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

A

acid - Variable in class edu.davidson.chm.equilibria.Solution
 
addAcidBaseSpecies(String, double, double, int, String, double) - Method in class chemEquilibria.ChemEquilibria
Creates a series of acid-base species and adds the species to a solution.
addBond(Atom) - Method in class showMol.Wire
Adds a wire from the central atom (defined in the constructor) to the specified atom.
addCellAtoms(float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Adds atoms centered on cell positions
addCircle(double, double, int, boolean) - Method in class electronDensity.ElectronDensity
Adds a circle to the electron density plot.
addCircle(double, double, int, boolean, int, int, int) - Method in class electronDensity.ElectronDensity
Adds a circle to the electron density plot.
addComplexes(String, double, double, String, double, double, int, String, double) - Method in class chemEquilibria.ChemEquilibria
Creates a series of metal-ligand complexes and adds the species to a solution.
addData(SDataSource, int, double[], double[]) - Method in class balance.Balance
Adds an array of data points via DataConnections.
addData(SDataSource, int, double[], double[]) - Method in class data.Data
SDataListener Method: Use to submit an array of data points Calls the JavaScript method addData
addData(double[], double[]) - Method in class data.DataSet
Adds an array of data points to the dataSet
addData(SDataSource, int, double[], double[]) - Method in class manometer.Manometer
Adds an array of data points via DataConnections.
addData(SDataSource, int, double[], double[]) - Method in class piston.Piston
Adds an array of data points via DataConnections.
addData(SDataSource, int, double[], double[]) - Method in class piston3.Piston3
Adds an array of data points via DataConnections.
addData(SDataSource, int, double[], double[]) - Method in class thermometer.Thermometer
Adds an array of data points via DataConnections.
addDataSet(String, int) - Method in class data.Data
Adds a new Data Set with identification id.
addDatum(SDataSource, int, double, double) - Method in class balance.Balance
The data source and id are not used.
addDatum(double, double) - Method in class chemEquilibria.ChemEquilibria
Adds a Vt, pX data point to the data set.
addDatum(double, double, double) - Method in class chemEquilibria.ChemEquilibria
Adds a Vt, pX data point to the data set.
addDatum(SDataSource, int, double, double) - Method in class data.Data
SDataListener Method: Use to submit a single data point Calls JavaScript method addDatum
addDatum(double, double) - Method in class data.DataSet
Adds a data point to the dataSet
addDatum(SDataSource, int, double, double) - Method in class manometer.Manometer
The data source and id are not used.
addDatum(SDataSource, int, double, double) - Method in class piston.Piston
The data source and id are not used.
addDatum(SDataSource, int, double, double) - Method in class piston3.Piston3
The data source and id are not used.
addDatum(SDataSource, int, double, double) - Method in class thermometer.Thermometer
Adds a data point via DataConnections.
addGaussian(int, double, double) - Method in class electronDensity.ElectronDensity
Adds an existing gaussian wave function to the collection of wave functions used to construct the hybrid orbital.
addHalfReaction(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Creates a half-reaction and adds it to the chemical system.
addHalfReaction(HalfReaction) - Method in class edu.davidson.chm.equilibria.ChemSystem
Adds a half-reaction to the chemical system
addHalfReaction(String, String, double) - Method in class edu.davidson.chm.equilibria.ChemSystem
Creates a new half-reaction and adds the half-reaction to the chemical system The reaction is described by a string in the conventional chemical notation.
addHoleAtoms(int, float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Adds atoms centered on hole positions
addLayer(int, int, float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Creates a layer of closest-packed atoms in the plane at z = 0;
addLine(double, double, double, double, double, double) - Method in class showMol.ShowMol
Creates a line between two points with the pre-defined emissive color.
addLineGroup(Point3d[]) - Method in class showStructure.ShowStructure
 
addLineGroup(double, double, double, double, double, double) - Method in class showStructure.ShowStructure
 
