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

S

S - Static variable in class showHybrid.OrbitalSet
 
scale(double) - Method in class edu.davidson.chm.equilibria.Gas
 
scale(double) - Method in class edu.davidson.chm.equilibria.Phase
Scales the amount of the phase.
scale(double) - Method in class edu.davidson.chm.equilibria.Solution
 
SegmentGroup - Class in showStructure
 
SegmentGroup() - Constructor for class showStructure.SegmentGroup
 
SegmentGroup(int, float, float, float, float, float, float, float) - Constructor for class showStructure.SegmentGroup
Constructs a set of sphere segments.
SegmentGroup(float, float, float, float, float, float, float, float) - Constructor for class showStructure.SegmentGroup
Constructs a set of sphere segments for atoms in center unit cell layer of an hcp structure
SegmentGroup(int, float, float, float, float, float, float, float, float) - Constructor for class showStructure.SegmentGroup
Constructs a set of sphere segments for atoms in center unit cell layer ns = 0 hexagonal unit cell ns = 1 a tetragonal unit cell
segmentRA - Variable in class showStructure.SegmentGroup
 
segmentTG - Variable in class showStructure.SegmentGroup
 
setAllIsosurfacesVisible(int, boolean) - Method in class showIsosurface.Atom
Determines whether all isosurfaces in the specified orbital are visible
setAllVisible(boolean) - Method in class showIsosurface.Orbital
Sets the visibility state for all of the isosurfaces
setAllVisible(boolean) - Method in class showStructure.AtomGroup
Sets the visibility of all atoms
setAllVisible(boolean) - Method in class showStructure.SegmentGroup
Sets the visibility of all segments
setAnalConc(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the analytical concentration (mole/L) of the ChemSpecies
setAnalConc(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the analytical concentration (moles/L).
setAnalMass(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the analytical mass (in grams) of the ChemSpecies in the Phase.
setAnalMass(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the analytical mass of the species
setAnalMoles(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the analytical moles of the ChemSpecies in the Phase.
setAnalMoles(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the analytical number of moles.
setAnalPressure(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the analytical partial pressure of the ChemSpecies in the Phase.
setAnalPressure(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the analytical partial pressure in atmospheres.
setAtomGroupRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for the entire set of AtomGroups
setAtomGroupRotation(int, float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for a specific AtomGroup
setAtomGroupTranslation(float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for the entire set of AtomGroups
setAtomGroupTranslation(int, float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for a specific AtomGroup
setAtomGroupVisible(int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of all atoms in a group
setAtomPosition(int, double, double, double) - Method in class showIsosurface.ShowIsosurface
Sets the position of the specified atom.
setAtomScale(int, double) - Method in class showIsosurface.ShowIsosurface
Scales the geometry objects for the specified atom
setAtomView(double, double, double, double, double, double, double) - Method in class showHybrid.ShowHybrid
Sets the rotation for a specific atom to view down the x axis.
setAtomView(int, double, double, double, double, double, double, double) - Method in class showIsosurface.ShowIsosurface
Sets the rotation for a specific atom to view down the x axis.
setAtomVisible(int, int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of the indicated atom
setAutoChargeBalance(String, boolean) - Method in class chemEquilibria.ChemEquilibria
Sets the autoChargeBalance property for the indicated phase.
setAutoChargeBalance(boolean) - Method in class edu.davidson.chm.equilibria.Phase
Sets the autoChargeBalance property.
setAutoMaxR(boolean) - Method in class electronDensity.ElectronDensity
Determines whether the maximum displacement is automatically estimated or is supplied by the user (default 3.0)
setAutoPlot(boolean) - Method in class electronDensity.ElectronDensity
Determines whether the plot is updated after every change in setting.
setAutoTimer(boolean) - Method in class spectrophotometer.Spectrophotometer
If true, the timer is automatically started when the first photon reaches the detector.
setAutoUpdate(boolean) - Method in class piston3.Piston3
Sets the autoUpdate parameter.
setAxesLength(float) - Method in class showHybrid.ShowHybrid
Sets the range of all axes from -r to r.
setAxesLength(float, float, float, float, float, float) - Method in class showHybrid.ShowHybrid
Sets the lengths of the axes.
setAxesLength(float) - Method in class showIsosurface.ShowIsosurface
Sets the range of all axes from -r to r.
setAxesLength(float, float, float, float, float, float) - Method in class showIsosurface.ShowIsosurface
Sets the lengths of the axes.
setAxesVisible(boolean) - Method in class showHybrid.ShowHybrid
Indicates whether axes are visible
setAxesVisible(boolean) - Method in class showIsosurface.ShowIsosurface
Indicates whether axes are visible
setBackgroundColor(String) - Method in class calorimeter.Calorimeter
Sets the background color of the applet
setBackgroundColor(String) - Method in class data.Data
Sets the background color of the applet
setBackgroundColor(String) - Method in class spectrophotometer.Spectrophotometer
Sets the background color of the applet.
setBackgroundColor(String) - Method in class thermometer.Thermometer
Sets the background color for the applet.
setBackgroundMode(boolean) - Method in class electronDensity.ElectronDensity
Sets the background mode.
setBackgroundScattering(double) - Method in class spectrophotometer.Spectrophotometer
Sets the probability of background scattering when a photon encounters the cell walls
setBombColor(String) - Method in class calorimeter.Calorimeter
Sets the color of the bomb in the bomb calorimeter
setBombHeight(int) - Method in class calorimeter.Calorimeter
Sets the height of the bomb.
setBombThickness(int) - Method in class calorimeter.Calorimeter
Sets the thickness of the walls of the bomb.
setBombWidth(int) - Method in class calorimeter.Calorimeter
Sets the width of the bomb.
setBrightness(double) - Method in class electronDensity.ElectronDensity
Sets the brightness factor.
setCalculationOnly(boolean) - Method in class stoppedFlow.StoppedFlow
Sets the calculation only flag.
setCalorimeterBodyCurvature(int) - Method in class calorimeter.Calorimeter
Sets the curvature used in drawing the rounded edges of the calorimeter.
setCalorimeterColor(String) - Method in class calorimeter.Calorimeter
Sets the color of the calorimeter body
setCalorimeterFraction(double) - Method in class calorimeter.Calorimeter
Sets the fraction of the applet region that is occupied by the calorimeter.
setCalorimeterTopHeight(int) - Method in class calorimeter.Calorimeter
Sets the thickness of the top of the calorimeter (Style 1 only).
setCalorimeterWallThickness(int) - Method in class calorimeter.Calorimeter
Sets the thickness of the walls of the calorimeter.
setCellAngles(float, float, float) - Method in class showStructure.UnitCell
 
setCellGroupRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for the cell group
setCellGroupTranslation(float, float, float) - Method in class showStructure.ShowStructure
Sets the translation of the cell group
setCellPathLength(double) - Method in class stoppedFlow.StoppedFlow
Sets the cell path length (in centimeters)
setCellSize(float, float, float) - Method in class showStructure.UnitCell
 
setCellType(int) - Method in class showStructure.UnitCell
 
setCharge(double) - Method in class edu.davidson.chm.equilibria.ChemSpecies
Sets the charge of the ChemicalSpecies.
setChemicalSystem(ChemSystem) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the chemical system
setChildMask(BitSet) - Method in class showHybrid.OrbitalSet
 
setChildMask(BitSet) - Method in class showIsosurface.Atom
Sets the ChildMask option to indicate which orbitals are displayed.
setChildMask(int, BitSet) - Method in class showIsosurface.ShowIsosurface
For the specified atom, sets the Switch child mask.
setChildMask(int, int, boolean) - Method in class showIsosurface.ShowIsosurface
For the specified atom, sets the Switch child mask for the specified orbital.
setChiSqTolerance(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the relative tolerance for chi-square.
setCoefficient(int, double) - Method in class stoppedFlow.StoppedFlow
Sets the stoichiometric coefficient for a single species.
setCoefficients(double[]) - Method in class stoppedFlow.StoppedFlow
Sets the stoichiometric coefficients for each species.
setColor(Color) - Method in class electronDensity.Circle
 
