META-INF/
META-INF/MANIFEST.MF
org/
org/jmol/
org/jmol/shapespecial/
org/jmol/shapespecial/Dipole.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Dipole extends java.lang.Object {
String thisID
short mad
short colix
short type
javax.vecmath.Point3f origin
javax.vecmath.Point3f center
javax.vecmath.Vector3f vector
String dipoleInfo
float dipoleValue
boolean isUserValue
float offsetSide
float offsetAngstroms
int offsetPercent
int visibilityFlags
int modelIndex
boolean visible
boolean noCross
boolean haveAtoms
boolean isValid
org.jmol.modelset.Atom[] atoms
javax.vecmath.Point3f[] coords
org.jmol.modelset.Bond bond
static final short DIPOLE_TYPE_UNKNOWN
static final short DIPOLE_TYPE_POINTS
static final short DIPOLE_TYPE_ATOMS
static final short DIPOLE_TYPE_BOND
static final short DIPOLE_TYPE_MOLECULAR
static final short DIPOLE_TYPE_POINTVECTOR
void <init> ()
void <init> (int, java.lang.String, java.lang.String, short, short, boolean)
void setTranslucent (boolean, float)
void set (java.lang.String, java.lang.String, org.jmol.modelset.Atom[], float, short, float, int, float, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private void set (javax.vecmath.Point3f, javax.vecmath.Point3f)
void set (float)
void set (javax.vecmath.Point3f, javax.vecmath.Point3f, float)
void set (javax.vecmath.Point3f, javax.vecmath.Vector3f)
void set (org.jmol.modelset.Atom, org.jmol.modelset.Atom, float)
void centerDipole ()
boolean isBondType ()
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/Dipoles.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Dipoles extends org.jmol.shape.Shape {
static final short DEFAULT_MAD
static final float DEFAULT_OFFSETSIDE
int dipoleCount
org.jmol.shapespecial.Dipole[] dipoles
private org.jmol.shapespecial.Dipole currentDipole
private org.jmol.shapespecial.Dipole tempDipole
private javax.vecmath.Point3f startCoord
private javax.vecmath.Point3f endCoord
private float dipoleValue
private boolean isUserValue
private boolean isBond
private boolean iHaveTwoEnds
private int atomIndex1
private int atomIndex2
private short colix
private javax.vecmath.Vector3f calculatedDipole
private String wildID
private static final float E_ANG_PER_DEBYE
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setProperty (int, boolean, int, float)
private void setProperty (int, org.jmol.shapespecial.Dipole, int, float)
public java.lang.Object getProperty (java.lang.String, int)
private void getBondDipoles ()
private boolean isBondDipole (int)
private void setColixDipole (short, short, java.util.BitSet)
private void setDipole ()
private void setDipole (org.jmol.modelset.Atom, org.jmol.modelset.Atom, float, float)
private int getDipoleIndex (java.lang.String, java.lang.String)
private boolean isSameAtoms (org.jmol.shapespecial.Dipole, java.lang.String)
private int getDipoleIndex (int, int)
private void deleteDipole (org.jmol.shapespecial.Dipole)
private org.jmol.shapespecial.Dipole findDipole (java.lang.String)
private org.jmol.shapespecial.Dipole findDipole (org.jmol.modelset.Atom, org.jmol.modelset.Atom, boolean)
private org.jmol.shapespecial.Dipole findBondDipole (org.jmol.modelset.Bond)
private org.jmol.shapespecial.Dipole findDipole (java.lang.String, java.lang.String)
private org.jmol.shapespecial.Dipole allocDipole (java.lang.String, java.lang.String)
private void dumpDipoles (java.lang.String)
private void clear (boolean)
public int getIndexFromName (java.lang.String)
public java.util.Vector getShapeDetail ()
private void setModelIndex ()
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/DipolesRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DipolesRenderer extends org.jmol.shape.ShapeRenderer {
private float dipoleVectorScale
private final javax.vecmath.Vector3f offset
private final javax.vecmath.Point3i[] screens
private final javax.vecmath.Point3f[] points
private javax.vecmath.Point3f cross0
private javax.vecmath.Point3f cross1
private static final int cylinderBase
private static final int cross
private static final int crossEnd
private static final int center
private static final int arrowHeadBase
private static final int arrowHeadTip
private int diameter
private int headWidthPixels
private int crossWidthPixels
private static final float arrowHeadOffset
private static final float arrowHeadWidthFactor
private static final float crossOffset
private static final float crossWidth
public void <init> ()
protected void render ()
