Package org.jmol.shapesurface
Class Isosurface
java.lang.Object
org.jmol.shape.Shape
org.jmol.shape.MeshCollection
org.jmol.shapesurface.Isosurface
- All Implemented Interfaces:
MeshDataServer
,VertexDataServer
- Direct Known Subclasses:
Contact
,LcaoCartoon
,MolecularOrbital
,Pmesh
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate String
(package private) boolean
private boolean
private int
private javajs.util.P3
private int
private float[]
private short
private boolean
protected boolean
private boolean
private boolean
protected IsosurfaceMesh[]
private boolean
private boolean
int[]
private javajs.util.P4
private static final int
private short
private float[]
private int
private String
private int
private String
private final javajs.util.P3i
private float
private String
private String
protected SurfaceGenerator
protected IsosurfaceMesh
private float
private javajs.util.Lst<javajs.util.P3>
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addMeshInfo
(IsosurfaceMesh mesh, Map<String, Object> info) void
addRequiredFile
(String fileName) int
addTriangleCheck
(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color) addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)int
addVertexCopy
(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.void
javajs.util.P3[]
calculateGeodesicSurface
(javajs.util.BS bsSelected, float envelopeRadius) private Object
calculateVolumeOrArea
(IsosurfaceMesh mesh, boolean isArea) checkObjectClicked
(int x, int y, int action, javajs.util.BS bsVisible, boolean drawPicking) boolean
checkObjectHovered
(int x, int y, javajs.util.BS bsVisible) protected void
clearSg()
private void
createLcaoLobe
(javajs.util.V3 lobeAxis, float factor, int nElectrons) protected void
discardTempData
(boolean discardAll) private void
drawLcaoCartoon
(javajs.util.V3 z, javajs.util.V3 x, javajs.util.V3 rotAxis, int nElectrons, boolean reverseColor) private void
void
fillMeshData
(MeshData meshData, int mode, IsosurfaceMesh mesh) private String
findValue
(int x, int y, boolean isPicking, javajs.util.BS bsVisible) protected void
getCapSlabInfo
(String script) private Object[]
getCapSlabObject
(String s, boolean isCap) legacy -- for some scripts with early isosurface slabbinggetCmd
(int index) private float[]
getDataRange
(IsosurfaceMesh mesh) private short
private Object
getFileReader
(String fileName) private void
getMeshCommand
(javajs.util.SB sb, int i) float[]
getPlane
(int x) static String
getPolygonColorData
(int ccount, short[] colixes, int[][] polygons, javajs.util.BS bsSlabDisplay) getProperty
(String property, int index) boolean
getPropertyData
(String property, Object[] data) protected Object
private boolean
getScriptBitSets
(String script, javajs.util.BS[] bsCmd) int
getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javajs.util.P3i offset, int vA, int vB, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, boolean isContourType, float[] fReturn) getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.float
getValue
(int x, int y, int z, int ptyz) for readers onlyprotected Object
protected Object
getVertices
(Mesh mesh) private void
hoverKey
(int x, int y) private void
void
private void
void
private boolean
isPickable
(IsosurfaceMesh m, javajs.util.BS bsVisible) protected void
newSg()
boolean
void
private void
setBsVdw()
private void
setColorPhase
(IsosurfaceMesh m, short colix0, short colix1) private void
setIsoMeshColor
(IsosurfaceMesh m, String color) private void
private void
setMeshI()
void
setOutputChannel
(javajs.api.GenericBinaryDocument binaryDoc, javajs.util.OC out) void
setProperty
(String propertyName, Object value, javajs.util.BS bs) private void
setPropertySuper
(String propertyName, Object value, javajs.util.BS bs) protected void
void
setRequiredFile
(String oldName, String fileName) protected void
setScriptInfo
(String strCommand) protected void
slabPolygons
(Object[] slabInfo) Methods inherited from class org.jmol.shape.MeshCollection
checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getMeshList, getPickedPoint, getPropDataMC, getPropMC, merge, 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
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Field Details
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isomeshes
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thisMesh
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actualID
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iHaveBitSets
protected boolean iHaveBitSets -
explicitContours
private boolean explicitContours -
atomIndex
private int atomIndex -
moNumber
private int moNumber -
moLinearCombination
private float[] moLinearCombination -
colorType
private int colorType -
defaultColix
private short defaultColix -
meshColix
private short meshColix -
center
private javajs.util.P3 center -
scale3d
private float scale3d -
isPhaseColored
private boolean isPhaseColored -
isColorExplicit
private boolean isColorExplicit -
scriptAppendix
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sg
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withinDistance2
private float withinDistance2 -
isWithinNot
private boolean isWithinNot -
withinPoints
private javajs.util.Lst<javajs.util.P3> withinPoints -
cutoffRange
private float[] cutoffRange -
allowMesh
boolean allowMesh -
script
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iHaveModelIndex
private boolean iHaveModelIndex -
nLCAO
private int nLCAO -
lcaoDir
private javajs.util.P4 lcaoDir -
associateNormals
private boolean associateNormals -
oldFileName
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newFileName
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MAX_OBJECT_CLICK_DISTANCE_SQUARED
private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED- See Also:
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ptXY
private final javajs.util.P3i ptXY -
keyXy
public int[] keyXy
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Constructor Details
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Isosurface
public Isosurface()
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Method Details
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allocMesh
- Overrides:
allocMesh
in classMeshCollection
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initShape
public void initShape()- Overrides:
initShape
in classMeshCollection
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newSg
protected void newSg() -
clearSg
protected void clearSg() -
setProperty
- Specified by:
setProperty
in classShape
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setPropI
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getFileReader
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setIsoMeshColor
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setColorPhase
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ensureMeshSource
private void ensureMeshSource() -
slabPolygons
