class CalculationsMMFF extends Calculations
Modifier and Type | Field and 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 |
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
Constructor and 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) |
Modifier and Type | Method and 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() |
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
static final double FPAR
public static final int DA_D
public static final int DA_DA
Calculation bondCalc
Calculation angleCalc
Calculation torsionCalc
Calculation oopCalc
Calculation vdwCalc
Calculation esCalc
Calculation sbCalc
ForceFieldMMFF mmff
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)
java.lang.String getUnits()
getUnits
in class Calculations
boolean setupCalculations()
setupCalculations
in class Calculations
protected boolean isLinear(int i)
isLinear
in class Calculations
private static boolean isInvertible(MinAtom a)
double compute(int iType, java.lang.Object[] dataIn)
compute
in class Calculations
java.lang.Object getParameterObj(MinObject a)
getParameterObj
in class Calculations
java.lang.String getDebugHeader(int iType)
getDebugHeader
in class Calculations
java.lang.String getDebugLine(int iType, Calculation c)
getDebugLine
in class Calculations