org.jmol.shapesurface

Class MolecularOrbital

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.MeshCollection

org.jmol.shapesurface.Isosurface

org.jmol.shapesurface.MolecularOrbital

All Implemented Interfaces:

MeshDataServer, VertexDataServer

public class MolecularOrbital
extends Isosurface

Field Summary

Fields

Modifier and Type	Field and Description
private Map<String,Map<String,Object>>	htModels
private Integer	moColorNeg
private Integer	moColorPos
private Float	moCutoff
private boolean	moDebug
private int	moDots
private int	moFill
private int	moFrontOnly
private boolean	moIsPositiveOnly
private float[]	moLinearCombination
private int	moMesh
private Integer	moMonteCarloCount
private int	moNumber
private javajs.util.P4	moPlane
private Integer	moRandomSeed
private Float	moResolution
private Float	moScale
private javajs.util.List<Object>	moSlab
private Integer	moSlabValue
private Boolean	moSquareData
private Boolean	moSquareLinear
private String	moTitleFormat
private String	moTranslucency
private Float	moTranslucentLevel
private int	myColorPt
private String	strID
private Map<String,Object>	thisModel

Fields inherited from class org.jmol.shapesurface.Isosurface

allowMesh, iHaveBitSets, jvxlData, keyXy, sg, thisMesh

Fields inherited from class org.jmol.shape.MeshCollection

bsDisplay, colix, color, connections, currentMesh, displayWithinDistance2, displayWithinPoints, explicitID, htObjects, isDisplayWithinNot, isFixed, linkedMesh, meshCount, meshes, modelIndex, myType, nUnnamed, pickedMesh, pickedModel, pickedPt, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title

Fields inherited from class org.jmol.shape.Shape

bsColixSet, bsSizeSet, gdata, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer

Constructor Summary

Constructors

Constructor and Description
MolecularOrbital()

Method Summary

Modifier and Type	Method and Description
protected void	clearSg()
private String	getId(int modelIndex)
private String	getMoState(int modelIndex)
Object	getProperty(String propertyName, int param)
private boolean	getSettings(String strID)
String	getShapeState()
void	initShape()
void	merge(Shape shape) called by ParallelProcessor at completion
private void	setOrbital(int moNumber, float[] linearCombination)
void	setProperty(String propertyName, Object value, BS bs) may come from any source -- executed AFTER a shape's own setProperty method

Methods inherited from class org.jmol.shapesurface.Isosurface

addMeshInfo, addRequiredFile, addTriangleCheck, addVertexCopy, allocMesh, calculateGeodesicSurface, checkObjectClicked, checkObjectHovered, discardTempData, fillMeshData, getCapSlabInfo, getCmd, getPlane, getPolygonColorData, getPropertyData, getPropI, getShapeDetail, getSurfacePointIndexAndFraction, getValue, invalidateTriangles, newSg, notifySurfaceGenerationCompleted, notifySurfaceMappingCompleted, setOutputChannel, setPropI, setScriptInfo, slabPolygons

Methods inherited from class org.jmol.shape.MeshCollection

checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getPickedPoint, getPropDataMC, getPropMC, setPropMC, setStatusPicked, setVisibilityFlags

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getSize, getSizeG, getTranslucentLabel, getViewer, initializeShape, initModelSet, setModelClickability, setModelSet, setPropS, setShapeSizeRD, setSize, setSizeRD, wasClicked

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

moTranslucency

private String moTranslucency

moTranslucentLevel

private Float moTranslucentLevel

moPlane

private javajs.util.P4 moPlane

moCutoff

private Float moCutoff

moResolution

private Float moResolution

moScale

private Float moScale

moColorPos

private Integer moColorPos

moColorNeg

private Integer moColorNeg

moMonteCarloCount

private Integer moMonteCarloCount

moIsPositiveOnly

private boolean moIsPositiveOnly

moSquareData

private Boolean moSquareData

moSquareLinear

private Boolean moSquareLinear

moRandomSeed

private Integer moRandomSeed

moFill

private int moFill

moMesh

private int moMesh

moDots

private int moDots

moFrontOnly

private int moFrontOnly

moTitleFormat

private String moTitleFormat

moDebug

private boolean moDebug

myColorPt

private int myColorPt

strID

private String strID

moNumber

private int moNumber

moLinearCombination

private float[] moLinearCombination

htModels

private Map<String,Map<String,Object>> htModels

thisModel

private Map<String,Object> thisModel

moSlab

private javajs.util.List<Object> moSlab

moSlabValue

private Integer moSlabValue

Constructor Detail

MolecularOrbital

public MolecularOrbital()

Method Detail

initShape

public void initShape()

Overrides:

initShape in class Isosurface

setProperty

public void setProperty(String propertyName,
                        Object value,
                        BS bs)

Description copied from class: Shape

may come from any source -- executed AFTER a shape's own setProperty method

Overrides:

setProperty in class Isosurface

getId

private String getId(int modelIndex)

getProperty

public Object getProperty(String propertyName,
                          int param)

Overrides:

getProperty in class Isosurface

Returns:

true if serviced

clearSg

protected void clearSg()

Overrides:

clearSg in class Isosurface

getSettings

private boolean getSettings(String strID)

setOrbital

private void setOrbital(int moNumber,
                        float[] linearCombination)

getShapeState

public String getShapeState()

Overrides:

getShapeState in class Isosurface

getMoState

private String getMoState(int modelIndex)

merge

public void merge(Shape shape)

Description copied from class: MeshCollection

called by ParallelProcessor at completion

Overrides:

merge in class Isosurface