setColor(int, int, int) - Method in class electronDensity.Circle
 
setColor(int, String) - Method in class piston3.Piston3
Sets the color of the indicated region (1, 2, or 3).
setColor(int, int, int, int) - Method in class piston3.Piston3
Sets the color of the indicated region (1, 2, or 3).
setColor(int, int, Color3f, Color3f, Color3f, Color3f) - Method in class showIsosurface.Atom
Sets the color of an isosurface
setColor(int, int, Color3f) - Method in class showIsosurface.Atom
Sets the diffuse color of an isosurface
setColor(Color3f, Color3f, Color3f, Color3f) - Method in class showIsosurface.Isosurface
Sets the color of the isosurface
setColor(Color3f) - Method in class showIsosurface.Isosurface
Sets the diffuse color of the isosurface
setColor(int, Color3f, Color3f, Color3f, Color3f) - Method in class showIsosurface.Orbital
Sets the color of an isosurface
setColor(int, Color3f) - Method in class showIsosurface.Orbital
Sets the diffuse color of an isosurface
setColor(int, int, int, Color3f, Color3f, Color3f, Color3f) - Method in class showIsosurface.ShowIsosurface
Sets the color of an isosurface
setColor(int, int, int, Color3f) - Method in class showIsosurface.ShowIsosurface
Sets the diffuse color of an isosurface
setColor(int, int, int, float, float, float) - Method in class showIsosurface.ShowIsosurface
Sets the diffuse color of an isosurface
setColor(int, Color) - Method in class stoppedFlow.StoppedFlow
Sets the color of a single species.
setColor(int, String) - Method in class stoppedFlow.StoppedFlow
Sets the color of a single species.
setColors(Color, Color) - Method in class electronDensity.ElectronDensity
Sets the colors used in the electron density plot.
setColors(int, int, int, int, int, int) - Method in class electronDensity.ElectronDensity
Sets the colors used in the electron density plot.
setColors(String, String, String) - Method in class piston3.Piston3
Sets the colors of all three regions.
setColors(int, int, int, int, int, int, int, int, int) - Method in class piston3.Piston3
Sets the colors of all three regions.
setColors(Color) - Method in class stoppedFlow.StoppedFlow
Sets the color of all species to the indicated color.
setColors(String) - Method in class stoppedFlow.StoppedFlow
Sets the color of all species to the indicated color.
setColors(Color[]) - Method in class stoppedFlow.StoppedFlow
Sets the colors of all species.
setColors(String[]) - Method in class stoppedFlow.StoppedFlow
Sets the colors of all species.
setComplexMode(int) - Method in class electronDensity.ElectronDensity
Sets the display mode for complex values (occurs only when the density mode is 1, which displays the wave function itself).
setConcentration(double) - Method in class spectrophotometer.Spectrophotometer
Sets the concentration of the absorbing species
setConcentrationA(int, double) - Method in class stoppedFlow.StoppedFlow
Sets the molar concentration of a single species in the liquid in syringe A.
setConcentrationB(int, double) - Method in class stoppedFlow.StoppedFlow
Sets the molar concentration of a single species in the liquid in syringe B.
setConcentrations(double[], double[]) - Method in class stoppedFlow.StoppedFlow
Sets the molar concentrations of species in the liquid in syringes.
setConcentrationsA(double[]) - Method in class stoppedFlow.StoppedFlow
Sets the molar concentrations of species in the liquid in syringe A.
setConcentrationsB(double[]) - Method in class stoppedFlow.StoppedFlow
Sets the molar concentrations of species in the liquid in syringe B.
setData(double[], double[]) - Method in class edu.davidson.chm.equilibria.Titration
Sets the experimental data to be fit.
setData(double[], double[], double[]) - Method in class edu.davidson.chm.equilibria.Titration
Sets the experimental data to be fit.
setDelay(long) - Method in class calorimeter.Calorimeter
Sets the delay time for the animation loop that starts the reaction or process.
setDensity(String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the density (in grams/mL) of the Phase.
setDensity(double) - Method in class edu.davidson.chm.equilibria.Gas
This method performs no action, because the density of a gas is dictated by the volume of the gas and the mass of the species in the gas.
setDensity(double) - Method in class edu.davidson.chm.equilibria.Liquid
Sets the density of the liquid.
setDensity(double) - Method in class edu.davidson.chm.equilibria.Phase
Sets the density of the phase.
setDensity(double) - Method in class edu.davidson.chm.equilibria.Solid
Sets the density of the solid.
setDensity(double) - Method in class edu.davidson.chm.equilibria.Solution
Sets the density of the solution.
setDensity(double) - Method in class manometer.Manometer
Sets the density of the liquid.
setDensityMode(int) - Method in class electronDensity.ElectronDensity
Sets the display mode (psi = wave function).
setDiameter(int) - Method in class bulb.Bulb
Sets the diameter of the bulb.
setDiameter(int) - Method in class electronDensity.Circle
 
setDiameters(int, int) - Method in class bulbs.Bulbs
Sets the diameters of the two bulbs.
setDielectricConstant(double) - Method in class edu.davidson.chm.equilibria.Phase
Sets the dielectric constant for the phase (solvent in a solution)
setDiffuseColor(float, float, float) - Method in class showMol.ShowMol
Sets the diffuse color for new spheres and lines.
setDisplayFitIterations(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the results of each iteration in the fit method are displayed on the Java console.
setDisplayFitResults(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the final results of the fit method are displayed on the Java console.
setDisplayFormat(int) - Method in class showMol.Molecule
Sets the display format.
setDisplayFormat(int) - Method in class showMol.ShowMol
Sets the display format for molecules that will be loaded.
setDisplayFormat(int, int) - Method in class showMol.ShowMol
Sets the display format for the indicated molecule, which must have previously been loaded.
setDisplayFormats(int) - Method in class showMol.ShowMol
Sets the display format for all molecules currently loaded.
setDisplayIterations(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the results of each iteration in the solve method are displayed on the Java console.
setDisplayIterations(boolean) - Method in class edu.davidson.chm.equilibria.Equilibria
If true, the results of each iteration in the solve() method are displayed.
setDisplayIterations(boolean) - Method in class edu.davidson.chm.equilibria.Titration
If true, the iteration results at each step of the curve-fitting procedure are displayed.
setDisplayLinearSystem(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the linear system of equations are displayed on the Java console at each iteration of the solve method.
setDisplayLinearSystem(boolean) - Method in class edu.davidson.chm.equilibria.Equilibria
If true, the linear system of equations are displayed at each iteration of the solve method.
setDisplayResults(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the final results of the solve method are displayed on the Java console.
setDisplayResults(boolean) - Method in class edu.davidson.chm.equilibria.Equilibria
If true, the final results of the solve method are displayed.
setDisplayResults(boolean) - Method in class edu.davidson.chm.equilibria.Titration
If true, the final results of the curve-fitting procedure are displayed.
setDisplaySign(boolean) - Method in class electronDensity.ElectronDensity
Determines whether the display shows the sign of the wave function.
setDisplayTime(boolean) - Method in class chemEquilibria.ChemEquilibria
If true, the time (in seconds) required to solve the equilibrium problem is displayed on the Java console (but only if the calculation was successful).
setDisplayTime(boolean) - Method in class edu.davidson.chm.equilibria.Equilibria
If true, the time in seconds required to solve an equilibrium problem via the solveProblem method is displayed on the Java console.
setDragable(boolean) - Method in class manometer.Manometer
Determines whether the user can drag the liquid level in the manometer.
setDragable(boolean) - Method in class piston.Piston
Determines whether the user can drag the barrier.
setDragable(boolean) - Method in class piston3.Piston3
Determines whether the user can drag the barrier.
setDragable(boolean) - Method in class thermometer.Thermometer
Determines whether the user can drag the liquid level in the thermometer.
setEmissiveColor(float, float, float) - Method in class showMol.ShowMol
Sets the emissive color for new spheres and lines.
setEquationTolerance(double) - Method in class chemEquilibria.ChemEquilibria
Sets the convergence tolerance for functions used in the solve method.
setEquationTolerance(double) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the convergence tolerance for functions.
setEquilibriaTolerance(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the relative tolerance for equilibrium calculations.
setFacesVisible(boolean) - Method in class showStructure.ShowStructure
Sets the visibility of the unit cell faces
setFacesVisible(boolean) - Method in class showStructure.UnitCell
Sets the visibility of the unit cell faces
setFactor(double) - Method in class showHybrid.MouseRot
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double, double) - Method in class showHybrid.MouseRot
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFilamentHeight(int) - Method in class calorimeter.Calorimeter
Sets the height of the filament above the bottom of the calorimeter.
setFilamentOffset(int) - Method in class calorimeter.Calorimeter
Sets the distance the left edge of the filament is positioned from the inside left wall of the calorimeter.
setFilamentSectionCount(int) - Method in class calorimeter.Calorimeter
Sets the number of sections in the filament, which has a zig-zag design.
setFilamentSectionWidth(int) - Method in class calorimeter.Calorimeter
Sets the width of each section in the filament, which has a zig-zag design.
setFilamentTime(double) - Method in class calorimeter.Calorimeter
Sets the time during which the filament is active.
setFileFormat(int) - Method in class showMol.ShowMol
Sets the default format for molecular structure files.
setFill(boolean) - Method in class electronDensity.Circle
 
