class CalculationsUFF extends Calculations
| Modifier and Type | Field and Description |
|---|---|
(package private) Calculation |
angleCalc |
(package private) Calculation |
bondCalc |
(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) Calculation |
oopCalc |
(package private) static int |
PAR_D |
(package private) static int |
PAR_HARD |
(package private) static int |
PAR_R |
(package private) static int |
PAR_RADIUS |
(package private) static int |
PAR_THETA |
(package private) static int |
PAR_U |
(package private) static int |
PAR_V |
(package private) static int |
PAR_X |
(package private) static int |
PAR_XI |
(package private) static int |
PAR_Z |
(package private) static int |
PAR_ZETA |
(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, 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 and Description |
|---|
CalculationsUFF(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) |
| 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) |
protected java.lang.Object |
getParameterObj(MinObject o) |
(package private) java.lang.String |
getUnits() |
private static boolean |
isInvertible(int n) |
(package private) boolean |
setupCalculations() |
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, setTorsionVariablesstatic final double KCAL332
static final double KCAL644
static final double KCAL6
static final double KCAL22
static final double KCAL44
static final int PAR_R
static final int PAR_THETA
static final int PAR_X
static final int PAR_D
static final int PAR_ZETA
static final int PAR_Z
static final int PAR_V
static final int PAR_U
static final int PAR_XI
static final int PAR_HARD
static final int PAR_RADIUS
Calculation bondCalc
Calculation angleCalc
Calculation torsionCalc
Calculation oopCalc
Calculation vdwCalc
CalculationsUFF(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)
java.lang.String getUnits()
getUnits in class Calculationsboolean setupCalculations()
setupCalculations in class Calculationsprivate static boolean isInvertible(int n)
static double calculateR0(double ri,
double rj,
double chiI,
double chiJ,
double bondorder)
double compute(int iType,
java.lang.Object[] dataIn)
compute in class Calculationsjava.lang.String getDebugHeader(int iType)
getDebugHeader in class Calculationsprotected java.lang.Object getParameterObj(MinObject o)
getParameterObj in class Calculations