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

C

calc(double[]) - Method in class edu.davidson.chm.equilibria.Titration

Calculates a titration curve at the titrant volumes contained in _Vt.

calcCurve(double) - Method in class edu.davidson.chm.equilibria.Titration

Calculates the titration curve.

calculate(double) - Method in class chemEquilibria.ChemEquilibria

Calculates a theoretical titration curve

callJavaScript(boolean) - Method in class data.Data

Determines whether JavaScript addData and addDatum functions are automatically called.

calorimeter - package calorimeter

Calorimeter - Class in calorimeter

This applet draws a calorimeter (there are three styles available) and simulates a calorimetry experiment.
Style 0 shows no calorimeter (blank applet box)
Style 1 shows a standard calorimeter.
Style 2 shows a thermos-type calorimeter.
Style 3 shows a bomb calorimeter.
Style 4 shows a thermos-type calorimeter with a reservoir that drains into the calorimeter.

Configurable Options include the sample, a heating filament, and a stirrer.

The applet serves as a DataSource (DataConnections) that supplies time-temperature data during the experiment.

Temperature and energy are in arbitrary units, but typically one would use ^oC and joules.

Calorimeter() - Constructor for class calorimeter.Calorimeter

CENTERED - Static variable in class showMol.ShowMol

centerMolecule() - Method in class showMol.Molecule

Positions the molecule so that the average atomic coordinates are at the origin.

centerMolecule(int) - Method in class showMol.ShowMol

Centers the specified molecule.

centerMoleculeOnAtom(int) - Method in class showMol.Molecule

Positions the molecule so that the specified atom is positioned at the origin.

centerMoleculeOnAtom(int, int) - Method in class showMol.ShowMol

Translates the indicated molecule so that the specified atom is at the origin.

centerSpheres() - Method in class showMol.ShowMol

Translates all spheres so that the center of the set lies at the origin.

chemEquilibria - package chemEquilibria

ChemEquilibria - Class in chemEquilibria

This applet provides a web page interface for the edu.davidson.chm.equilibria package.

ChemEquilibria() - Constructor for class chemEquilibria.ChemEquilibria

ChemSpecies - Class in edu.davidson.chm.equilibria

A ChemicalSpecies is a molecule or ion.

ChemSpecies() - Constructor for class edu.davidson.chm.equilibria.ChemSpecies

ChemSpecies(String, double, double) - Constructor for class edu.davidson.chm.equilibria.ChemSpecies

ChemSystem - Class in edu.davidson.chm.equilibria

Chemical Equilibria Problem Solver

ChemSystem() - Constructor for class edu.davidson.chm.equilibria.ChemSystem

Creates a chemical system using the default parameters

ChemSystem(String) - Constructor for class edu.davidson.chm.equilibria.ChemSystem

Creates a chemical system using user-defined parameters

ChemSystem(String, double, double) - Constructor for class edu.davidson.chm.equilibria.ChemSystem

Creates a chemical system using user-defined parameters

Circle - Class in electronDensity

This class paints a circle on the electron density plot

Circle() - Constructor for class electronDensity.Circle

Circle(double, double) - Constructor for class electronDensity.Circle

Circle(double, double, int) - Constructor for class electronDensity.Circle

Circle(double, double, int, Color) - Constructor for class electronDensity.Circle

Circle(double, double, int, Color, boolean) - Constructor for class electronDensity.Circle

clear() - Method in class chemEquilibria.ChemEquilibria

Clears the entire chemical system and resets the properties for a new calculation.

clear() - Method in class edu.davidson.chm.waveFunction.HybridWaveFunction

Clears the wave functions making up the hybrid wave function.

clearBonds() - Method in class showMol.Wire

Removes all bonds to the central atom.

clearCircles() - Method in class electronDensity.ElectronDensity

Clears all circles

clearCoefficients() - Method in class stoppedFlow.StoppedFlow

Sets all stoichiometric coefficients to zero, except for that of species 0, which is set to -1.

clearColors() - Method in class stoppedFlow.StoppedFlow

Sets the color for all species to the background color

clearConcentrationsA() - Method in class stoppedFlow.StoppedFlow

Sets the concentrations of all species in the syringe A solution to zero.

clearConcentrationsB() - Method in class stoppedFlow.StoppedFlow

Sets the concentrations of all species in the syringe B solution to zero.

clearData() - Method in class chemEquilibria.ChemEquilibria

Clears the data to be fit in the curve-fitting procedure.

clearData() - Method in class data.DataSet

Clears all of the data in the set

clearMessages() - Method in class edu.davidson.chm.equilibria.Equilibria

Clears the message list

clearMolarAbsorptivities() - Method in class stoppedFlow.StoppedFlow

Sets all molar absorptivities to zero.

clearMouse() - Method in class showMol.ShowMol

Clears the mouse transformations.

clearParameters() - Method in class chemEquilibria.ChemEquilibria

Clears the parameters to be optimized in the curve-fitting procedure.

clearRateLaw() - Method in class stoppedFlow.StoppedFlow

Sets all exponents in the rate law to zero.

clearReactions() - Method in class edu.davidson.chm.equilibria.Titration

Clears all reactions to be used in the curve-fitting procedure

clearRotation() - Method in class showMol.Molecule

Resets the rotation portion of the transform.

clearRotation(int) - Method in class showMol.ShowMol

Clears the rotation component of the transform for this specified molecule.

clearSeries(int) - Method in class balance.Balance

This method is required by SDataListener but is not used in this class.