private boolean transform (org.jmol.shapespecial.Dipole)
private void renderDipoleVector (org.jmol.shapespecial.Dipole)
}
org/jmol/shapespecial/Draw.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Draw extends org.jmol.shape.MeshCollection {
org.jmol.shapespecial.DrawMesh[] dmeshes
org.jmol.shapespecial.DrawMesh thisMesh
private javax.vecmath.Point3f[] ptList
private javax.vecmath.Vector3f offset
private int nPoints
private int diameter
private float width
private float newScale
private float length
private boolean isCurve
private boolean isArc
private boolean isArrow
private boolean isLine
private boolean isVector
private boolean isCircle
private boolean isPerpendicular
private boolean isCylinder
private boolean isVertices
private boolean isPlane
private boolean isReversed
private boolean isRotated45
private boolean isCrossed
private boolean isValid
private boolean noHead
private int indicatedModelIndex
private int[] modelInfo
private boolean makePoints
private int nidentifiers
private int nbitsets
private javax.vecmath.Point4f plane
private java.util.BitSet bsAllModels
private java.util.Vector vData
private static final int PT_COORD
private static final int PT_IDENTIFIER
private static final int PT_BITSET
private static final int PT_MODEL_INDEX
private static final int PT_MODEL_BASED_POINTS
private final javax.vecmath.Vector3f vAB
private final javax.vecmath.Vector3f vAC
private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED
private org.jmol.shapespecial.DrawMesh pickedMesh
private int pickedModel
private int pickedVertex
private final javax.vecmath.Point3i ptXY
public void <init> ()
public void allocMesh (java.lang.String)
void setPropertySuper (java.lang.String, java.lang.Object, java.util.BitSet)
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void resetObjects ()
public java.lang.Object getProperty (java.lang.String, int)
private javax.vecmath.Point3f getSpinCenter (java.lang.String, int, int)
private javax.vecmath.Vector3f getSpinAxis (java.lang.String, int)
private boolean setDrawing ()
private void addPoint (javax.vecmath.Point3f, int)
private boolean setPoints (int, int)
private void setPolygon (int)
private static void scaleDrawing (org.jmol.shapespecial.DrawMesh, float)
private static final void setAxes (org.jmol.shapespecial.DrawMesh)
public void setVisibilityFlags (java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
private org.jmol.util.Point3fi getPickedPoint (javax.vecmath.Point3f)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public synchronized boolean checkObjectDragged (int, int, int, int, int, java.util.BitSet)
private void move2D (org.jmol.shapespecial.DrawMesh, int[], int, int, int, boolean)
private boolean findPickedObject (int, int, boolean, java.util.BitSet)
private java.lang.String getDrawCommand (org.jmol.shapespecial.DrawMesh)
private java.lang.String getDrawCommand (org.jmol.shapespecial.DrawMesh, int)
static boolean isPolygonDisplayable (org.jmol.shape.Mesh, int)
private static java.lang.String getVertexList (org.jmol.shapespecial.DrawMesh, int, int)
public java.util.Vector getShapeDetail ()
public java.lang.String getShapeState ()
static javax.vecmath.Point3f randomPoint ()
}
org/jmol/shapespecial/DrawMesh.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DrawMesh extends org.jmol.shape.Mesh {
java.util.BitSet modelFlags
int drawType
int[] drawTypes
javax.vecmath.Point3f[] ptCenters
javax.vecmath.Vector3f axis
javax.vecmath.Vector3f[] axes
int drawVertexCount
int[] drawVertexCounts
boolean isFixed
boolean isVector
float drawArrowScale
boolean nohead
java.util.BitSet bsMeshesVisible
void <init> (java.lang.String, org.jmol.g3d.Graphics3D, short, int)
final void setCenter (int)
void offset (javax.vecmath.Vector3f)
public void deleteAtoms (int)
}
org/jmol/shapespecial/DrawRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DrawRenderer extends org.jmol.shape.MeshRenderer {
private int drawType
private org.jmol.shapespecial.DrawMesh dmesh
private javax.vecmath.Point3f[] controlHermites
private final javax.vecmath.Point3f vpt0
private final javax.vecmath.Point3f vpt1
private final javax.vecmath.Point3f vpt2
private final javax.vecmath.Vector3f vTemp
private final javax.vecmath.Vector3f vTemp2
private final javax.vecmath.Point3f pt0f
private final javax.vecmath.Point3i pt0i
public void <init> ()
protected void render ()
protected boolean isPolygonDisplayable (int)
protected void render2 (boolean)
