org.jmol.minimize.forcefield

Class CalculationsUFF

java.lang.Object

org.jmol.minimize.forcefield.Calculations

org.jmol.minimize.forcefield.CalculationsUFF

 class CalculationsUFF
extends Calculations

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	CalculationsUFF.AngleCalc
(package private) class	CalculationsUFF.DistanceCalc
(package private) class	CalculationsUFF.OOPCalc
(package private) class	CalculationsUFF.TorsionCalc
(package private) class	CalculationsUFF.VDWCalc

Nested classes/interfaces inherited from class org.jmol.minimize.forcefield.Calculations

Calculations.PairCalc

Field Summary

Fields

Modifier and Type	Field and Description
(package private) CalculationsUFF.AngleCalc	angleCalc
(package private) CalculationsUFF.DistanceCalc	bondCalc
private java.util.Map<java.lang.Object,FFParam>	ffParams
(package private) static double	KCAL22
(package private) static double	KCAL332
(package private) static double	KCAL44
(package private) static double	KCAL6
(package private) static double	KCAL644
(package private) CalculationsUFF.OOPCalc	oopCalc
static int	PAR_D
static int	PAR_HARD
static int	PAR_R
static int	PAR_RADIUS
static int	PAR_THETA
static int	PAR_U
static int	PAR_V
static int	PAR_X
static int	PAR_XI
static int	PAR_Z
static int	PAR_ZETA
protected FFParam	parA
protected FFParam	parB
protected FFParam	parC
(package private) CalculationsUFF.TorsionCalc	torsionCalc
(package private) CalculationsUFF.VDWCalc	vdwCalc

Fields inherited from class org.jmol.minimize.forcefield.Calculations

angleCount, atomCount, bondCount, CALC_ANGLE, CALC_DISTANCE, CALC_ES, CALC_MAX, CALC_OOP, CALC_STRETCH_BEND, CALC_TORSION, CALC_VDW, calculations, constraints, da, db, dc, dd, DEG_TO_RAD, ff, gradients, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, minAngles, minAtoms, minBonds, minTorsions, RAD_TO_DEG, silent, torsionCount, v1, v2, v3

Constructor Summary

Constructors

Constructor and Description
CalculationsUFF(ForceField ff, java.util.Map<java.lang.Object,FFParam> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, java.util.List<java.lang.Object[]> constraints)

Method Summary

Methods

Modifier and Type	Method and Description
(package private) static double	calculateR0(double ri, double rj, double chiI, double chiJ, double bondorder)
(package private) double	compute(int iType, java.lang.Object[] dataIn)
(package private) java.lang.String	getDebugHeader(int iType)
(package private) FFParam	getParameter(java.lang.Object a)
(package private) java.lang.String	getUnits()
private static boolean	isInvertible(int n)
(package private) boolean	setupCalculations()

Methods inherited from class org.jmol.minimize.forcefield.Calculations

addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugLine, getLogData, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ffParams

private java.util.Map<java.lang.Object,FFParam> ffParams

parA

protected FFParam parA

parB

protected FFParam parB

parC

protected FFParam parC

PAR_R

public static final int PAR_R

See Also:

Constant Field Values

PAR_THETA

public static final int PAR_THETA

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Constant Field Values

PAR_X

public static final int PAR_X

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Constant Field Values

PAR_D

public static final int PAR_D

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Constant Field Values

PAR_ZETA

public static final int PAR_ZETA

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Constant Field Values

PAR_Z

public static final int PAR_Z

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Constant Field Values

PAR_V

public static final int PAR_V

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Constant Field Values

PAR_U

public static final int PAR_U

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Constant Field Values

PAR_XI

public static final int PAR_XI

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Constant Field Values

PAR_HARD

public static final int PAR_HARD

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Constant Field Values

PAR_RADIUS

public static final int PAR_RADIUS

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Constant Field Values

bondCalc

CalculationsUFF.DistanceCalc bondCalc

angleCalc

CalculationsUFF.AngleCalc angleCalc

torsionCalc

CalculationsUFF.TorsionCalc torsionCalc

oopCalc

CalculationsUFF.OOPCalc oopCalc

vdwCalc

CalculationsUFF.VDWCalc vdwCalc

KCAL332

static final double KCAL332

See Also:

Constant Field Values

KCAL644

static final double KCAL644

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Constant Field Values

KCAL6

static final double KCAL6

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Constant Field Values

KCAL22

static final double KCAL22

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Constant Field Values

KCAL44

static final double KCAL44

See Also:

Constant Field Values

Constructor Detail

CalculationsUFF

CalculationsUFF(ForceField ff,
               java.util.Map<java.lang.Object,FFParam> ffParams,
               MinAtom[] minAtoms,
               MinBond[] minBonds,
               MinAngle[] minAngles,
               MinTorsion[] minTorsions,
               java.util.List<java.lang.Object[]> constraints)

Method Detail

getUnits

java.lang.String getUnits()

Specified by:

getUnits in class Calculations

setupCalculations

boolean setupCalculations()

Specified by:

setupCalculations in class Calculations

isInvertible

private static boolean isInvertible(int n)

calculateR0

static double calculateR0(double ri,
                 double rj,
                 double chiI,
                 double chiJ,
                 double bondorder)

compute

double compute(int iType,
             java.lang.Object[] dataIn)

Specified by:

compute in class Calculations

getParameter

FFParam getParameter(java.lang.Object a)

getDebugHeader

java.lang.String getDebugHeader(int iType)

Overrides:

getDebugHeader in class Calculations