Package org.jmol.minimize.forcefield
Class CalculationsUFF
java.lang.Object
org.jmol.minimize.forcefield.Calculations
org.jmol.minimize.forcefield.CalculationsUFF
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Field Summary
FieldsModifier and TypeFieldDescription(package private) Calculation
(package private) Calculation
(package private) static final double
(package private) static final double
(package private) static final double
(package private) static final double
(package private) static final double
(package private) Calculation
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) Calculation
(package private) Calculation
Fields inherited from class org.jmol.minimize.forcefield.Calculations
ac, angleCount, bondCount, CALC_ANGLE, CALC_DISTANCE, CALC_ES, CALC_MAX, CALC_OOP, CALC_STRETCH_BEND, CALC_TORSION, CALC_VDW, calculations, da, db, dc, dd, DEG_TO_RAD, ff, ffParams, gradients, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, minAngles, minAtoms, minBonds, minTorsions, parA, parB, parC, RAD_TO_DEG, silent, torsionCount, v1, v2, v3
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Constructor Summary
ConstructorsConstructorDescriptionCalculationsUFF
(ForceField ff, Map<Object, Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints) -
Method Summary
Modifier and TypeMethodDescription(package private) static double
calculateR0
(double ri, double rj, double chiI, double chiJ, double bondorder) (package private) double
(package private) String
getDebugHeader
(int iType) protected Object
(package private) String
getUnits()
private static boolean
isInvertible
(int n) (package private) boolean
Methods inherited from class org.jmol.minimize.forcefield.Calculations
addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugHeader2, getDebugLine, getDebugLineC, getLogData, getParameter, isLinear, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables
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Field Details
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KCAL332
static final double KCAL332- See Also:
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KCAL644
static final double KCAL644- See Also:
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KCAL6
static final double KCAL6- See Also:
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KCAL22
static final double KCAL22- See Also:
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KCAL44
static final double KCAL44- See Also:
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PAR_R
static final int PAR_R- See Also:
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PAR_THETA
static final int PAR_THETA- See Also:
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PAR_X
static final int PAR_X- See Also:
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PAR_D
static final int PAR_D- See Also:
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PAR_ZETA
static final int PAR_ZETA- See Also:
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PAR_Z
static final int PAR_Z- See Also:
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PAR_V
static final int PAR_V- See Also:
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PAR_U
static final int PAR_U- See Also:
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PAR_XI
static final int PAR_XI- See Also:
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PAR_HARD
static final int PAR_HARD- See Also:
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PAR_RADIUS
static final int PAR_RADIUS- See Also:
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bondCalc
Calculation bondCalc -
angleCalc
Calculation angleCalc -
torsionCalc
Calculation torsionCalc -
oopCalc
Calculation oopCalc -
vdwCalc
Calculation vdwCalc
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Constructor Details
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CalculationsUFF
CalculationsUFF(ForceField ff, Map<Object, Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
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Method Details
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getUnits
String getUnits()- Specified by:
getUnits
in classCalculations
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setupCalculations
boolean setupCalculations()- Specified by:
setupCalculations
in classCalculations
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isInvertible
private static boolean isInvertible(int n) -
calculateR0
static double calculateR0(double ri, double rj, double chiI, double chiJ, double bondorder) -
compute
- Specified by:
compute
in classCalculations
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getDebugHeader
- Specified by:
getDebugHeader
in classCalculations
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getParameterObj
- Specified by:
getParameterObj
in classCalculations
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