org.jmol.shapespecial
Class Dipoles

java.lang.Object
  extended by org.jmol.shape.Shape
      extended by org.jmol.shapespecial.Dipoles

public class Dipoles
extends Shape


Field Summary
private  int atomIndex1
           
private  int atomIndex2
           
private  Vector3f calculatedDipole
           
private  short colix
           
private  Dipole currentDipole
           
(package private) static short DEFAULT_MAD
           
(package private) static float DEFAULT_OFFSETSIDE
           
(package private)  int dipoleCount
           
(package private)  Dipole[] dipoles
           
private  float dipoleValue
           
private static float E_ANG_PER_DEBYE
           
private  Point3f endCoord
           
private  boolean iHaveTwoEnds
           
private  boolean isBond
           
private  boolean isUserValue
           
private  Point3f startCoord
           
private  Dipole tempDipole
           
private  String wildID
           
 
Fields inherited from class org.jmol.shape.Shape
g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties
 
Constructor Summary
Dipoles()
           
 
Method Summary
private  Dipole allocDipole(String thisID, String dipoleInfo)
           
private  void clear(boolean clearBondDipolesOnly)
           
private  void deleteDipole(Dipole dipole)
           
private  void dumpDipoles(String msg)
           
private  Dipole findBondDipole(Bond bond)
           
private  Dipole findDipole(Atom atom1, Atom atom2, boolean doAllocate)
           
private  Dipole findDipole(String thisID)
           
private  Dipole findDipole(String thisID, String dipoleInfo)
           
private  void getBondDipoles()
           
private  int getDipoleIndex(int atomIndex1, int atomIndex2)
           
private  int getDipoleIndex(String dipoleInfo, String thisID)
           
 int getIndexFromName(String thisID)
           
 Object getProperty(String property, int index)
           
 boolean getProperty(String property, Object[] data)
           
 List getShapeDetail()
           
 String getShapeState()
           
private  boolean isBondDipole(int i)
           
private  boolean isSameAtoms(Dipole dipole, String dipoleInfo)
           
private  void setColixDipole(short colix, int bondTypeMask, BitSet bs)
           
private  void setDipole()
           
private  void setDipole(Atom atom1, Atom atom2, float c1, float c2)
           
private  void setModelIndex()
           
private  void setProperty(int tok, boolean bondOnly, int iValue, float fValue)
           
private  void setProperty(int tok, Dipole dipole, int iValue, float fValue)
           
 void setProperty(String propertyName, Object value, BitSet bs)
          may come from any source -- executed AFTER a shape's own setProperty method
 void setVisibilityFlags(BitSet bs)
           
 
Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getShapeCommands, getShapeCommands, getSize, getSize, getViewer, initializeShape, initModelSet, initShape, merge, setColix, setColix, setColix, setModelClickability, setModelSet, setShapeProperty, setShapeSize, setSize, setSize, setStateInfo, setStateInfo, wasClicked
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DEFAULT_MAD

static final short DEFAULT_MAD
See Also:
Constant Field Values

DEFAULT_OFFSETSIDE

static final float DEFAULT_OFFSETSIDE
See Also:
Constant Field Values

dipoleCount

int dipoleCount

dipoles

Dipole[] dipoles

currentDipole

private Dipole currentDipole

tempDipole

private Dipole tempDipole

startCoord

private Point3f startCoord

endCoord

private Point3f endCoord

dipoleValue

private float dipoleValue

isUserValue

private boolean isUserValue

isBond

private boolean isBond

iHaveTwoEnds

private boolean iHaveTwoEnds

atomIndex1

private int atomIndex1

atomIndex2

private int atomIndex2

colix

private short colix

calculatedDipole

private Vector3f calculatedDipole

wildID

private String wildID

E_ANG_PER_DEBYE

private static final float E_ANG_PER_DEBYE
See Also:
Constant Field Values
Constructor Detail

Dipoles

public Dipoles()
Method Detail

setProperty

public void setProperty(String propertyName,
                        Object value,
                        BitSet bs)
Description copied from class: Shape
may come from any source -- executed AFTER a shape's own setProperty method

Overrides:
setProperty in class Shape

setProperty

private void setProperty(int tok,
                         boolean bondOnly,
                         int iValue,
                         float fValue)

setProperty

private void setProperty(int tok,
                         Dipole dipole,
                         int iValue,
                         float fValue)

getProperty

public boolean getProperty(String property,
                           Object[] data)
Overrides:
getProperty in class Shape

getProperty

public Object getProperty(String property,
                          int index)
Overrides:
getProperty in class Shape

getBondDipoles

private void getBondDipoles()

isBondDipole

private boolean isBondDipole(int i)

setColixDipole

private void setColixDipole(short colix,
                            int bondTypeMask,
                            BitSet bs)

setDipole

private void setDipole()

setDipole

private void setDipole(Atom atom1,
                       Atom atom2,
                       float c1,
                       float c2)

getDipoleIndex

private int getDipoleIndex(String dipoleInfo,
                           String thisID)

isSameAtoms

private boolean isSameAtoms(Dipole dipole,
                            String dipoleInfo)

getDipoleIndex

private int getDipoleIndex(int atomIndex1,
                           int atomIndex2)

deleteDipole

private void deleteDipole(Dipole dipole)

findDipole

private Dipole findDipole(String thisID)

findDipole

private Dipole findDipole(Atom atom1,
                          Atom atom2,
                          boolean doAllocate)

findBondDipole

private Dipole findBondDipole(Bond bond)

findDipole

private Dipole findDipole(String thisID,
                          String dipoleInfo)

allocDipole

private Dipole allocDipole(String thisID,
                           String dipoleInfo)

dumpDipoles

private void dumpDipoles(String msg)

clear

private void clear(boolean clearBondDipolesOnly)

getIndexFromName

public int getIndexFromName(String thisID)
Overrides:
getIndexFromName in class Shape

getShapeDetail

public List getShapeDetail()
Overrides:
getShapeDetail in class Shape

setModelIndex

private void setModelIndex()

setVisibilityFlags

public void setVisibilityFlags(BitSet bs)
Overrides:
setVisibilityFlags in class Shape

getShapeState

public String getShapeState()
Overrides:
getShapeState in class Shape