org.jmol.minimize.forcefield
Class CalculationsUFF

java.lang.Object
  extended by org.jmol.minimize.forcefield.Calculations
      extended by org.jmol.minimize.forcefield.CalculationsUFF

 class CalculationsUFF
extends Calculations


Nested Class Summary
(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
           
 
Field Summary
(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
           
 
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
 
Constructor Summary
CalculationsUFF(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, java.util.Vector constraints)
           
 
Method Summary
(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.Vector calc, CalculationsUFF.PairCalc type)
           
(package private)  boolean setupCalculations()
           
(package private)  boolean setupElectrostatics()
           
 
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
 

Field Detail

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
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Constant Field Values

PAR_D

public static final int PAR_D
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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
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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
Constructor Detail

CalculationsUFF

CalculationsUFF(ForceField ff,
                MinAtom[] minAtoms,
                MinBond[] minBonds,
                int[][] angles,
                int[][] torsions,
                double[] partialCharges,
                java.util.Vector constraints)
Method Detail

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.Vector 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