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, 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 |
---|
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<java.lang.Object[]> 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, setTorsionVariables
static 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<java.lang.Object[]> constraints)
java.lang.String getUnits()
getUnits
in class Calculations
boolean setupCalculations()
setupCalculations
in class Calculations
private 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 Calculations
java.lang.String getDebugHeader(int iType)
getDebugHeader
in class Calculations
protected java.lang.Object getParameterObj(MinObject o)
getParameterObj
in class Calculations