clearSeries(int) - Method in class data.Data

SDataListener Method: Clears the specified data set.

clearSeries(int) - Method in class manometer.Manometer

This method is required by SDataListener but is not used in this class.

clearSeries(int) - Method in class piston.Piston

This method is required by SDataListener but is not used in this class.

clearSeries(int) - Method in class piston3.Piston3

This method is required by SDataListener but is not used in this class.

clearSeries(int) - Method in class thermometer.Thermometer

This method is required by SDataListener but is not used in this class.

clearSpecies() - Method in class edu.davidson.chm.equilibria.Titration

Clears all species to be used in the curve-fitting procedure

COM - Static variable in class showMol.ShowMol

compile() - Method in class showIsosurface.Orbital

Compiles the orbital BranchGroup.

copyOf(String) - Method in class edu.davidson.chm.equilibria.ChemSystem

Returns a new ChemSystem with the indicated label.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Gas

Creates a copy of this phase and places it in the indicated ChemSystem.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.HalfReaction

Returns a copy of the HalfReaction.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Liquid

Creates a copy of this phase and places it in the indicated ChemSystem.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Phase

Creates a copy of the phase and places it in the indicated ChemSystem.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Reaction

Returns a copy of the Reaction.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Solid

Creates a copy of this phase and places it in the indicated ChemSystem.

copyOf(ChemSystem) - Method in class edu.davidson.chm.equilibria.Solution

Creates a copy of this phase and places it in the indicated ChemSystem.

createAcidBase(String, double, double, int) - Static method in class edu.davidson.chm.equilibria.ChemSpecies

Returns an array of ChemSpecies for a sequence of acid-base reactions.

createAcidBaseSpecies(Phase, ChemSpecies[], double[], double[], String) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates a series of acid-base species and adds the acid-base species to _phase and the acid-base reactions to the chemical system.

createAqueousPhase(String, double) - Method in class chemEquilibria.ChemEquilibria

Creates an aqueous solution phase.

createAqueousPhase(String, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds an aqueous solution to the chemical system.

createBonds(Vector<Atom>, Vector<Bond>, Vector<Wire>) - Static method in class showMol.MoleculeLoader

Creates Bonds for the a set of atoms based upon proximity.

CREATEBONDS - Static variable in class showMol.ShowMol

createChemSpecies(String, double, double) - Method in class chemEquilibria.ChemEquilibria

Creates a new ChemSpecies.

createChemSpecies(String) - Static method in class edu.davidson.chm.equilibria.ChemSpecies

Returns a ChemSpecies based upon the properties defined by the string (_data).

createComplexationSpecies(Phase, ChemSpecies[], double[], double[], String) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates a series of complex species and adds the complex species to _phase and the complexation reactions to the chemical system.

createComplexes(String, double, double, String, double, double, int) - Static method in class edu.davidson.chm.equilibria.ChemSpecies

Returns an array of ChemSpecies for a sequence of complexation reactions.

createGasPhase(String, double) - Method in class chemEquilibria.ChemEquilibria

Creates a gas phase containing no species (i.e., a vacuum).

createGasPhase(String) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a gas to the chemical system.

createGasPhase(String, ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a gas to the chemical system.

createGaussian(int, int, String) - Method in class electronDensity.ElectronDensity

Creates a Gaussian basis function with the given id number.

createLiquidPhase(String, String, double) - Method in class chemEquilibria.ChemEquilibria

Creates a liquid phase (pure substance).

createLiquidPhase(ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a liquid to the chemical system.

createLiquidPhase(String, ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a liquid to the chemical system.

createOrbital(int) - Method in class showIsosurface.Atom

Creates a new Orbital object containing no isosurfaces

createOrbital(int, URL) - Method in class showIsosurface.Atom

Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file

createOrbital(int, URL, int) - Method in class showIsosurface.Atom

Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files

createOrbital(int, int) - Method in class showIsosurface.ShowIsosurface

Creates a new Orbital object containing no isosurfaces

createOrbital(int, int, String) - Method in class showIsosurface.ShowIsosurface

Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file

createOrbital(int, int, String, int) - Method in class showIsosurface.ShowIsosurface

Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files

createSolidPhase(String, String, double) - Method in class chemEquilibria.ChemEquilibria

Creates a solid phase (pure substance).

createSolidPhase(ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a solid to the chemical system.

createSolidPhase(String, ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a solid to the chemical system.

createSolutionPhase(String, String, double) - Method in class chemEquilibria.ChemEquilibria

Creates an aprotic solution phase.

createSolutionPhase(String, String, double, double) - Method in class chemEquilibria.ChemEquilibria

Creates a protic solution phase.

createSolutionPhase(String, String, String, String, double, double) - Method in class chemEquilibria.ChemEquilibria

Creates a protic solution phase.

createSolutionPhase(String, ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a solution to the chemical system.

createSolutionPhase(String, ChemSpecies, double, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a solution to the chemical system.

createSolutionPhase(String, ChemSpecies, ChemSpecies, ChemSpecies, double, double) - Method in class edu.davidson.chm.equilibria.ChemSystem

Creates and adds a solution to the chemical system.

createSpecies(ChemSpecies[], double[]) - Method in class edu.davidson.chm.equilibria.Phase

Creates a series of new Species and adds them to the Phase.

createSpecies(ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.Phase

Creates a new Species and adds it to the Phase.

createTitration(String, String) - Method in class chemEquilibria.ChemEquilibria

Create a Titration object using the current chemical system.

CUBE - Static variable in class showMol.ShowMol