org.jmol.quantum
Class MepCalculation

java.lang.Object
  extended by org.jmol.quantum.QuantumCalculation
      extended by org.jmol.quantum.MepCalculation
All Implemented Interfaces:
MepCalculationInterface
Direct Known Subclasses:
MlpCalculation

public class MepCalculation
extends QuantumCalculation
implements MepCalculationInterface


Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.quantum.QuantumCalculation
QuantumCalculation.QMAtom
 
Field Summary
private  Point3f[] atomCoordAngstroms
           
private  BitSet bsSelected
           
protected  int distanceMode
           
protected static int E_MINUS_D
           
protected static int E_MINUS_D_OVER_2
           
protected  Hashtable htAtomicPotentials
           
protected static int ONE_OVER_D
           
protected static int ONE_OVER_ONE_PLUS_D
           
private  float[] potentials
           
protected  String resourceName
           
 
Fields inherited from class org.jmol.quantum.QuantumCalculation
atomIndex, bohr_per_angstrom, doDebug, nX, nY, nZ, originBohr, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, volume, voxelData, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin
 
Constructor Summary
MepCalculation()
           
 
Method Summary
 void assignPotentials(Atom[] atoms, float[] potentials, BitSet bsAromatic, BitSet bsCarbonyl, BitSet bsIgnore, String data)
           
 void calculate(VolumeDataInterface volumeData, BitSet bsSelected, Point3f[] atomCoordAngstroms, float[] potentials, int calcType)
           
protected  void getAtomicPotentials(String data, String resourceName)
           
protected  float getTabulatedPotential(Atom atom)
           
 float getValueAtPoint(Point3f pt)
           
private  void processMep()
           
 void setup(int calcType, float[] potentials, Point3f[] atomCoordAngstroms, BitSet bsSelected)
           
 float valueFor(float x0, float d2, int distanceMode)
           
 
Methods inherited from class org.jmol.quantum.QuantumCalculation
initialize, setupCoordinates
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ONE_OVER_D

protected static final int ONE_OVER_D
See Also:
Constant Field Values

E_MINUS_D_OVER_2

protected static final int E_MINUS_D_OVER_2
See Also:
Constant Field Values

ONE_OVER_ONE_PLUS_D

protected static final int ONE_OVER_ONE_PLUS_D
See Also:
Constant Field Values

E_MINUS_D

protected static final int E_MINUS_D
See Also:
Constant Field Values

distanceMode

protected int distanceMode

potentials

private float[] potentials

atomCoordAngstroms

private Point3f[] atomCoordAngstroms

bsSelected

private BitSet bsSelected

htAtomicPotentials

protected Hashtable htAtomicPotentials

resourceName

protected String resourceName
Constructor Detail

MepCalculation

public MepCalculation()
Method Detail

assignPotentials

public void assignPotentials(Atom[] atoms,
                             float[] potentials,
                             BitSet bsAromatic,
                             BitSet bsCarbonyl,
                             BitSet bsIgnore,
                             String data)
Specified by:
assignPotentials in interface MepCalculationInterface

setup

public void setup(int calcType,
                  float[] potentials,
                  Point3f[] atomCoordAngstroms,
                  BitSet bsSelected)

calculate

public void calculate(VolumeDataInterface volumeData,
                      BitSet bsSelected,
                      Point3f[] atomCoordAngstroms,
                      float[] potentials,
                      int calcType)
Specified by:
calculate in interface MepCalculationInterface

getValueAtPoint

public float getValueAtPoint(Point3f pt)

processMep

private void processMep()

valueFor

public float valueFor(float x0,
                      float d2,
                      int distanceMode)
Specified by:
valueFor in interface MepCalculationInterface

getTabulatedPotential

protected float getTabulatedPotential(Atom atom)

getAtomicPotentials

protected void getAtomicPotentials(String data,
                                   String resourceName)