org.jmol.minimize.forcefield
Class CalculationsUFF
java.lang.Object
org.jmol.minimize.forcefield.Calculations
org.jmol.minimize.forcefield.CalculationsUFF
class CalculationsUFF
- extends Calculations
Fields inherited from class org.jmol.minimize.forcefield.Calculations |
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 |
Methods inherited from class org.jmol.minimize.forcefield.Calculations |
addForce, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyTorsion, energyVDW, getLogData, getParameter, haveParams, setConstraints, setLoggingEnabled, setParams, setPreliminary, setSilent |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PAR_R
public static final int PAR_R
- See Also:
- Constant Field Values
PAR_THETA
public static final int PAR_THETA
- See Also:
- Constant Field Values
PAR_X
public static final int PAR_X
- See Also:
- Constant Field Values
PAR_D
public static final int PAR_D
- See Also:
- Constant Field Values
PAR_ZETA
public static final int PAR_ZETA
- See Also:
- Constant Field Values
PAR_Z
public static final int PAR_Z
- See Also:
- Constant Field Values
PAR_V
public static final int PAR_V
- See Also:
- Constant Field Values
PAR_U
public static final int PAR_U
- See Also:
- Constant Field Values
PAR_XI
public static final int PAR_XI
- See Also:
- Constant Field Values
PAR_HARD
public static final int PAR_HARD
- See Also:
- Constant Field Values
PAR_RADIUS
public static final int PAR_RADIUS
- See Also:
- Constant Field Values
bondCalc
CalculationsUFF.DistanceCalc bondCalc
angleCalc
CalculationsUFF.AngleCalc angleCalc
torsionCalc
CalculationsUFF.TorsionCalc torsionCalc
oopCalc
CalculationsUFF.OOPCalc oopCalc
vdwCalc
CalculationsUFF.VDWCalc vdwCalc
esCalc
CalculationsUFF.ESCalc esCalc
KCAL644
static final double KCAL644
- See Also:
- Constant Field Values
KCAL6
static final double KCAL6
- See Also:
- Constant Field Values
KCAL22
static final double KCAL22
- See Also:
- Constant Field Values
KCAL44
static final double KCAL44
- See Also:
- Constant Field Values
KCAL332
static final double KCAL332
- See Also:
- Constant Field Values
CalculationsUFF
CalculationsUFF(ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds,
int[][] angles,
int[][] torsions,
double[] partialCharges,
java.util.List constraints)
getUnit
java.lang.String getUnit()
- Specified by:
getUnit
in class Calculations
setupCalculations
boolean setupCalculations()
- Specified by:
setupCalculations
in class Calculations
isInvertible
private boolean isInvertible(int n)
pairSearch
private void pairSearch(java.util.List calc,
CalculationsUFF.PairCalc type)
setupElectrostatics
boolean setupElectrostatics()
- Specified by:
setupElectrostatics
in class Calculations
calculateR0
static double calculateR0(double ri,
double rj,
double chiI,
double chiJ,
double bondorder)
compute
double compute(int iType,
java.lang.Object[] dataIn)
- Specified by:
compute
in class Calculations
getAtomList
java.lang.String getAtomList(java.lang.String title)
- Specified by:
getAtomList
in class Calculations
getDebugHeader
java.lang.String getDebugHeader(int iType)
- Specified by:
getDebugHeader
in class Calculations
getDebugLine
java.lang.String getDebugLine(int iType,
Calculation c)
getDebugFooter
java.lang.String getDebugFooter(int iType,
double energy)
- Specified by:
getDebugFooter
in class Calculations