setFinalSlope(double) - Method in class calorimeter.Calorimeter
Sets the slope of the time-temperature plot after the reaction or process has started.
setFitChiSqTolerance(double) - Method in class chemEquilibria.ChemEquilibria
Sets the relative tolerance for the minimization of chi-square in the curve-fitting procedure.
setFitTolerance(double) - Method in class chemEquilibria.ChemEquilibria
Sets the relative tolerance for parameters (ln K or ln n) in the curve-fitting procedure.
setFont(String, String, int) - Method in class manometer.Manometer
Sets the font for the manometers labels.
setFontSize(int) - Method in class showHybrid.ShowHybrid
Sets the font size for the axes labels
setFontSize(int) - Method in class showIsosurface.ShowIsosurface
Sets the font size for the axes labels
setFractionLiquid(double) - Method in class manometer.Manometer
Sets the fraction of the functional volume of the manometer occupied by the liquid.
setFractions(double, double) - Method in class stoppedFlow.StoppedFlow
Sets the initial fractions of the total syringe volumes.
setFractionsDelivered(double, double) - Method in class stoppedFlow.StoppedFlow
Sets the fractions of the total syringe volumes that are delivered in the simulation.
setFunction(int, double, double, double) - Method in class edu.davidson.chm.waveFunction.Gaussian
Adds a gaussian function to the basis function.
setFW(double) - Method in class edu.davidson.chm.equilibria.ChemSpecies
Sets the formula weight of the ChemicalSpecies.
setFW(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the formula weight of the species by calling the setFW method of the ChemSpecies.
setGasColor(String) - Method in class bulb.Bulb
Sets the color of the gas in the bulb.
setGasColor(int, int, int) - Method in class bulb.Bulb
Sets the color of the gas in the bulb.
setGaussian(int) - Method in class electronDensity.ElectronDensity
Sets the wave function to be the previously defined gaussian basis function with the indicated id.
setGaussian(int, double, double) - Method in class electronDensity.ElectronDensity
Sets the wave function to be the previously defined gaussian basis function with the indicated id.
setGaussianOrigin(int, double, double, double) - Method in class electronDensity.ElectronDensity
Sets the origin (in spherical coordinates) for the gaussian basis function
setGaussianOriginXYZ(int, double, double, double) - Method in class electronDensity.ElectronDensity
Sets the origin (in cartesian coordinates) for the gaussian basis function
setGeometry(String) - Method in class edu.davidson.chm.waveFunction.Gaussian
 
