Package org.jmol.minimize.forcefield
Class CalculationsMMFF
- java.lang.Object
-
- org.jmol.minimize.forcefield.Calculations
-
- org.jmol.minimize.forcefield.CalculationsMMFF
-
class CalculationsMMFF extends Calculations
- Author:
- Bob Hanson 5/10/12 - 5/15/12
-
-
Field Summary
Fields Modifier and Type Field Description (package private) Calculation
angleCalc
(package private) Calculation
bondCalc
static int
DA_D
static int
DA_DA
(package private) Calculation
esCalc
(package private) static double
FPAR
(package private) ForceFieldMMFF
mmff
(package private) Calculation
oopCalc
(package private) Calculation
sbCalc
(package private) Calculation
torsionCalc
(package private) Calculation
vdwCalc
-
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
-
-
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<MMConstraint> constraints)
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) double
compute(int iType, java.lang.Object[] dataIn)
(package private) java.lang.String
getDebugHeader(int iType)
(package private) java.lang.String
getDebugLine(int iType, Calculation c)
(package private) java.lang.Object
getParameterObj(MinObject a)
(package private) java.lang.String
getUnits()
private static boolean
isInvertible(MinAtom a)
protected boolean
isLinear(int i)
(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, getDebugHeader2, getDebugLineC, getLogData, getParameter, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables
-
-
-
-
Field Detail
-
FPAR
static final double FPAR
- See Also:
- Constant Field Values
-
DA_D
public static final int DA_D
- See Also:
- Constant Field Values
-
DA_DA
public static final int DA_DA
- See Also:
- Constant Field Values
-
bondCalc
Calculation bondCalc
-
angleCalc
Calculation angleCalc
-
torsionCalc
Calculation torsionCalc
-
oopCalc
Calculation oopCalc
-
vdwCalc
Calculation vdwCalc
-
esCalc
Calculation esCalc
-
sbCalc
Calculation sbCalc
-
mmff
ForceFieldMMFF mmff
-
-
Constructor Detail
-
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<MMConstraint> constraints)
-
-
Method Detail
-
getUnits
java.lang.String getUnits()
- Specified by:
getUnits
in classCalculations
-
setupCalculations
boolean setupCalculations()
- Specified by:
setupCalculations
in classCalculations
-
isLinear
protected boolean isLinear(int i)
- Overrides:
isLinear
in classCalculations
- Returns:
- T/F
-
isInvertible
private static boolean isInvertible(MinAtom a)
-
compute
double compute(int iType, java.lang.Object[] dataIn)
- Specified by:
compute
in classCalculations
-
getParameterObj
java.lang.Object getParameterObj(MinObject a)
- Specified by:
getParameterObj
in classCalculations
-
getDebugHeader
java.lang.String getDebugHeader(int iType)
- Specified by:
getDebugHeader
in classCalculations
-
getDebugLine
java.lang.String getDebugLine(int iType, Calculation c)
- Overrides:
getDebugLine
in classCalculations
-
-