Package org.jmol.minimize.forcefield
Class CalculationsMMFF
- java.lang.Object
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- org.jmol.minimize.forcefield.Calculations
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- org.jmol.minimize.forcefield.CalculationsMMFF
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class CalculationsMMFF extends Calculations
- Author:
- Bob Hanson 5/10/12 - 5/15/12
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Field Summary
Fields Modifier and Type Field Description (package private) CalculationangleCalc(package private) CalculationbondCalcstatic intDA_Dstatic intDA_DA(package private) CalculationesCalc(package private) static doubleFPAR(package private) ForceFieldMMFFmmff(package private) CalculationoopCalc(package private) CalculationsbCalc(package private) CalculationtorsionCalc(package private) CalculationvdwCalc-
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, constraints, da, db, dc, dd, DEG_TO_RAD, ff, ffParams, gradients, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, minAngles, minAtoms, minBonds, minPositions, minTorsions, parA, parB, parC, RAD_TO_DEG, silent, torsionCount, v1, v2, v3
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Constructor Summary
Constructors Constructor Description CalculationsMMFF(ForceField ff, java.util.Map<java.lang.Object,java.lang.Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<java.lang.Object[]> constraints)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) doublecompute(int iType, java.lang.Object[] dataIn)(package private) java.lang.StringgetDebugHeader(int iType)(package private) java.lang.StringgetDebugLine(int iType, Calculation c)(package private) java.lang.ObjectgetParameterObj(MinObject a)(package private) java.lang.StringgetUnits()private static booleanisInvertible(MinAtom a)protected booleanisLinear(int i)(package private) booleansetupCalculations()-
Methods inherited from class org.jmol.minimize.forcefield.Calculations
addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugHeader2, getDebugLineC, getLogData, getParameter, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables
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Field Detail
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FPAR
static final double FPAR
- See Also:
- Constant Field Values
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DA_D
public static final int DA_D
- See Also:
- Constant Field Values
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DA_DA
public static final int DA_DA
- See Also:
- Constant Field Values
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bondCalc
Calculation bondCalc
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angleCalc
Calculation angleCalc
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torsionCalc
Calculation torsionCalc
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oopCalc
Calculation oopCalc
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vdwCalc
Calculation vdwCalc
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esCalc
Calculation esCalc
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sbCalc
Calculation sbCalc
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mmff
ForceFieldMMFF mmff
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Constructor Detail
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CalculationsMMFF
CalculationsMMFF(ForceField ff, java.util.Map<java.lang.Object,java.lang.Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<java.lang.Object[]> constraints)
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Method Detail
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getUnits
java.lang.String getUnits()
- Specified by:
getUnitsin classCalculations
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setupCalculations
boolean setupCalculations()
- Specified by:
setupCalculationsin classCalculations
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isLinear
protected boolean isLinear(int i)
- Overrides:
isLinearin classCalculations- Returns:
- T/F
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isInvertible
private static boolean isInvertible(MinAtom a)
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compute
double compute(int iType, java.lang.Object[] dataIn)- Specified by:
computein classCalculations
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getParameterObj
java.lang.Object getParameterObj(MinObject a)
- Specified by:
getParameterObjin classCalculations
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getDebugHeader
java.lang.String getDebugHeader(int iType)
- Specified by:
getDebugHeaderin classCalculations
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getDebugLine
java.lang.String getDebugLine(int iType, Calculation c)- Overrides:
getDebugLinein classCalculations
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