Package org.jmol.shapesurface
Class IsosurfaceMesh
java.lang.Object
org.jmol.util.MeshSurface
org.jmol.shape.Mesh
org.jmol.shapesurface.IsosurfaceMesh
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
int
int
boolean
float[]
int
Fields inherited from class org.jmol.shape.Mesh
atomIndex, bsTemp, cappingObject, checkByteCount, color, colorCommand, colorDensity, colorType, connectedAtoms, diameter, drawTriangles, fillTriangles, frontOnly, havePlanarContours, haveXyPoints, hoverLabel, index, insideOut, isModelConnected, isShell, isTwoSided, isValid, lattice, lighting, lineData, linkedMesh, meshColix, modelIndex, normixes, PREVIOUS_MESH_ID, ptCenter, recalcAltVertices, reverseColor, scale3d, scriptCommand, showContourLines, showPoints, showTriangles, slabbingObject, symopColixes, symopNormixes, symops, thisID, title, unitCell, useColix, vAB, vertexColorMap, visibilityFlags, visible, volumeRenderPointSize, vTemp, width
Fields inherited from class org.jmol.util.MeshSurface
altVertices, bsDisplay, bsPolygons, bsSlabDisplay, bsSlabGhost, colix, colixBack, colorsExplicit, dataOnly, haveQuads, iA, iB, iC, isColorSolid, isDrawPolygon, isMerged, mat4, mergePolygonCount0, mergeVertexCount0, meshType, normalCount, normals, normalsTemp, normixCount, nSets, oabc, offset, P_CHECK, P_CONTOUR, P_EXPLICIT_COLOR, pc, pcs, pis, polygonCount0, SEED_COUNT, slabColix, slabMeshType, slabOptions, surfaceAtoms, surfaceSet, vc, vcs, vertexCount0, vertexSets, vertexSource, vs, vvs, vwr
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Method Summary
Modifier and TypeMethodDescriptionstatic void
addContourPoints
(Lst<Object> v, BS bsContour, int i, SB fData, T3[] vertices, float[] vertexValues, int iA, int iB, int iC, float value) P3[]
create a set of contour data.getInfo
(boolean isAll) protected float
getPmeshData
(boolean isBinary) float
float[]
getValidValues
(BS bs) T3[]
getValidVertices
(BS bs) protected void
void
void
setBoundingBox
(P3[] pts) static void
setContourVector
(Lst<Object> v, int nPolygons, BS bsContour, float value, short colix, int color, SB fData) void
setDiscreteColixes
(float[] values, short[] colixes) void
setMerged
(boolean TF) void
setTranslucent
(boolean isTranslucent, float iLevel) protected void
sumVertexNormals
(T3[] vertices, V3[] vectorSums) void
updateCoordinates
(M4 m, BS bs) bs will be null if this is a set from the new isosurface MOVE [mat4] commandMethods inherited from class org.jmol.shape.Mesh
checkWithin, clear, clearMesh, getNormals, getNormalsTemp, getOffsetVertices, getRendering, getState, getVertexIndexFromNumber, getVisibleVBS, initialize, mesh1, rotateTranslate, setLighting, setNormixes, setShowWithin, setTokenProperty, setVisibilityFlags, sumVertexNormals2
Methods inherited from class org.jmol.util.MeshSurface
addPolygon, addPolygonC, addQuad, addTriangle, addTriangleCheck, addV, addVCVal, getFaces, getMeshSlicer, getSlabColor, getSlabType, getSphereData, getSphericalInterpolationFraction, getVertices, invalidatePolygons, newMesh, resetSlab, setABC, setBox, setColix, setColixBack, setPolygonCount, setTranslucentVertices, slabBrillouin, slabPolygonsList
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Field Details
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jvxlData
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vertexIncrement
public int vertexIncrement -
firstRealVertex
public int firstRealVertex -
dataType
public int dataType -
hasGridPoints
public boolean hasGridPoints -
colorEncoder
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colorPhased
public boolean colorPhased -
probeValues
public float[] probeValues
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Method Details
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getResolution
public float getResolution()- Overrides:
getResolution
in classMeshSurface
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setTranslucent
public void setTranslucent(boolean isTranslucent, float iLevel) - Overrides:
setTranslucent
in classMesh
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setMerged
public void setMerged(boolean TF) -
sumVertexNormals
- Overrides:
sumVertexNormals
in classMesh
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getContours
create a set of contour data. Each contour is a Vector containing: 0 Integer number of polygons (length of BitSet) 1 BitSet of critical triangles 2 Float value 3 int[] [colorArgb] 4 StringXBuilder containing encoded data for each segment: char type ('3', '6', '5') indicating which two edges of the triangle are connected: '3' 0x011 AB-BC '5' 0x101 AB-CA '6' 0x110 BC-CA char fraction along first edge (jvxlFractionToCharacter) char fraction along second edge (jvxlFractionToCharacter) 5- stream of pairs of points for rendering- Returns:
- contour vector set
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getPmeshData
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setContourVector
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addContourPoints
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setDiscreteColixes
public void setDiscreteColixes(float[] values, short[] colixes) -
reinitializeLightingAndColor
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getBoundingBox
- Overrides:
getBoundingBox
in classMesh
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setBoundingBox
- Overrides:
setBoundingBox
in classMeshSurface
- Parameters:
pts
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merge
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getUnitCell
- Overrides:
getUnitCell
in classMesh
- Returns:
- unitcell
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getMinDistance2ForVertexGrouping
protected float getMinDistance2ForVertexGrouping()- Overrides:
getMinDistance2ForVertexGrouping
in classMesh
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getVisibleVertexBitSet
- Overrides:
getVisibleVertexBitSet
in classMesh
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updateCoordinates
bs will be null if this is a set from the new isosurface MOVE [mat4] command- Parameters:
m
-bs
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getInfo
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getValidValues
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getValidVertices
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