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setPropertySuper
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getPropertyData
- Overrides:
getPropertyData
in classShape
- Returns:
- true if serviced
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getProperty
- Overrides:
getProperty
in classShape
- Returns:
- true if serviced
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getPropI
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getDataRange
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calculateVolumeOrArea
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getPolygonColorData
public static String getPolygonColorData(int ccount, short[] colixes, int[][] polygons, javajs.util.BS bsSlabDisplay) -
getShapeState
- Specified by:
getShapeState
in classShape
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getMeshCommand
private void getMeshCommand(javajs.util.SB sb, int i) -
getScriptBitSets
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getCapSlabInfo
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getCapSlabObject
legacy -- for some scripts with early isosurface slabbing- Parameters:
s
-isCap
-- Returns:
- slabInfo object
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initializeIsosurface
private void initializeIsosurface() -
initState
private void initState() -
setMeshI
private void setMeshI() -
discardTempData
protected void discardTempData(boolean discardAll) -
getDefaultColix
private short getDefaultColix() -
drawLcaoCartoon
private void drawLcaoCartoon(javajs.util.V3 z, javajs.util.V3 x, javajs.util.V3 rotAxis, int nElectrons, boolean reverseColor) -
createLcaoLobe
private void createLcaoLobe(javajs.util.V3 lobeAxis, float factor, int nElectrons) -
invalidateTriangles
public void invalidateTriangles()- Specified by:
invalidateTriangles
in interfaceMeshDataServer
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setOutputChannel
public void setOutputChannel(javajs.api.GenericBinaryDocument binaryDoc, javajs.util.OC out) - Specified by:
setOutputChannel
in interfaceMeshDataServer
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fillMeshData
- Specified by:
fillMeshData
in interfaceMeshDataServer
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notifySurfaceGenerationCompleted
public boolean notifySurfaceGenerationCompleted()- Specified by:
notifySurfaceGenerationCompleted
in interfaceMeshDataServer
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notifySurfaceMappingCompleted
public void notifySurfaceMappingCompleted()- Specified by:
notifySurfaceMappingCompleted
in interfaceMeshDataServer
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setBsVdw
private void setBsVdw() -
calculateGeodesicSurface
public javajs.util.P3[] calculateGeodesicSurface(javajs.util.BS bsSelected, float envelopeRadius) - Specified by:
calculateGeodesicSurface
in interfaceMeshDataServer
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getSurfacePointIndexAndFraction
public int getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javajs.util.P3i offset, int vA, int vB, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, boolean isContourType, float[] fReturn) Description copied from interface:VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge. If a vertex is discarded, then Integer.MAX_VALUE should be returned. the 3D coordinate of the point can be calculated using surfacePoint.scaleAdd(fraction, edgeVector, pointA); where fraction is generally calculated as: fraction = (cutoff - valueA) / (valueB - valueA); if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) fraction = (-cutoff - valueA) / (valueB - valueA); This method is also used by MarchingCubes to deliver the appropriate oblique planar coordinate to MarchingSquares for later contouring.- Specified by:
getSurfacePointIndexAndFraction
in interfaceVertexDataServer
vA
- [0:7]vB
- [0:7]edgeVector
- vector from A to B- Returns:
- new vertex index or Integer.MAX_VALUE
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addVertexCopy
public int addVertexCopy(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) Description copied from interface:VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane. The implementing method should COPY the Point3f using Point3f.set(). The data consumer can use the association key to group this vertex with others near the same gridpoint.- Specified by:
addVertexCopy
in interfaceVertexDataServer
assocVertex
- unique association vertex or -1- Returns:
- new vertex index
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addTriangleCheck
public int addTriangleCheck(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color) Description copied from interface:VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)- Specified by:
addTriangleCheck
in interfaceVertexDataServer
iContour
- TODO- Returns:
- polygon index or -1
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setScriptInfo
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addRequiredFile
- Specified by:
addRequiredFile
in interfaceMeshDataServer
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setRequiredFile
- Specified by:
setRequiredFile
in interfaceMeshDataServer
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setJvxlInfo
private void setJvxlInfo() -
getShapeDetail
- Overrides:
getShapeDetail
in classShape
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addMeshInfo
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getPlane
public float[] getPlane(int x) - Specified by:
getPlane
in interfaceVertexDataServer
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getValue
public float getValue(int x, int y, int z, int ptyz) Description copied from interface:VertexDataServer
for readers only- Specified by:
getValue
in interfaceVertexDataServer
- Returns:
- value[x][y][z]
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checkObjectHovered
public boolean checkObjectHovered(int x, int y, javajs.util.BS bsVisible) - Overrides:
checkObjectHovered
in classShape
- Returns:
- T/F
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hoverKey
private void hoverKey(int x, int y) -
checkObjectClicked
public Map<String,Object> checkObjectClicked(int x, int y, int action, javajs.util.BS bsVisible, boolean drawPicking) - Overrides:
checkObjectClicked
in classShape
drawPicking
- TODO- Returns:
- Hashtable containing information about pt clicked
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isPickable
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findValue
- Parameters:
x
-y
-isPicking
- IGNOREDbsVisible
-- Returns:
- value found
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getCmd
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getValues
- Overrides:
getValues
in classMeshCollection
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getVertices
- Overrides:
getVertices
in classMeshCollection
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