addMolecule(String) - Method in class showMol.ShowMol
Adds a molecule to the display.
addMolecule(String, int) - Method in class showMol.ShowMol
Adds a molecule to the display.
addMolecule(String, int, int) - Method in class showMol.ShowMol
Adds a molecule to the display.
addMoleculeRotation(int, double, double, double, double) - Method in class showMol.ShowMol
Rotates the selected molecule.
addNLM(int, int, int, double, double) - Method in class electronDensity.ElectronDensity
Adds a new hydrogenic wave function using the user-supplied quantum numbers.
addNML(int, int, int, double, double) - Method in class edu.davidson.chm.waveFunction.HybridWaveFunction
Adds a hydrogenic wave function to the hybrid wave function
addPar(String, String, String) - Method in class chemEquilibria.ChemEquilibria
Adds a parameter to be optimized in the curve-fitting procedure.
addPhase(Phase) - Method in class edu.davidson.chm.equilibria.ChemSystem
Adds a existing phase to the chemical system
addPoints(float, int, int) - Method in class showStructure.ShowStructure
Adds a layer of points for a closest-packed structure
addReaction(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Creates a chemical reaction and adds it to the chemical system.
addReaction(Reaction) - Method in class edu.davidson.chm.equilibria.ChemSystem
Adds an existing reaction to the chemical system
addReaction(String, String, double) - Method in class edu.davidson.chm.equilibria.ChemSystem
Creates a new reaction and adds the reaction to the chemical system The reaction is described by a string in the conventional chemical notation.
addReaction(Reaction) - Method in class edu.davidson.chm.equilibria.Titration
Adds a reaction to the collection of reactions whose equilibrium constants are to be determined by the curve-fitting procedure.
addRotation(double, double, double, double) - Method in class showMol.Molecule
Rotates the molecule about its center.
addSegments(int, float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Creates a set of sphere segments (sphere center at the origin) ns = -1 atoms in center unit cell layer of an hcp structure ns = 0 atoms on vertices of hexagonal cell ns = 2 sphere cut into halves by xy plane ns = 4 sphere cut into quarters by xy and xz planes ns = 6 sphere cut into sixths by xy plane and phi = 0, 120, and 240 degrees ns = 8 sphere cut into eighths by xy, xz, and yz planes
addSegmentsD(float, float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer of an hcp structure
addSegmentsS(float, float, float, float, float, float, float, float) - Method in class showStructure.ShowStructure
Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer in a tetragonal cell
addSpecial(int) - Method in class showMol.ShowMol
Adds a Molecule based upon one of the special, pre-defined settings.
addSpecies(String, String, double) - Method in class chemEquilibria.ChemEquilibria
Adds the specified amount of a ChemSpecies to a Phase.
addSpecies(String, double, String, double) - Method in class chemEquilibria.ChemEquilibria
Adds the specified amount of a ChemSpecies to a Phase.
addSpecies(Species) - Method in class edu.davidson.chm.equilibria.Phase
Adds a Species to the phase.
addSpecies(ChemSpecies, double) - Method in class edu.davidson.chm.equilibria.Phase
Adds more of an existing ChemSpecies to the phase.
addSpecies(String, double) - Method in class edu.davidson.chm.equilibria.Phase
Adds more of an existing ChemSpecies to the phase.
addSpecies(Species) - Method in class edu.davidson.chm.equilibria.Titration
Adds a species to the collection of species whose analytical moles are to be determined by the curve-fitting procedure.
addSphere(float, float, float, float) - Method in class showMol.ShowMol
Adds a sphere to the display.
addWaveFunction(WaveFunction, double, double) - Method in class edu.davidson.chm.waveFunction.HybridWaveFunction
Adds a wave function to the hybrid wave function.
addWaveFunction(WaveFunction, double, double) - Method in class electronDensity.ElectronDensity
Adds a new wave function to the collection of wave functions used to construct the hybrid orbital.
alignAtomAndPoint(int, int, int) - Method in class showStructure.ShowStructure
 
alignOrbitals() - Method in class showHybrid.ShowHybrid
For matched sphere geometries and orbitals sets, rotates the orbitals to place the z-axis along the highest axis of symmetry for the sphere geometry.
alpha - Variable in class showStructure.UnitCell
 
ambientColor - Variable in class showStructure.PointGroup
 
ambientColor - Variable in class showStructure.SegmentGroup
 
ambientColor - Variable in class showStructure.UnitCell
 
analMoles - Variable in class edu.davidson.chm.equilibria.Species
 
apply() - Method in class chemEquilibria.ChemEquilibria
Applies the best-fit parameters from the last curve-fitting procedure to the Reaction and Species objects.
apply() - Method in class edu.davidson.chm.equilibria.Titration
Applies the best-fit parameters to the original ChemSystem.
AqueousSolution - Class in edu.davidson.chm.equilibria
Creates an aqueous solution phase.
AqueousSolution() - Constructor for class edu.davidson.chm.equilibria.AqueousSolution
 
AqueousSolution(ChemSystem) - Constructor for class edu.davidson.chm.equilibria.AqueousSolution
Creates an aqueous solution.
AqueousSolution(String, ChemSystem) - Constructor for class edu.davidson.chm.equilibria.AqueousSolution
Creates an aqueous solution.
Arrow - Class in showHybrid
 
Arrow() - Constructor for class showHybrid.Arrow
 
Arrow(int) - Constructor for class showHybrid.Arrow
Creates a single or double arrow
assemblePieces() - Method in class showStructure.ShowStructure
 
Atom - Class in showIsosurface
The Atom class creates a TransformGroup object that locates the position of the atom and a Switch object that contains one or more Orbital Representations.
Atom() - Constructor for class showIsosurface.Atom
Creates an Atom object with the atom located at the origin.
Atom(double, double, double) - Constructor for class showIsosurface.Atom
Creates an Atom object with the atom located at the specified position.
Atom - Class in showMol
Atom contains the coordinate and display properties for an atom.
Atom() - Constructor for class showMol.Atom
The default constructor creates an Atom object for an unspecified element (X) located at the origin.
Atom(String, double, double, double) - Constructor for class showMol.Atom
The Atom object is created for the element identified by its symbol at the specified location.
Atom(int, double, double, double) - Constructor for class showMol.Atom
The Atom object is created for the element identified by its atomic number at the specified location.
AtomGroup - Class in showStructure
 
AtomGroup() - Constructor for class showStructure.AtomGroup
Default constructor is not usable
AtomGroup(UnitCell, int, float, Color3f, Color3f) - Constructor for class showStructure.AtomGroup
Creates sets of atoms for a unit cell.
AtomGroup(int, int, float, Color3f, Color3f) - Constructor for class showStructure.AtomGroup
Creates a single layer of closest-packed atoms
atomRA - Variable in class showStructure.AtomGroup
 
atomTG - Variable in class showStructure.AtomGroup
 
atomTransformGroup - Variable in class showStructure.AtomGroup
 
autoChargeBalance - Variable in class edu.davidson.chm.equilibria.Phase
 
autodissociation - Variable in class edu.davidson.chm.equilibria.Solution
 
autoScaleMax(boolean) - Method in class thermometer.Thermometer
Sets autoscale feature for the maximum temperature.
autoScaleMin(boolean) - Method in class thermometer.Thermometer
Sets autoscale feature for the minimum temperature.

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