org.jmol.shapespecial

Class Dipoles

java.lang.Object

org.jmol.shape.Shape

org.jmol.shapespecial.Dipoles

public class Dipoles
extends Shape

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomIndex1
private int	atomIndex2
private javax.vecmath.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 javax.vecmath.Point3f	endCoord
private boolean	iHaveTwoEnds
private boolean	isBond
private boolean	isUserValue
private javax.vecmath.Point3f	startCoord
private Dipole	tempDipole
private java.lang.String	wildID

Fields inherited from class org.jmol.shape.Shape

g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties

Constructor Summary

Constructors

Constructor and Description
Dipoles()

Method Summary

Methods

Modifier and Type	Method and Description
private Dipole	allocDipole(java.lang.String thisID, java.lang.String dipoleInfo)
private void	clear(boolean clearBondDipolesOnly)
private void	deleteDipole(Dipole dipole)
private void	dumpDipoles(java.lang.String msg)
private Dipole	findBondDipole(Bond bond)
private Dipole	findDipole(Atom atom1, Atom atom2, boolean doAllocate)
private Dipole	findDipole(java.lang.String thisID)
private Dipole	findDipole(java.lang.String thisID, java.lang.String dipoleInfo)
private void	getBondDipoles()
private int	getDipoleIndex(int atomIndex1, int atomIndex2)
private int	getDipoleIndex(java.lang.String dipoleInfo, java.lang.String thisID)
int	getIndexFromName(java.lang.String thisID)
java.lang.Object	getProperty(java.lang.String property, int index)
boolean	getProperty(java.lang.String property, java.lang.Object[] data)
java.util.List<java.util.Map<java.lang.String,java.lang.Object>>	getShapeDetail()
java.lang.String	getShapeState()
private boolean	isBondDipole(int i)
private boolean	isSameAtoms(Dipole dipole, java.lang.String dipoleInfo)
private void	setColixDipole(short colix, int bondTypeMask, java.util.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(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs) may come from any source -- executed AFTER a shape's own setProperty method
void	setVisibilityFlags(java.util.BitSet bs)

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getShapeCommands, getShapeCommands, getSize, getSize, getTranslucentLabel, 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 javax.vecmath.Point3f startCoord

endCoord

private javax.vecmath.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 javax.vecmath.Vector3f calculatedDipole

wildID

private java.lang.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(java.lang.String propertyName,
               java.lang.Object value,
               java.util.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(java.lang.String property,
                  java.lang.Object[] data)

Overrides:

getProperty in class Shape

Returns:

true if serviced

getProperty

public java.lang.Object getProperty(java.lang.String property,
                           int index)

Overrides:

getProperty in class Shape

Returns:

true if serviced

getBondDipoles

private void getBondDipoles()

isBondDipole

private boolean isBondDipole(int i)

setColixDipole

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

setDipole

private void setDipole()

setDipole

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

getDipoleIndex

private int getDipoleIndex(java.lang.String dipoleInfo,
                 java.lang.String thisID)

isSameAtoms

private boolean isSameAtoms(Dipole dipole,
                  java.lang.String dipoleInfo)

getDipoleIndex

private int getDipoleIndex(int atomIndex1,
                 int atomIndex2)

deleteDipole

private void deleteDipole(Dipole dipole)

findDipole

private Dipole findDipole(java.lang.String thisID)

findDipole

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

findBondDipole

private Dipole findBondDipole(Bond bond)

findDipole

private Dipole findDipole(java.lang.String thisID,
                java.lang.String dipoleInfo)

allocDipole

private Dipole allocDipole(java.lang.String thisID,
                 java.lang.String dipoleInfo)

dumpDipoles

private void dumpDipoles(java.lang.String msg)

clear

private void clear(boolean clearBondDipolesOnly)

getIndexFromName

public int getIndexFromName(java.lang.String thisID)

Overrides:

getIndexFromName in class Shape

Returns:

index

getShapeDetail

public java.util.List<java.util.Map<java.lang.String,java.lang.Object>> getShapeDetail()

Overrides:

getShapeDetail in class Shape

setModelIndex

private void setModelIndex()

setVisibilityFlags

public void setVisibilityFlags(java.util.BitSet bs)

Overrides:

setVisibilityFlags in class Shape

getShapeState

public java.lang.String getShapeState()

Overrides:

getShapeState in class Shape