setGeometry(int, double) - Method in class showHybrid.ShowHybrid
Orients the spheres for a specific geometry:
g = 2     linear
g = 3     trigonal planar
g = 4     tetrahedral
g = 5     trigonal bipyramidal
g = 6     octahedral
g = 7     square planar
setHeatCapacity(double) - Method in class calorimeter.Calorimeter
Sets the heat capacity of the calorimeter (includes the calorimeter body and the liquid in the calorimeter.
setHeatFlow(double) - Method in class calorimeter.Calorimeter
Sets the heat flow for the calorimeter attributable to the reaction or process.
setHeatingRate(double) - Method in class calorimeter.Calorimeter
Sets the heating rate for the filament, which must be a possible value.
setID(int) - Method in class edu.davidson.chm.waveFunction.WaveFunction
Sets the id of the wave function
setIndex(int) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the index of this reaction (used in Equilibria.class)
setIndex(int) - Method in class edu.davidson.chm.equilibria.Species
Sets the index of this species (used in Equilibria.class)
setInitialSlope(double) - Method in class calorimeter.Calorimeter
Sets the slope of the time-temperature plot prior to the start of the reaction or process.
setInitialTemperature(double) - Method in class calorimeter.Calorimeter
Sets the initial temperature for the calorimeter (the temperature when the simulation begins).
setIntensity(double) - Method in class spectrophotometer.Spectrophotometer
Sets the source intensity, the rate at which photons are emitted from the light source.
setInterpolation(int) - Method in class electronDensity.ElectronDensity
Sets the interpolation level.
setIonSize(String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the ion-size parameter (used in the Extended Debye-Huckel Equation) for the chemical species.
setIonSize(double) - Method in class edu.davidson.chm.equilibria.ChemSpecies
Sets the Debye-Huckel ion-size parameter in angstroms.
setIonSize(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the Debye-Huckel ion size parameter in angstroms by calling the setIonSize method of the ChemSpecies.
setIsAcid(boolean) - Method in class edu.davidson.chm.equilibria.Species
Sets the isAcid property
setIsAuto(boolean) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the isAuto property to identify autodissociation reactions
setIsBase(boolean) - Method in class edu.davidson.chm.equilibria.Species
Sets the isBase property
setIsIdeal(boolean) - Method in class chemEquilibria.ChemEquilibria
Sets the isIdeal property.
setIsIdeal(boolean) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the isIdeal property.
setIsIsobaric(boolean) - Method in class chemEquilibria.ChemEquilibria
Sets the isIsobaric property.
setIsIsobaric(boolean) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the isIsobaric property.
setIsosurfaceVisible(int, int, boolean) - Method in class showIsosurface.Atom
Determines whether the specified isosurface in the specified orbital is visible
setIsosurfaceVisible(int, int, int, boolean) - Method in class showIsosurface.ShowIsosurface
Indicates whether an isosurface is visible
setIsReactive(boolean) - Method in class edu.davidson.chm.equilibria.Species
Sets the isReactive status
setIsSolvent(boolean) - Method in class edu.davidson.chm.equilibria.Species
Sets the isSolvent status
setIsValid(boolean) - Method in class edu.davidson.chm.equilibria.HalfReaction
Sets the isValid property
setIsValid(boolean) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the isValid property
setK(String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the equilibrium constant for the reaction identified by the label.
setK(double) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the thermodynamic equilibrium constant at the reference temperature
setLabel(String) - Method in class edu.davidson.chm.equilibria.ChemSpecies
Sets the descriptive label of the ChemicalSpecies.
setLabel(String) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the label
setLabel(String) - Method in class edu.davidson.chm.equilibria.Phase
Sets the label for a phase
setLabel(String) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the descriptive label for the reaction
setLabel(String) - Method in class edu.davidson.chm.equilibria.Species
Sets the label for the species by calling the setLabel method of the ChemSpecies.
setLabel(int) - Method in class thermometer.Thermometer
Sets the label for the thermometer
0 = no label 1 = K
2 = Kelvin
3 = oC
4 = Celcius
5 = oF
6 = Fahrenheit
setLabelFont(Font) - Method in class data.Data
Sets the font for the label.
setLabelFormat(int, int) - Method in class data.Data
Sets the format for the values displayed in the label
setLabelSize(int, int) - Method in class data.Data
Sets the size of the label.
setLabelText(String) - Method in class data.Data
Sets the text in the label.
setLambda(double) - Method in class chemEquilibria.ChemEquilibria
Sets the initial value of lambda, which controls the transition from the steepest-descent to Hessian methods in the Levenberg-Marquardt algorithm.
setLambda(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the initial value of lambda, the parameter that controls the transition from steepest-descent to Hessian method in the Levenberg-Marquardt algorithm.
setLambdaScaleFactor(double) - Method in class chemEquilibria.ChemEquilibria
Sets the lambda scaling factor.
setLambdaScaleFactor(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the lambda scaling factor.
setLeftColor(String) - Method in class bulbs.Bulbs
Sets the color of the gas in the left bulb.
setLeftColor(int, int, int) - Method in class bulbs.Bulbs
Sets the color of the gas in the left bulb.
setLeftVolume(double) - Method in class bulbs.Bulbs
Sets the volume of the left bulb.
setLightColor(double) - Method in class stoppedFlow.StoppedFlow
Sets the light beam to the color corresponding with the indicated wavelength.
setLightColor(Color) - Method in class stoppedFlow.StoppedFlow
Sets the light color.
setLineGroupRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for the entire set of LineGroups
setLineGroupRotation(int, float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for a specific LineGroup
setLineGroupsVisible(boolean) - Method in class showStructure.ShowStructure
Sets the visibility of all LineGroups
setLineGroupTranslation(float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for the entire set of LineGroups
setLineGroupTranslation(int, float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for a specific LineGroup
setLineGroupVisible(int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of the indicated LineGroup
setLinesVisible(boolean) - Method in class showStructure.ShowStructure
Sets the visibility of the unit cell lines
setLinesVisible(boolean) - Method in class showStructure.UnitCell
Sets the visibility of the unit cell lines
setLiquidColor(int, int, int) - Method in class bulb.Bulb
Sets the color of the liquid at the bottom of the bulb
setLiquidColor(String) - Method in class calorimeter.Calorimeter
Sets the color of the liquid in the calorimeter (Style 1 and 2 only).
setLiquidColor(String) - Method in class spectrophotometer.Spectrophotometer
Sets the color of the liquid in the cell.
setLiquidColor(String) - Method in class thermometer.Thermometer
Sets the color of the liquid in the thermometer (default is red).
setLiquidFraction(double) - Method in class bulb.Bulb
Sets the amount of liquid shown at the bottom of the bulb
setLiquidFraction(double) - Method in class calorimeter.Calorimeter
Sets the fraction of the calorimeter body that is filled with the liquid.
setMass(double) - Method in class balance.Balance
Sets the mass.
setMass(double) - Method in class edu.davidson.chm.equilibria.Gas
This method performs no action, because the mass of a gas is dictated by the masses of each species in the gas and cannot be set globally.
setMass(double) - Method in class edu.davidson.chm.equilibria.Liquid
Sets the mass of the liquid.
setMass(double) - Method in class edu.davidson.chm.equilibria.Phase
Sets the mass for the phase.
setMass(double) - Method in class edu.davidson.chm.equilibria.Solid
Sets the mass of the solid.
setMass(double) - Method in class edu.davidson.chm.equilibria.Solution
Sets the mass of the solvent.
setMaxCnt(int) - Method in class calorimeter.Calorimeter
Sets the number of increments in the animation loop.
setMaxCnt(int) - Method in class chemEquilibria.ChemEquilibria
Sets the maximum number of iterations to be used in solving the nonlinear system of equations in the solve method.
setMaxCnt(int) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the maximum number of iterations to be used in solving the nonlinear system of equations.
setMaximum(double) - Method in class manometer.Manometer
Sets the maximum scale value.
setMaxInc(double) - Method in class chemEquilibria.ChemEquilibria
Sets the maximum amount a variable can change during a single iteration in the solve method.
setMaxInc(double) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the maximum amount a variable can change during a single iteration.
setMaxIncrement(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the maximum amount by which a parameter (ln K or ln n) may change during an iteration of the Levenberg-Marquardt algorithm.
setMaxR(double) - Method in class electronDensity.ElectronDensity
Sets the maximum displacement to be used is autoMaxR = false.
setMaxTemperature(double) - Method in class thermometer.Thermometer
Sets the maximum temperature on the thermometer.
setMaxVolume(double) - Method in class piston.Piston
Sets the maximum volume for the piston.
setMaxVolume(double, double) - Method in class piston.Piston
Sets the maximum volume for the piston based upon the volume at a given scale reading.
setMaxVolume(double) - Method in class piston3.Piston3
Sets the maximum volume for the piston.
setMaxVolume(double, double) - Method in class piston3.Piston3
Sets the maximum volume for the piston based upon the volume at a given scale reading.
setMinimumStepSize(double) - Method in class stoppedFlow.StoppedFlow
Sets the minimum step size in seconds for the Fourth Order Runge-Kutta-Fehlberg algorithm.
setMinMaxIncrement(double, double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the minimum and maximum volume increment for a titration calculation
setMinMaxTemperature(double, double) - Method in class thermometer.Thermometer
Sets the minimum and maximum temperatures on the thermometer.
setMinTemperature(double) - Method in class thermometer.Thermometer
Sets the minimum temperature on the thermometer.
setMinVolume(double) - Method in class piston.Piston
Sets the minimum volume for the piston.
setMinVolume(double) - Method in class piston3.Piston3
Sets the minimum volume for the piston.
setMixtureColor(String) - Method in class bulbs.Bulbs
Sets the color of the gas mixture.
setMixtureColor(int, int, int) - Method in class bulbs.Bulbs
Sets the color of the gas mixture.
setMolarAbsorptivities(double[]) - Method in class stoppedFlow.StoppedFlow
Sets the molar absorptivities of the various species.
setMolarAbsorptivity(double) - Method in class spectrophotometer.Spectrophotometer
Sets the molar absorptivity of the absorbing species
setMolarAbsorptivity(int, double) - Method in class stoppedFlow.StoppedFlow
Sets the molar absorptivity of a single species.
setMoleculeRotation(int, double, double, double, double) - Method in class showMol.ShowMol
Rotates the selected molecule.
setMoleculeRotationOnAtom(int, int, double, double, double, double) - Method in class showMol.ShowMol
Rotates the selected molecule.
setMoleculesVisible(boolean) - Method in class showMol.ShowMol
Sets all or none of the molecules to be visible
setMoleculeTranslation(int, double, double, double) - Method in class showMol.ShowMol
Sets the location of the selected molecule.
setMoleculeVisible(int, boolean) - Method in class showMol.ShowMol
Determines whether the specified molecule is displayed.
setMoles(double) - Method in class edu.davidson.chm.equilibria.Species
Sets the number of moles of the species.
setMoles(double) - Method in class manometer.Manometer
Sets the moles of trapped gas.
setMonitor(String) - Method in class chemEquilibria.ChemEquilibria
Sets the species whose pX value is monitored during a titration
setMonitor(String, String) - Method in class chemEquilibria.ChemEquilibria
Sets the electrodes whose potential is monitored during a titration.
setMonitor(String) - Method in class edu.davidson.chm.equilibria.Titration
Sets the titration to monitor pX where X is the chemical species identified by the label _chemSpecies
setMonitor(String, String) - Method in class edu.davidson.chm.equilibria.Titration
Sets the titration to monitor a half-cell or cell potential where _label identifies the phase whose potential is to be monitored.
setName(String) - Method in class showIsosurface.Atom
Sets the name of the atom
setName(String) - Method in class showIsosurface.Orbital
Sets the name of the orbital
setNLM(int, int, int) - Method in class edu.davidson.chm.waveFunction.HydrogenicWaveFunction
Sets the quantum numbers
setNLM(int, int, int) - Method in class electronDensity.ElectronDensity
Creates a new hydrogenic wave function using the user-supplied quantum numbers.
setNLM(int, int, int, double, double) - Method in class electronDensity.ElectronDensity
Creates a new hydrogenic wave function using the user-supplied quantum numbers.
setNucleusColor(float, float, float) - Method in class showIsosurface.Atom
Sets the emissive color of the nucleus and sets the nucleus to be visible
setNucleusColor(int, float, float, float) - Method in class showIsosurface.ShowIsosurface
Sets the emissive color of the nucleus of the specified atom and sets the nucleus to be visible
setNucleusVisible(boolean) - Method in class showIsosurface.Atom
Determines whether the nucleus is visible as a small where sphere
setNucleusVisible(int, boolean) - Method in class showIsosurface.ShowIsosurface
Determines whether the nucleus is visible as a small where sphere
setOrbital(String) - Method in class electronDensity.ElectronDensity
Sets the orbital to be displayed.
setOrbital(int) - Method in class showHybrid.OrbitalSet
Determines which orbital or atom is displayed.
setOrbital(int) - Method in class showHybrid.ShowHybrid
Determines which arrows or orbitals are displayed.
setOrbitalActive(int) - Method in class showIsosurface.Atom
The orbital's BranchGroup is compiled and added to the atom's Switch node.
setOrbitalActive(int, int) - Method in class showIsosurface.ShowIsosurface
The orbital's BranchGroup is compiled and added to the atom's Switch node.
setOrbitalSet(int) - Method in class showHybrid.ShowHybrid
Determines which orbital set is active.
setOrbitalTransparency(int, int, float) - Method in class showIsosurface.ShowIsosurface
Sets the transparency of an orbital
setOrbTG(TransformGroup) - Method in class showHybrid.PickRotate
 
