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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
 
cellA - Variable in class showStructure.UnitCell
 
cellB - Variable in class showStructure.UnitCell
 
cellC - Variable in class showStructure.UnitCell
 
cellPts - Variable in class showStructure.UnitCell
 
cellTG - Variable in class showStructure.UnitCell
 
cellType - Variable in class showStructure.UnitCell
 
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.
charge - Variable in class edu.davidson.chm.equilibria.ChemSpecies
 
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
 
chemSpecies - Variable in class edu.davidson.chm.equilibria.Species
 
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
chemSystem - Variable in class edu.davidson.chm.equilibria.Phase
 
chemSystem - Variable in class edu.davidson.chm.equilibria.Species
 
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.
creaseAngle - Variable in class showStructure.SegmentGroup
 
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.
createArrays() - Method in class edu.davidson.chm.waveFunction.Gaussian
 
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.
createEquations() - Method in class edu.davidson.chm.equilibria.Equilibria
Constructs the mass balance, charge-balance, and equilibrium equations for this chemical system.
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
 

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