class starfish.chemistry.AtomProperty

Z

z - Variable in class starfish.chemistry.AtomParser

z - Variable in class starfish.chemistry.Point3

Zn - Static variable in class starfish.chemistry.AtomProperty

Zr - Static variable in class starfish.chemistry.AtomProperty

A B C D E F G H I K L M N O P R S T U V W X Y Z