setOrigin(double, double, double) - Method in class edu.davidson.chm.waveFunction.Gaussian
Sets the position of the origin for the basis function.
setOriginXYZ(double, double, double) - Method in class edu.davidson.chm.waveFunction.Gaussian
Sets the position of the origin for the basis function.
setOutputIncrement(double) - Method in class stoppedFlow.StoppedFlow
Sets the output increment for simulation data.
setOwner(SApplet) - Method in class balance.Balance
Sets the owner for SDataListener
setOwner(SApplet) - Method in class calorimeter.Calorimeter
Sets the owner for the data source.
setOwner(SApplet) - Method in class data.Data
SDataListener Method: Sets the owner of this SDataListener
setOwner(SApplet) - Method in class manometer.Manometer
Sets the owner for SDataListener and SDataSource
setOwner(SApplet) - Method in class piston.Piston
Sets the owner for SDataListener and SDataSource
setOwner(SApplet) - Method in class piston3.Piston3
Sets the owner for SDataListener and SDataSource
setOwner(SApplet) - Method in class spectrophotometer.Spectrophotometer
Sets the owner for the SDataSource.
setOwner(SApplet) - Method in class stoppedFlow.StoppedFlow
Sets the owner for the SDataSource.
setOwner(SApplet) - Method in class thermometer.Thermometer
Sets the owner for SDataListener and SDataSource
setPath(String) - Method in class showMol.ShowMol
Sets the default path for files.
setPathLength(double) - Method in class spectrophotometer.Spectrophotometer
Sets the cell path length.
setPhotonRadius(int) - Method in class spectrophotometer.Spectrophotometer
Sets the radius of the photons.
setPixelsPerCM(int) - Method in class spectrophotometer.Spectrophotometer
Sets the number of pixels per centimeter.
setPointGroupRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for the entire set of PointGroups
setPointGroupRotation(int, float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for a specific PointGroup
setPointGroupTranslation(float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for the entire set of PointGroups
setPointGroupTranslation(int, float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for a specific PointGroup
setPointGroupVisible(boolean) - Method in class showStructure.ShowStructure
Sets the visibility of all points in all groups
setPointGroupVisible(int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of all points in a group
setPointsVisible(boolean) - Method in class showStructure.PointGroup
Sets the visibility of the lattice points.
setPosition(double, double) - Method in class electronDensity.Circle
 
setPosition(double, double, double) - Method in class showIsosurface.Atom
Sets the position of the atom
setPosition(double, double, double) - Method in class showIsosurface.ShowIsosurface
Sets the position of the root transform.
setPrecision(double) - Method in class stoppedFlow.StoppedFlow
Sets the relative precision for the numerical calculations for the user-defined reaction order.
setPressure(double) - Method in class chemEquilibria.ChemEquilibria
Sets the pressure (in atm) of the system.
setPressure(double) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the system pressure.
setPressure(double) - Method in class manometer.Manometer
Sets the pressure.
setRadius(double) - Method in class showHybrid.ShowHybrid
Sets the radius for the spheres.
setRandom(long) - Method in class calorimeter.Calorimeter
Sets the seed value for the random number generator.
setRandom(long) - Method in class stoppedFlow.StoppedFlow
Sets the seed value for the random number generator.
setRateConstant(double) - Method in class stoppedFlow.StoppedFlow
Sets the rate constant based upon species 0.
setRateLaw(double[]) - Method in class stoppedFlow.StoppedFlow
Sets the rate law for the user-defined kinetics option (see setReactionOrder).
setRateLaw(int, double) - Method in class stoppedFlow.StoppedFlow
Sets the exponent in the rate law for a given species for the user-defined kinetics option (see setReactionOrder).
setReactionOrder(int) - Method in class stoppedFlow.StoppedFlow
Sets the reaction order for the kinetics.
setRedundantTolerance(double) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the tolerance for aborting analysis when redundant chemical equations are encountered.
setReferenceIntensity(double) - Method in class spectrophotometer.Spectrophotometer
Sets the reference intensity.
setReferenceTemperature(double) - Method in class chemEquilibria.ChemEquilibria
Sets the reference potential for all reactions and half-reaction.
setReferenceTemperature(String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the reference potential for a reaction or half-reaction.
setReferenceTemperature(double) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the reference temperature for all reactions and half-reactions in the chemical system
setReferenceTemperature(double) - Method in class edu.davidson.chm.equilibria.HalfReaction
Sets the reference temperature (in Kelvin)
setReferenceTemperature(double) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the reference temperature, which is used to calculate the equilibrium constant at temperatures other than the reference temperature.
setReservoirHeight(int) - Method in class calorimeter.Calorimeter
Sets the height of the reservoir.
setReservoirLiquidFraction(double) - Method in class calorimeter.Calorimeter
Sets the fraction of the reservoir filled with liquid.
setReservoirOffset(int) - Method in class calorimeter.Calorimeter
Sets the offset of the reservoir from the left edge of the calorimeter.
setReservoirThickness(int) - Method in class calorimeter.Calorimeter
Sets the thickness of the reservoir walls.
setReservoirWidth(int) - Method in class calorimeter.Calorimeter
Sets the width of the reservoir.
setRightColor(String) - Method in class bulbs.Bulbs
Sets the color of the gas in the right bulb.
setRightColor(int, int, int) - Method in class bulbs.Bulbs
Sets the color of the gas in the right bulb.
setRightVolume(double) - Method in class bulbs.Bulbs
Sets the volume of the right bulb.
setRootTG(TransformGroup) - Method in class showHybrid.PickRotate
 
