java.lang.Object

org.jmol.minimize.forcefield.Calculations

org.jmol.minimize.forcefield.CalculationsMMFF

class CalculationsMMFF extends Calculations

Author:: Bob Hanson 5/10/12 - 5/15/12

Field Summary

Fields

Modifier and Type

Field

Description

(package private) Calculation

angleCalc

(package private) Calculation

bondCalc

static final int

DA_D

static final int

DA_DA

(package private) Calculation

esCalc

(package private) static final double

FPAR

(package private) ForceFieldMMFF

mmff

(package private) Calculation

oopCalc

(package private) Calculation

sbCalc

(package private) Calculation

torsionCalc

(package private) Calculation

vdwCalc

Fields inherited from class org.jmol.minimize.forcefield.Calculations
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 Summary

Constructors

Constructor

Description

CalculationsMMFF(ForceField ff, Map<Object,Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
Method Summary

Modifier and Type

Method

Description

(package private) double

compute(int iType, Object[] dataIn)

(package private) String

getDebugHeader(int iType)

(package private) String

getDebugLine(int iType, Calculation c)

(package private) Object

getParameterObj(MinObject a)

(package private) String

getUnits()

private static boolean

isInvertible(MinAtom a)

protected boolean

isLinear(int i)

(package private) boolean

setupCalculations()

Methods inherited from class org.jmol.minimize.forcefield.Calculations
addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugHeader2, getDebugLineC, getLogData, getParameter, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- FPAR
  
  static final double FPAR
  See Also:
  
  Constant Field Values
- DA_D
  
  public static final int DA_D
  See Also:
  
  Constant Field Values
- DA_DA
  
  public static final int DA_DA
  See Also:
  
  Constant Field Values
- bondCalc
  
  Calculation bondCalc
- angleCalc
  
  Calculation angleCalc
- torsionCalc
  
  Calculation torsionCalc
- oopCalc
  
  Calculation oopCalc
- vdwCalc
  
  Calculation vdwCalc
- esCalc
  
  Calculation esCalc
- sbCalc
  
  Calculation sbCalc
- mmff
  
  ForceFieldMMFF mmff
Constructor Details
- CalculationsMMFF
  
  CalculationsMMFF(ForceField ff, Map<Object,Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
Method Details
- getUnits
  
  String getUnits()
  
  Specified by:
  
  getUnits in class Calculations
- setupCalculations
  
  boolean setupCalculations()
  
  Specified by:
  
  setupCalculations in class Calculations
- isLinear
  
  protected boolean isLinear(int i)
  
  Overrides:
  
  isLinear in class Calculations
  
  Returns:
  
  T/F
- isInvertible
  
  private static boolean isInvertible(MinAtom a)
- compute
  
  double compute(int iType, Object[] dataIn)
  
  Specified by:
  
  compute in class Calculations
- getParameterObj
  
  Object getParameterObj(MinObject a)
  
  Specified by:
  
  getParameterObj in class Calculations
- getDebugHeader
  
  String getDebugHeader(int iType)
  
  Specified by:
  
  getDebugHeader in class Calculations
- getDebugLine
  
  String getDebugLine(int iType, Calculation c)
  
  Overrides:
  
  getDebugLine in class Calculations

Class CalculationsMMFF

Field Summary

Fields inherited from class org.jmol.minimize.forcefield.Calculations

Constructor Summary

Method Summary

Methods inherited from class org.jmol.minimize.forcefield.Calculations

Methods inherited from class java.lang.Object

Field Details

FPAR

DA_D

DA_DA

bondCalc

angleCalc

torsionCalc

oopCalc

vdwCalc

esCalc

sbCalc

mmff

Constructor Details

CalculationsMMFF

Method Details

getUnits

setupCalculations

isLinear

isInvertible

compute

getParameterObj

getDebugHeader

getDebugLine