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Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Member Functions | Protected Attributes | Static Package Functions | Private Member Functions | Private Attributes

org::jmol::shapesurface::MolecularOrbital Class Reference

Inheritance diagram for org::jmol::shapesurface::MolecularOrbital:
Inheritance graph
Collaboration diagram for org::jmol::shapesurface::MolecularOrbital:
Collaboration graph

List of all members.

Public Member Functions

int addTriangleCheck (int iA, int iB, int iC, int check, int check2, boolean isAbsolute, int color)
int addVertexCopy (Point3f vertexXYZ, float value, int assocVertex)
void allocMesh (String thisID, Mesh m)
Point3f[] calculateGeodesicSurface (BitSet bsSelected, float envelopeRadius)
void checkBoundsMinMax (Point3f pointMin, Point3f pointMax)
Point3fi checkObjectClicked (int x, int y, int action, BitSet bsVisible)
boolean checkObjectDragged (int prevX, int prevY, int x, int y, int modifiers, BitSet bsVisible)
boolean checkObjectHovered (int x, int y, BitSet bsVisible)
void deleteMesh (int i)
void fillMeshData (MeshData meshData, int mode, IsosurfaceMesh mesh)
void findNearestAtomIndex (int xMouse, int yMouse, Atom[] closest, BitSet bsNot)
String getColorCommand (String type, short colix)
String getColorCommand (String type, byte pid, short colix)
int getIndexFromName (String thisID)
Mesh getMesh (String thisID)
void getPlane (int x)
Object getProperty (String propertyName, int param)
boolean getProperty (String property, Object[] data)
List getShapeDetail ()
String getShapeState ()
int getSize (Group group)
int getSize (int atomIndex)
int getSurfacePointIndexAndFraction (float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType, float[] fReturn)
float getValue (int x, int y, int z, int ptyz)
Viewer getViewer ()
final void initializeShape (Viewer viewer, Graphics3D g3d, ModelSet modelSet, int shapeID)
void initShape ()
void invalidateTriangles ()
void merge (Shape shape)
void notifySurfaceGenerationCompleted ()
void notifySurfaceMappingCompleted ()
short setColix (short colix, byte paletteID, int atomIndex)
void setModelClickability ()
void setModelIndex (int atomIndex, int modelIndex)
void setModelSet (ModelSet modelSet)
void setProperty (String propertyName, Object value, BitSet bs)
void setShapeProperty (String propertyName, Object value, BitSet bsSelected)
void setShapeSize (int size, RadiusData rd, BitSet bsSelected)
void setVisibilityFlags (BitSet bs)
boolean wasClicked (int x, int y)

Static Public Member Functions

static void appendCmd (StringBuffer s, String cmd)
static short getColix (short[] colixes, int i, Atom atom)
static String getFontCommand (String type, Font3D font)
static String getPolygonColorData (int ccount, short[] colixes)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore, String selectCmd)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore)
static void setStateInfo (Hashtable ht, int i1, int i2, String key)
static void setStateInfo (Hashtable ht, int i, String key)

Public Attributes

String actualID
short colix
Mesh currentMesh
boolean explicitID
Graphics3D g3d
boolean isBioShape
boolean isFixed
int meshCount
Mesh[] meshes = new Mesh[4]
int modelCount
ModelSet modelSet
String myType
int myVisibilityFlag
int nUnnamed
String script
int shapeID
String[] title
Viewer viewer

Static Public Attributes

static final float RADIUS_MAX = 4

Protected Member Functions

void checkExplicit (String id)
void clean ()
void clearSg ()
int coordinateInRange (int x, int y, Point3f vertex, int dmin2, Point3i ptXY)
void deleteMesh (String key)
void getCapSlabInfo (String script)
void getModelIndex (String script)
void initModelSet ()
short setColix (short colix, byte paletteID, Atom atom)
short setColix (short colix, byte paletteID, Bond bond)
void setScriptInfo (String strCommand)
void setSize (int size, BitSet bsSelected)
void setSize (RadiusData rd, BitSet bsSelected)
void setStatusPicked (int flag, Point3f v)

Protected Attributes

boolean allowContourLines
boolean allowMesh = true
boolean haveContours = false
Hashtable htObjects
boolean iHaveModelIndex
JvxlData jvxlData
Mesh linkedMesh
int modelIndex
Mesh pickedMesh = null
int pickedModel
int pickedVertex
String previousMeshID
SurfaceGenerator sg
IsosurfaceMesh thisMesh
boolean translucentAllowed = true
float translucentLevel
List xmlProperties

Static Package Functions

static String encodeColor (short colix)

Private Member Functions

String getId (int modelIndex)
String getMoState (int modelIndex)
boolean getSettings (String strID)
void setOrbital (int moNumber)

Private Attributes

Hashtable htModels
Integer moColorNeg = null
Integer moColorPos = null
Float moCutoff = null
boolean moDebug
int moDots = Token.nodots
int moFill = Token.nofill
int moFrontOnly = Token.frontonly
boolean moIsPositiveOnly = false
int moMesh = Token.mesh
int moNumber
Point4f moPlane = null
Float moResolution = null
Float moScale = null
String moTitleFormat = null
String moTranslucency = null
Float moTranslucentLevel = null
int myColorPt
String strID
Hashtable thisModel

Detailed Description

Definition at line 43 of file MolecularOrbital.java.

The documentation for this class was generated from the following file:

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