setRootTr(TransformGroup) - Method in class showHybrid.MouseRot
Before processing mouse rotation for local motion, call this method with the root TransformGroup as the argument to pass the root transform
setRootTrIdentity() - Method in class showHybrid.MouseRot
Before processing mouse rotation for global motion, call this method to set the root transform to the identity matrix
setRotation(double, double, double, double) - Method in class electronDensity.ElectronDensity
Sets the rotation parameters for the display.
setRotation(double, double, double, double) - Method in class showHybrid.ShowHybrid
Set the rotation for the display.
setRotation(double, double, double, double) - Method in class showMol.Molecule
Rotates the molecule about its center.
setRotation(double, double, double, double) - Method in class showMol.ShowMol
Rotates the scene.
setRotation(float, float, float, float) - Method in class showStructure.AtomGroup
Set rotation for the entire group.
setRotation(float, float, float, float) - Method in class showStructure.LineGroup
Set rotation for the entire group.
setRotation(float, float, float, float) - Method in class showStructure.PointGroup
Set rotation for the entire group.
setRotation(float, float, float, float) - Method in class showStructure.SegmentGroup
Set rotation for the entire group.
setRotation(int, float, float, float, float) - Method in class showStructure.SegmentGroup
Set rotation for the indicated segment.
setRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Set rotation for the entire structure.
setRotation(float, float, float, float) - Method in class showStructure.UnitCell
Sets the UnitCell rotation
setRotationOnAtom(int, double, double, double, double) - Method in class showMol.Molecule
Rotates the molecule about the specified atom.
setSampleColor(String) - Method in class calorimeter.Calorimeter
Sets the color of the sample in the calorimeter (Style 1 and 2 only).
setSampleDiameter(int) - Method in class calorimeter.Calorimeter
Sets the diameter of the sample itself.
setSampleHeight(int) - Method in class calorimeter.Calorimeter
Sets the height of the sample region.
setSampleOffset(int) - Method in class calorimeter.Calorimeter
Sets the distance the sample is positioned from the inside wall.
setSampleWidth(int) - Method in class calorimeter.Calorimeter
Sets the width (thickness)of hammer.
setScale(int, int) - Method in class balance.Balance
Sets the scale and precision of the balance
setScale(double) - Method in class showIsosurface.Atom
Sets the transform scale
setScaleMaximum(double) - Method in class piston.Piston
Sets the maximum value of the scale.
setScaleMaximum(double) - Method in class piston3.Piston3
Sets the maximum value of the scale.
setScalingFactor(double) - Method in class spectrophotometer.Spectrophotometer
Sets the scaling factor.
setSegmentGroupRotation(float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for the entire set of SegmentGroups
setSegmentGroupRotation(int, float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for a specific SegmentGroup
setSegmentGroupRotation(int, int, float, float, float, float) - Method in class showStructure.ShowStructure
Sets the rotation for a specific SegmentGroup
setSegmentGroupTranslation(float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for the entire set of SegmentGroups
setSegmentGroupTranslation(int, float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for a specific SegmentGroup
setSegmentGroupTranslation(int, int, float, float, float) - Method in class showStructure.ShowStructure
Sets the translation for a specific SegmentGroup
setSegmentGroupVisible(int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of all segments in a group
setSegmentVisible(int, int, boolean) - Method in class showStructure.ShowStructure
Sets the visibility of the indicated segment
setShowArrow(Boolean) - Method in class showHybrid.OrbitalSet
 
setShowArrow(Boolean) - Method in class showHybrid.ShowHybrid
Determines whether arrows or orbitals are displayed
setShowAxes(boolean) - Method in class electronDensity.ElectronDensity
Sets the showAxes property.
setShowLiquid(boolean) - Method in class bulb.Bulb
Determines whether the liquid at the bottom of the bulb is shown or not.
setShowOverlay(Boolean) - Method in class showHybrid.OrbitalSet
 
setShowOverlay(Boolean) - Method in class showHybrid.ShowHybrid
Determines whether arrows/orbitals are overlaid.
setSpeed(double) - Method in class spectrophotometer.Spectrophotometer
Sets the speed with which a photon moves across the screen.
setSphereDistance(double) - Method in class showHybrid.ShowHybrid
Sets the distance of the spheres from the origin.
setStandardDeviation(double) - Method in class balance.Balance
Sets the standard deviation for the mass value.
setStandardDeviation(double) - Method in class calorimeter.Calorimeter
Sets the standard deviation for the Gaussian noise applied to the temperature.
setStandardDeviation(double) - Method in class chemEquilibria.ChemEquilibria
Sets the standard deviation for pX values for the curve-fitting procedure.
setStandardDeviation(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the standard deviation to be used for all pX or E values if the individual standard deviations are not defined.
setStandardDeviation(double) - Method in class stoppedFlow.StoppedFlow
Sets the standard deviation for the Gaussian error applied to the absorbance.
setStandardPotential(double) - Method in class edu.davidson.chm.equilibria.HalfReaction
Sets the standard potential at the reference temperature
setStartTime(double) - Method in class calorimeter.Calorimeter
Sets the time at which the reaction or process starts.
setStartTime(double) - Method in class stoppedFlow.StoppedFlow
Sets the starting time for the chemical reaction.
setStirrerColor(String) - Method in class calorimeter.Calorimeter
Sets the color of the stirrer
setStirrerOffsetX(int) - Method in class calorimeter.Calorimeter
Sets the distance the stirrer is offset from the inside left wall of the calorimeter.
setStirrerOffsetY(int) - Method in class calorimeter.Calorimeter
Sets the distance the stirrer is offset from the bottom of the calorimeter.
setStirrerWidth(int) - Method in class calorimeter.Calorimeter
Sets the width and height of the vanes on the stirrer.
setStopcockState(boolean) - Method in class bulb.Bulb
Sets the state of the stopcock.
setStopcockState(boolean) - Method in class bulbs.Bulbs
Sets the state of the stopcock.
setStopTime(double) - Method in class calorimeter.Calorimeter
Sets the time at which the simulation stops.
setStopTime(double) - Method in class stoppedFlow.StoppedFlow
Sets the stopping time for the simulation reaction.
setSVDThreshold(double) - Method in class chemEquilibria.ChemEquilibria
Sets the threshold value in the solve method for setting the diagonal elements from svd to zero.
setSVDThreshold(double) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the threshold value for setting the diagonal elements from svd to zero.
setTargetIncrement(double) - Method in class chemEquilibria.ChemEquilibria
Sets the target change for pX or E in a titration.
setTargetIncrement(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the target change in pX or E for a titration.
setTemperature(double) - Method in class chemEquilibria.ChemEquilibria
Sets the temperature (in Kelvin) of the system.
setTemperature(double) - Method in class edu.davidson.chm.equilibria.ChemSystem
Sets the system temperature
setTemperature(double) - Method in class manometer.Manometer
Sets the temperature
setTemperature(double) - Method in class thermometer.Thermometer
Sets the temperature and updates the thermometer graphics.
setTemperatureDependence(String, double, double) - Method in class chemEquilibria.ChemEquilibria
Sets the parameters controlling the temperature-dependence of the equilibrium constant for a reaction.
setTemperatureDependence(String, double, double, double) - Method in class chemEquilibria.ChemEquilibria
Sets the parameters used to determine the temperature-dependence of the standard potential for a half-reaction.
setTemperatureDependence(double, double, double) - Method in class edu.davidson.chm.equilibria.HalfReaction
Sets the parameters used to determine the temperature-dependence of the standard potential.
setTemperatureDependence(double, double) - Method in class edu.davidson.chm.equilibria.Reaction
Sets the parameters controlling the temperature-dependence of the equilibrium constant.
setThermometerFraction(double) - Method in class calorimeter.Calorimeter
Sets the height of the liquid in the thermometer as a fraction of the length of the thermometer
setThermometerOffsetX(int) - Method in class calorimeter.Calorimeter
Sets the position of the right edge of the thermometer from the inside right wall of the calorimeter
setThermometerOffsetY(int) - Method in class calorimeter.Calorimeter
Sets the position of the bottom of the thermometer from the inside bottom of the calorimeter
setTimeConstant(double) - Method in class calorimeter.Calorimeter
Sets the time constant for the simulation.
setTimeIncrement(double) - Method in class calorimeter.Calorimeter
Sets the simulation time increment, the time between points in the simulation.
setTimeIncrement(double) - Method in class spectrophotometer.Spectrophotometer
Sets the simulation time increment, the time between points in the simulation.
setTimeIncrement(double) - Method in class stoppedFlow.StoppedFlow
Sets the time increment for the simulation.
setTolerance(double) - Method in class chemEquilibria.ChemEquilibria
Sets the relative tolerance in the solve method for convergence of the amounts of each species.
setTolerance(double) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the relative tolerance for convergence of the amounts of each species
setTolerance(double) - Method in class edu.davidson.chm.equilibria.Titration
Sets the absolute tolerance for convergence of parameters.
setTransform(Transform3D) - Method in class showIsosurface.Atom
Sets the transform of the atom
setTranslation(double, double, double) - Method in class showMol.Molecule
Sets the position of the molecule.
setTranslation(double, double, double) - Method in class showMol.ShowMol
Shifts the position of the scene.
setTranslation(float, float, float) - Method in class showStructure.AtomGroup
Set the translation for the entire group.
setTranslation(float, float, float) - Method in class showStructure.LineGroup
Set the translation for the entire group.
setTranslation(float, float, float) - Method in class showStructure.PointGroup
Set the translation for the entire group.
setTranslation(float, float, float) - Method in class showStructure.SegmentGroup
Set the translation for the entire group.
setTranslation(int, float, float, float) - Method in class showStructure.SegmentGroup
Set the translation for the indicated segment.
setTranslation(float, float, float) - Method in class showStructure.ShowStructure
Set the translation for the entire structure.
setTranslation(float, float, float) - Method in class showStructure.UnitCell
Sets the UnitCell translation.
setTransparency(int, float) - Method in class showIsosurface.Atom
Sets the transparency of the specified orbital
setTransparency(float) - Method in class showIsosurface.Isosurface
Sets the transparency of the isosurface
setTransparency(float) - Method in class showIsosurface.Orbital
Sets the transparency of the orbital
setUnitCellRotation(float, float, float, float) - Method in class showStructure.ShowStructure
 
