class CalculationsUFF extends Calculations
Modifier and Type | Class and Description |
---|---|
(package private) class |
CalculationsUFF.AngleCalc |
(package private) class |
CalculationsUFF.DistanceCalc |
(package private) class |
CalculationsUFF.ESCalc |
(package private) class |
CalculationsUFF.OOPCalc |
(package private) class |
CalculationsUFF.PairCalc |
(package private) class |
CalculationsUFF.TorsionCalc |
(package private) class |
CalculationsUFF.VDWCalc |
Modifier and Type | Field and Description |
---|---|
(package private) CalculationsUFF.AngleCalc |
angleCalc |
(package private) CalculationsUFF.DistanceCalc |
bondCalc |
(package private) CalculationsUFF.ESCalc |
esCalc |
(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) CalculationsUFF.OOPCalc |
oopCalc |
static int |
PAR_D |
static int |
PAR_HARD |
static int |
PAR_R |
static int |
PAR_RADIUS |
static int |
PAR_THETA |
static int |
PAR_U |
static int |
PAR_V |
static int |
PAR_X |
static int |
PAR_XI |
static int |
PAR_Z |
static int |
PAR_ZETA |
(package private) CalculationsUFF.TorsionCalc |
torsionCalc |
(package private) CalculationsUFF.VDWCalc |
vdwCalc |
angles, atomCount, atoms, bondCount, bonds, CALC_ANGLE, CALC_DISTANCE, CALC_ES, CALC_MAX, CALC_OOP, CALC_TORSION, CALC_VDW, calculations, constraints, da, db, dc, dd, DEG_TO_RAD, ff, ffParams, gradients, havePartialCharges, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, partialCharges, RAD_TO_DEG, silent, torsions, v1, v2, v3
Constructor and Description |
---|
CalculationsUFF(ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds,
int[][] angles,
int[][] torsions,
double[] partialCharges,
java.util.List<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 |
getAtomList(java.lang.String title) |
(package private) java.lang.String |
getDebugFooter(int iType,
double energy) |
(package private) java.lang.String |
getDebugHeader(int iType) |
(package private) java.lang.String |
getDebugLine(int iType,
Calculation c) |
(package private) java.lang.String |
getUnit() |
private boolean |
isInvertible(int n) |
private void |
pairSearch(java.util.List<java.lang.Object[]> calc,
CalculationsUFF.PairCalc type) |
(package private) boolean |
setupCalculations() |
(package private) boolean |
setupElectrostatics() |
addForce, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyTorsion, energyVDW, getConstraintList, getLogData, getParameter, haveParams, setConstraints, setLoggingEnabled, setParams, setPreliminary, setSilent
public static final int PAR_R
public static final int PAR_THETA
public static final int PAR_X
public static final int PAR_D
public static final int PAR_ZETA
public static final int PAR_Z
public static final int PAR_V
public static final int PAR_U
public static final int PAR_XI
public static final int PAR_HARD
public static final int PAR_RADIUS
CalculationsUFF.DistanceCalc bondCalc
CalculationsUFF.AngleCalc angleCalc
CalculationsUFF.TorsionCalc torsionCalc
CalculationsUFF.OOPCalc oopCalc
CalculationsUFF.VDWCalc vdwCalc
CalculationsUFF.ESCalc esCalc
static final double KCAL644
static final double KCAL6
static final double KCAL22
static final double KCAL44
static final double KCAL332
CalculationsUFF(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, java.util.List<java.lang.Object[]> constraints)
java.lang.String getUnit()
getUnit
in class Calculations
boolean setupCalculations()
setupCalculations
in class Calculations
private boolean isInvertible(int n)
private void pairSearch(java.util.List<java.lang.Object[]> calc, CalculationsUFF.PairCalc type)
boolean setupElectrostatics()
setupElectrostatics
in class Calculations
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 getAtomList(java.lang.String title)
getAtomList
in class Calculations
java.lang.String getDebugHeader(int iType)
getDebugHeader
in class Calculations
java.lang.String getDebugLine(int iType, Calculation c)
java.lang.String getDebugFooter(int iType, double energy)
getDebugFooter
in class Calculations