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, keyXy, sg, thisMesh

Fields inherited from class org.jmol.shape.MeshCollection
bsDisplay, colix, color, connections, currentMesh, displayWithinDistance2, displayWithinPoints, explicitID, htObjects, isDisplayWithinNot, isFixed, jvxlData, 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, getValues, getVertices, 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, setTitle, 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 Details
- 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 Details
- MolecularOrbital
  
  public MolecularOrbital()
Method Details
- 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

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 Details

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 Details

MolecularOrbital

Method Details

initShape

setProperty

getId

getProperty

getMoInfo

clearSg

getSettings

setOrbital

getShapeState

merge