setUnitCellTranslation(float, float, float) - Method in class showStructure.ShowStructure
 
setUnits(String, String) - Method in class balance.Balance
Sets the units displayed on the balance.
setupCallback(MouseBehaviorCallback) - Method in class showHybrid.MouseRot
The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(PickingCallback) - Method in class showHybrid.PickRotate
Register the class @param callback to be called each time the picked object moves
setUseFilament(boolean) - Method in class calorimeter.Calorimeter
Determines whether the filament is used during a simulation (Style 1 only).
setUsePrevious(boolean) - Method in class chemEquilibria.ChemEquilibria
Sets the usePrevious property for the solve method.
setUsePrevious(boolean) - Method in class edu.davidson.chm.equilibria.Equilibria
Sets the usePrevious property.
setVaporPressure(double) - Method in class manometer.Manometer
Sets the vapor pressure of the liquid.
setView(double, double, double, double) - Method in class showHybrid.ShowHybrid
Sets the orbital orientation to a specific value.
setView(double, double, double, double) - Method in class showIsosurface.ShowIsosurface
Sets the orientation to a specific value.
setViewDistance(float) - Method in class showHybrid.ShowHybrid
Sets the viewing distance.
setViewDistance(float) - Method in class showIsosurface.ShowIsosurface
Sets the viewing distance.
setViewDistance(float) - Method in class showMol.ShowMol
Sets the viewing distance.
setViewDistance(float) - Method in class showStructure.ShowStructure
Sets the viewing distance.
setViewXY() - Method in class electronDensity.ElectronDensity
Sets the plot to display the xy plane
setViewXZ() - Method in class electronDensity.ElectronDensity
Sets the plot to display the xz plane
setViewYZ() - Method in class electronDensity.ElectronDensity
Sets the plot to display the xz plane
setVisible(Boolean) - Method in class showHybrid.Arrow
 
setVisible(boolean) - Method in class showIsosurface.Isosurface
Determines whether the isosurface is visible
setVisible(int, boolean) - Method in class showIsosurface.Orbital
Sets the visibility state of a specific isosurface
setVisible(int, boolean) - Method in class showStructure.AtomGroup
Sets the visibility of the indicated atom
setVisible(boolean) - Method in class showStructure.LineGroup
Sets the visibility of the lines
setVisible(int, boolean) - Method in class showStructure.SegmentGroup
Sets the visibility of the indicated segment
setVolume(String, double) - Method in class chemEquilibria.ChemEquilibria
Sets the volume (in liters) of the phase
setVolume(double) - Method in class edu.davidson.chm.equilibria.Gas
Sets the volume for the phase.
setVolume(double) - Method in class edu.davidson.chm.equilibria.Liquid
Sets the volume of the liquid.
setVolume(double) - Method in class edu.davidson.chm.equilibria.Phase
Sets the volume for the phase.
setVolume(double) - Method in class edu.davidson.chm.equilibria.Solid
Sets the volume of the solid.
setVolume(double) - Method in class edu.davidson.chm.equilibria.Solution
Sets the volume of the solution.
setVolume(double) - Method in class piston.Piston
Sets the volume (in mL) of the piston.
setVolume(double) - Method in class piston3.Piston3
Sets the volume (in mL) of the piston.
setVolume(int, double) - Method in class piston3.Piston3
Sets the volume (in mL) of a region (1, 2, or 3)
setVolumes(double, double, double) - Method in class piston3.Piston3
Sets the volumes (in mL) of all three regions.
setWaveFunction(WaveFunction, double, double) - Method in class electronDensity.ElectronDensity
Creates a new hybrid wave function using the user-supplied wave function.
setWavelength(double) - Method in class spectrophotometer.Spectrophotometer
Sets the wavelength of the photons.
setWhichChild(int) - Method in class showHybrid.OrbitalSet
 
setWhichOrbital(int) - Method in class showIsosurface.Atom
Indicates which orbital is to be displayed May also specify Switch.CHILD_ALL, Switch.CHILD_NONE, or Switch.CHILD_MASK.
setWhichOrbital(int, int) - Method in class showIsosurface.ShowIsosurface
For the selected atom, specifies the orbital to be displayed.
setXView() - Method in class showHybrid.ShowHybrid
Sets the orbital orientation to view down the orbital x axis.
setXView() - Method in class showIsosurface.ShowIsosurface
Sets the orientation to view down the x axis.
setYView() - Method in class showHybrid.ShowHybrid
Sets the orbital orientation to view down the orbital y axis.
setYView() - Method in class showIsosurface.ShowIsosurface
Sets the orientation to view down the y axis.
setZView() - Method in class showHybrid.ShowHybrid
Sets the orbital orientation to view down the orbital z axis.
setZView() - Method in class showIsosurface.ShowIsosurface
Sets the orientation to view down the z axis.
shininess - Variable in class showStructure.PointGroup
 
shininess - Variable in class showStructure.SegmentGroup
 
shininess - Variable in class showStructure.UnitCell
 
showFilament(boolean) - Method in class calorimeter.Calorimeter
Determines whether the filament is shown in the calorimeter (Style 1 only).
showHybrid - package showHybrid
 
