Package 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

Direct Known Subclasses:

NBO

public class MolecularOrbital
extends Isosurface

Field Summary

Fields

Modifier and Type	Field	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 int	moShell
private javajs.util.Lst<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	nboType
private String	strID
private Map<String,Object>	thisModel

Fields inherited from class org.jmol.shapesurface.Isosurface

allowMesh, iHaveBitSets, isomeshes, 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, nUnnamed, pickedMesh, pickedModel, pickedPt, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title

Fields inherited from class org.jmol.shape.Shape

bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr

Constructor Summary

Constructors

Constructor	Description
MolecularOrbital()

Method Summary

Modifier and Type	Method	Description
protected void	clearSg()
private String	getId(int modelIndex)
String	getMoInfo(int modelIndex)
Object	getProperty(String propertyName, int index)
private boolean	getSettings(String strID)
String	getShapeState()
void	initShape()
void	merge(MeshCollection shape)	called by ParallelProcessor at completion
private void	setOrbital(int moNumber, float[] linearCombination)
void	setProperty(String propertyName, Object value, javajs.util.BS bs)

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, setRequiredFile, setScriptInfo, slabPolygons

Methods inherited from class org.jmol.shape.MeshCollection

checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getMeshList, getPickedPoint, getPropDataMC, getPropMC, resetObjects, setModelVisibilityFlags, setPropMC, setStatusPicked, setTokenProperty

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getPropShape, getSize, getSizeG, getTranslucentLabel, initializeShape, initModelSet, replaceGroup, setAtomClickability, 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

moShell

private int moShell

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.Lst<Object> moSlab

moSlabValue

private Integer moSlabValue

nboType

private String nboType

Constructor Detail

MolecularOrbital

public MolecularOrbital()

Method Detail

initShape

public void initShape()

Overrides:

initShape in class Isosurface

setProperty

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

Overrides:

setProperty in class Isosurface

getId

private String getId(int modelIndex)

getProperty

public Object getProperty(String propertyName,
                          int index)

Overrides:

getProperty in class Isosurface

Returns:

true if serviced

getMoInfo

public String getMoInfo(int modelIndex)

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

merge

public void merge(MeshCollection shape)

Description copied from class: MeshCollection

called by ParallelProcessor at completion

Overrides:

merge in class MeshCollection