Package org.jmol.shapesurface
Class MolecularOrbital
- java.lang.Object
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- org.jmol.shape.Shape
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- org.jmol.shape.MeshCollection
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- org.jmol.shapesurface.Isosurface
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- org.jmol.shapesurface.MolecularOrbital
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- All Implemented Interfaces:
MeshDataServer
,VertexDataServer
- Direct Known Subclasses:
NBO
public class MolecularOrbital extends Isosurface
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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
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Fields inherited from class org.jmol.shapesurface.Isosurface
allowMesh, iHaveBitSets, isomeshes, jvxlData, keyXy, sg, thisMesh
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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
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Fields inherited from class org.jmol.shape.Shape
bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
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Constructor Summary
Constructors Constructor Description MolecularOrbital()
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Method Summary
All Methods Instance Methods Concrete Methods 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 completionprivate void
setOrbital(int moNumber, float[] linearCombination)
void
setProperty(String propertyName, Object value, javajs.util.BS bs)
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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
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Methods inherited from class org.jmol.shape.MeshCollection
checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getMeshList, getPickedPoint, getPropDataMC, getPropMC, resetObjects, setModelVisibilityFlags, setPropMC, setStatusPicked, setTokenProperty
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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
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Field Detail
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moTranslucency
private String moTranslucency
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moTranslucentLevel
private Float moTranslucentLevel
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moPlane
private javajs.util.P4 moPlane
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moCutoff
private Float moCutoff
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moResolution
private Float moResolution
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moScale
private Float moScale
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moColorPos
private Integer moColorPos
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moColorNeg
private Integer moColorNeg
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moMonteCarloCount
private Integer moMonteCarloCount
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moIsPositiveOnly
private boolean moIsPositiveOnly
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moSquareData
private Boolean moSquareData
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moSquareLinear
private Boolean moSquareLinear
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moRandomSeed
private Integer moRandomSeed
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moFill
private int moFill
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moMesh
private int moMesh
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moDots
private int moDots
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moFrontOnly
private int moFrontOnly
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moShell
private int moShell
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moTitleFormat
private String moTitleFormat
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moDebug
private boolean moDebug
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myColorPt
private int myColorPt
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strID
private String strID
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moNumber
private int moNumber
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moLinearCombination
private float[] moLinearCombination
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moSlab
private javajs.util.Lst<Object> moSlab
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moSlabValue
private Integer moSlabValue
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nboType
private String nboType
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Method Detail
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initShape
public void initShape()
- Overrides:
initShape
in classIsosurface
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setProperty
public void setProperty(String propertyName, Object value, javajs.util.BS bs)
- Overrides:
setProperty
in classIsosurface
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getId
private String getId(int modelIndex)
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getProperty
public Object getProperty(String propertyName, int index)
- Overrides:
getProperty
in classIsosurface
- Returns:
- true if serviced
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getMoInfo
public String getMoInfo(int modelIndex)
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clearSg
protected void clearSg()
- Overrides:
clearSg
in classIsosurface
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getSettings
private boolean getSettings(String strID)
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setOrbital
private void setOrbital(int moNumber, float[] linearCombination)
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getShapeState
public String getShapeState()
- Overrides:
getShapeState
in classIsosurface
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merge
public void merge(MeshCollection shape)
Description copied from class:MeshCollection
called by ParallelProcessor at completion- Overrides:
merge
in classMeshCollection
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