ShowHybrid - Class in showHybrid
Displays orbital isosurfaces given a point set.
ShowHybrid() - Constructor for class showHybrid.ShowHybrid
 
showIsosurface - package showIsosurface
 
ShowIsosurface - Class in showIsosurface
Displays orbital isosurfaces given a point set.
ShowIsosurface() - Constructor for class showIsosurface.ShowIsosurface
 
showMol - package showMol
 
ShowMol - Class in showMol
ShowMol is a molecular viewer for the following file types: PDB (Brookhaven Protein Database format)
ShowMol() - Constructor for class showMol.ShowMol
 
showPieces() - Method in class showStructure.ShowStructure
 
showSample(boolean) - Method in class calorimeter.Calorimeter
Determines whether the sample is shown in the calorimeter (Styles 1 and 2 only).
showStirrer(boolean) - Method in class calorimeter.Calorimeter
Determines whether the stirrer is shown in the calorimeter (all Styles).
showStructure - package showStructure
 
ShowStructure - Class in showStructure
Displays unit cell structure.
ShowStructure() - Constructor for class showStructure.ShowStructure
 
Solid - Class in edu.davidson.chm.equilibria
This project contains the files necessary to solve arbitrary equilibrium problems
Solid() - Constructor for class edu.davidson.chm.equilibria.Solid
 
Solid(String, ChemSystem, ChemSpecies) - Constructor for class edu.davidson.chm.equilibria.Solid
The minimal requirements for defining a Solid phase are a descriptive label, the chemical system containing the phase, and the chemical species the constitutes the solid.
Solid(String, ChemSystem, ChemSpecies, double) - Constructor for class edu.davidson.chm.equilibria.Solid
The minimal requirements for defining a Solid phase are a descriptive label, the chemical system containing the phase, and the chemical species the constitutes the solid.
Solution - Class in edu.davidson.chm.equilibria
Creates a solution phase.
Solution() - Constructor for class edu.davidson.chm.equilibria.Solution
 
Solution(String, ChemSystem, ChemSpecies) - Constructor for class edu.davidson.chm.equilibria.Solution
The minimal requirements for defining a Solution phase are a descriptive label, the chemical system containing the phase, and the chemical species that constitutes the solvent.
Solution(String, ChemSystem, ChemSpecies, double) - Constructor for class edu.davidson.chm.equilibria.Solution
The minimal requirements for defining a Solution phase are a descriptive label, the chemical system containing the phase, and the chemical species the constitutes the solvent.
Solution(String, ChemSystem, ChemSpecies, ChemSpecies, ChemSpecies, double) - Constructor for class edu.davidson.chm.equilibria.Solution
The minimal requirements for defining a Solution phase are a descriptive label, the chemical system containing the phase, and the chemical species the constitutes the solvent.
solve() - Method in class chemEquilibria.ChemEquilibria
Solves the equilibrium problem.
solve() - Method in class edu.davidson.chm.equilibria.Equilibria
Solves the mathematical problem and automatically updates number of moles for all species.
solvent - Variable in class edu.davidson.chm.equilibria.Solution
 
solveProblem() - Method in class edu.davidson.chm.equilibria.Equilibria
Solves the equilibrium problem.
SP - Static variable in class showHybrid.OrbitalSet
 
SP2 - Static variable in class showHybrid.OrbitalSet
 
SP3 - Static variable in class showHybrid.OrbitalSet
 
SPACEFILLING - Static variable in class showMol.Molecule
 
SPACEFILLING - Static variable in class showMol.ShowMol
 
species - Variable in class edu.davidson.chm.equilibria.Phase
 
Species - Class in edu.davidson.chm.equilibria
A Species object contains the information necessary to describe a chemical species
Species() - Constructor for class edu.davidson.chm.equilibria.Species
The default constructor should never be used.
Species(ChemSpecies, Phase) - Constructor for class edu.davidson.chm.equilibria.Species
Creates a species consisting of the indicated ChemSpecies in the indicated Phase.
Species(ChemSpecies, Phase, double) - Constructor for class edu.davidson.chm.equilibria.Species
Creates a species consisting of the indicated ChemSpecies in the indicated Phase.
spectrophotometer - package spectrophotometer
 
Spectrophotometer - Class in spectrophotometer
Simulation of a spectrophotometer.
Spectrophotometer() - Constructor for class spectrophotometer.Spectrophotometer
 
specularColor - Variable in class showStructure.PointGroup
 
specularColor - Variable in class showStructure.SegmentGroup
 
specularColor - Variable in class showStructure.UnitCell
 
start() - Method in class balance.Balance
 
start() - Method in class bulb.Bulb
 
start() - Method in class bulbs.Bulbs
 
start() - Method in class calorimeter.Calorimeter
 
start() - Method in class chemEquilibria.ChemEquilibria
 
start() - Method in class data.Data
 
start() - Method in class electronDensity.ElectronDensity
 
start() - Method in class manometer.Manometer
 
start() - Method in class piston.Piston
 
start() - Method in class piston3.Piston3
 
start() - Method in class showHybrid.ShowHybrid
 
start() - Method in class showIsosurface.ShowIsosurface
 
start() - Method in class showMol.ShowMol
 
start() - Method in class showStructure.ShowStructure
 
start() - Method in class spectrophotometer.Spectrophotometer
 
start() - Method in class stoppedFlow.StoppedFlow
 
start() - Method in class thermometer.Thermometer
 
startSimulation() - Method in class calorimeter.Calorimeter
Starts the simulation.
startSimulation() - Method in class spectrophotometer.Spectrophotometer
Starts the simulation by starting the clock.
startSimulation() - Method in class stoppedFlow.StoppedFlow
Starts the simulation.
startTimer() - Method in class spectrophotometer.Spectrophotometer
Starts the timer.
step(double, double) - Method in class calorimeter.Calorimeter
The step method required for the SStepable interface.
step(double, double) - Method in class spectrophotometer.Spectrophotometer
Calculates state of system at each step in the simulation.
step(double, double) - Method in class stoppedFlow.StoppedFlow
Calculates state of system at each step in the simulation.
stop() - Method in class balance.Balance
 
stop() - Method in class bulb.Bulb
 
stop() - Method in class bulbs.Bulbs
 
stop() - Method in class calorimeter.Calorimeter
 
stop() - Method in class chemEquilibria.ChemEquilibria
 
stop() - Method in class data.Data
 
stop() - Method in class electronDensity.ElectronDensity
 
stop() - Method in class manometer.Manometer
 
stop() - Method in class piston.Piston
 
stop() - Method in class piston3.Piston3
 
stop() - Method in class showHybrid.ShowHybrid
 
stop() - Method in class showIsosurface.ShowIsosurface
 
stop() - Method in class showMol.ShowMol
 
stop() - Method in class showStructure.ShowStructure
 
stop() - Method in class spectrophotometer.Spectrophotometer
 
stop() - Method in class stoppedFlow.StoppedFlow
 
stop() - Method in class thermometer.Thermometer
 
stoppedFlow - package stoppedFlow
 
StoppedFlow - Class in stoppedFlow
This applet simulates a stopped-flow apparatus for performing kinetics studies.
StoppedFlow() - Constructor for class stoppedFlow.StoppedFlow
 
stopSimulation() - Method in class calorimeter.Calorimeter
Stops the simulation, but not change is made to the temperature or to the appearance of the calorimeter
stopSimulation() - Method in class spectrophotometer.Spectrophotometer
Stops the simulation.
stopSimulation() - Method in class stoppedFlow.StoppedFlow
Stops the simulation.
stopTimer() - Method in class spectrophotometer.Spectrophotometer
Stops the timer.
submitData() - Method in class chemEquilibria.ChemEquilibria
Submits experimental data to a titration object

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