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 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>>`	`htModels`
`private java.lang.Integer`	`moColorNeg`
`private java.lang.Integer`	`moColorPos`
`private java.lang.Float`	`moCutoff`
`private boolean`	`moDebug`
`private int`	`moDots`
`private int`	`moFill`
`private int`	`moFrontOnly`
`private boolean`	`moIsPositiveOnly`
`private float[]`	`moLinearCombination`
`private int`	`moMesh`
`private java.lang.Integer`	`moMonteCarloCount`
`private int`	`moNumber`
`private javajs.util.P4`	`moPlane`
`private java.lang.Integer`	`moRandomSeed`
`private java.lang.Float`	`moResolution`
`private java.lang.Float`	`moScale`
`private int`	`moShell`
`private javajs.util.Lst<java.lang.Object>`	`moSlab`
`private java.lang.Integer`	`moSlabValue`
`private java.lang.Boolean`	`moSquareData`
`private java.lang.Boolean`	`moSquareLinear`
`private java.lang.String`	`moTitleFormat`
`private java.lang.String`	`moTranslucency`
`private java.lang.Float`	`moTranslucentLevel`
`private int`	`myColorPt`
`private java.lang.String`	`nboType`
`private java.lang.String`	`strID`
`private java.util.Map<java.lang.String,java.lang.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, 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`clearSg()`
`private java.lang.String`	`getId(int modelIndex)`
`java.lang.String`	`getMoInfo(int modelIndex)`
`java.lang.Object`	`getProperty(java.lang.String propertyName, int index)`
`private boolean`	`getSettings(java.lang.String strID)`
`java.lang.String`	`getShapeState()`
`void`	`initShape()`
`void`	`merge(MeshCollection shape)`	called by ParallelProcessor at completion
`private void`	`setOrbital(int moNumber, float[] linearCombination)`
`void`	`setProperty(java.lang.String propertyName, java.lang.Object value, 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, 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 java.lang.String moTranslucency

moTranslucentLevel

private java.lang.Float moTranslucentLevel

moPlane
```
private javajs.util.P4 moPlane
```

moCutoff
```
private java.lang.Float moCutoff
```

moResolution
```
private java.lang.Float moResolution
```

moScale
```
private java.lang.Float moScale
```

moColorPos
```
private java.lang.Integer moColorPos
```

moColorNeg
```
private java.lang.Integer moColorNeg
```

moMonteCarloCount

private java.lang.Integer moMonteCarloCount

moIsPositiveOnly
```
private boolean moIsPositiveOnly
```

moSquareData
```
private java.lang.Boolean moSquareData
```

moSquareLinear

private java.lang.Boolean moSquareLinear

moRandomSeed
```
private java.lang.Integer moRandomSeed
```

moFill
```
private int moFill
```

moMesh
```
private int moMesh
```

moDots
```
private int moDots
```

moFrontOnly
```
private int moFrontOnly
```

moShell
```
private int moShell
```

moTitleFormat
```
private java.lang.String moTitleFormat
```

moDebug
```
private boolean moDebug
```

myColorPt
```
private int myColorPt
```

strID
```
private java.lang.String strID
```

moNumber
```
private int moNumber
```

moLinearCombination
```
private float[] moLinearCombination
```

htModels

private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htModels

thisModel

private java.util.Map<java.lang.String,java.lang.Object> thisModel

moSlab

private javajs.util.Lst<java.lang.Object> moSlab

moSlabValue
```
private java.lang.Integer moSlabValue
```

nboType
```
private java.lang.String nboType
```

Constructor Detail
- MolecularOrbital
```
public MolecularOrbital()
```

Method Detail

initShape
```
public void initShape()
```
Overrides:

initShape in class Isosurface

setProperty

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

Overrides:: setProperty in class Isosurface

getId

private java.lang.String getId(int modelIndex)

getProperty

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

Overrides:: getProperty in class Isosurface
Returns:: true if serviced

getMoInfo

public java.lang.String getMoInfo(int modelIndex)

clearSg
```
protected void clearSg()
```
Overrides:

clearSg in class Isosurface

getSettings

private boolean getSettings(java.lang.String strID)

setOrbital

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

getShapeState
```
public java.lang.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

Class MolecularOrbital

Field Summary

Fields inherited from class org.jmol.shapesurface.Isosurface

Fields inherited from class org.jmol.shape.MeshCollection

Fields inherited from class org.jmol.shape.Shape

Constructor Summary

Method Summary

Methods inherited from class org.jmol.shapesurface.Isosurface

Methods inherited from class org.jmol.shape.MeshCollection

Methods inherited from class org.jmol.shape.Shape

Methods inherited from class java.lang.Object

Field Detail

moTranslucency

moTranslucentLevel

moPlane

moCutoff

moResolution

moScale

moColorPos

moColorNeg

moMonteCarloCount

moIsPositiveOnly

moSquareData

moSquareLinear

moRandomSeed

moFill

moMesh

moDots

moFrontOnly

moShell

moTitleFormat

moDebug

myColorPt

strID

moNumber

moLinearCombination

htModels

thisModel

moSlab

moSlabValue

nboType

Constructor Detail

MolecularOrbital

Method Detail

initShape

setProperty

getId

getProperty

getMoInfo

clearSg

getSettings

setOrbital

getShapeState

merge