private void renderXyArrow (int)
private void renderArrowHead (javax.vecmath.Point3f, javax.vecmath.Point3f, float, boolean, boolean)
private void renderHandles ()
private void renderInfo ()
}
org/jmol/shapespecial/Ellipsoids$Ellipsoid.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Ellipsoids$Ellipsoid extends java.lang.Object {
String id
javax.vecmath.Vector3f[] axes
float[] lengths
javax.vecmath.Point3f center
double[] coef
short colix
int modelIndex
float scale
boolean visible
boolean isValid
boolean isOn
void <init> (java.lang.String, int)
}
org/jmol/shapespecial/Ellipsoids.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Ellipsoids extends org.jmol.shape.AtomShape {
java.util.Hashtable htEllipsoids
boolean haveEllipsoids
org.jmol.shapespecial.Ellipsoids$Ellipsoid ellipsoid
private static float[] crtval
public void <init> ()
public int getIndexFromName (java.lang.String)
public void setSize (int, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void updateEquation (org.jmol.shapespecial.Ellipsoids$Ellipsoid)
public java.lang.String getShapeState ()
public void setVisibilityFlags (java.util.BitSet)
static final float getRadius (int)
static void <clinit> ()
}
org/jmol/shapespecial/EllipsoidsRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.EllipsoidsRenderer extends org.jmol.shape.ShapeRenderer {
private org.jmol.shapespecial.Ellipsoids ellipsoids
private boolean drawDots
private boolean drawArcs
private boolean drawAxes
private boolean drawFill
private boolean drawBall
private boolean wireframeOnly
private int dotCount
private int[] coords
private javax.vecmath.Vector3f[] axes
private final float[] factoredLengths
private int diameter
private int diameter0
private int selectedOctant
private javax.vecmath.Point3i[] selectedPoints
private int iCutout
private javax.vecmath.Matrix3f mat
private javax.vecmath.Matrix3f mTemp
private javax.vecmath.Matrix4f mDeriv
private javax.vecmath.Matrix3f matScreenToCartesian
private javax.vecmath.Matrix3f matScreenToEllipsoid
private javax.vecmath.Matrix3f matEllipsoidToScreen
private double[] coef
private final javax.vecmath.Vector3f v1
private final javax.vecmath.Vector3f v2
private final javax.vecmath.Vector3f v3
private final javax.vecmath.Point3f pt1
private final javax.vecmath.Point3f pt2
private final javax.vecmath.Point3i s0
private final javax.vecmath.Point3i s1
private final javax.vecmath.Point3i s2
private static final float toRadians
private static final float[] cossin
private final javax.vecmath.Point3i[] screens
private final javax.vecmath.Point3f[] points
private static int[] axisPoints
private static int[] octants
private int dx
private float perspectiveFactor
private javax.vecmath.Point3f center
private static final javax.vecmath.Vector3f[] unitVectors
private static final javax.vecmath.Vector3f[] unitAxisVectors
public void <init> ()
protected void render ()
private void render1 (org.jmol.modelset.Atom, java.lang.Object[])
private void setMatrices ()
private void setAxes (float)
private void renderAxes ()
private void renderDots (javax.vecmath.Point3f)
private void renderArcs (javax.vecmath.Point3f)
private void renderArc (javax.vecmath.Point3f, int, int)
protected void renderEllipsoid (org.jmol.shapespecial.Ellipsoids$Ellipsoid)
protected void renderBall ()
private void setSelectedOctant ()
static void <clinit> ()
}
org/jmol/shapespecial/GeoSurface.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.GeoSurface extends org.jmol.shape.Dots {
public void <init> ()
public void initShape ()
}
org/jmol/shapespecial/GeoSurfaceRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.GeoSurfaceRenderer extends org.jmol.shape.DotsRenderer {
private javax.vecmath.Point3i facePt1
private javax.vecmath.Point3i facePt2
private javax.vecmath.Point3i facePt3
public void <init> ()
protected void render ()
protected void renderConvex (short, int[], int)
private void renderSurface (int[])
}
org/jmol/shapespecial/Polyhedra$Polyhedron.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Polyhedra$Polyhedron extends java.lang.Object {
int modelIndex
final org.jmol.modelset.Atom centralAtom
final org.jmol.modelset.Atom[] vertices
int ptCenter
boolean visible
final short[] normixes
byte[] planes
int visibilityFlags
boolean collapsed
float myFaceCenterOffset
float myDistanceFactor
private final org.jmol.shapespecial.Polyhedra this$0
void <init> (org.jmol.shapespecial.Polyhedra, org.jmol.modelset.Atom, int, int, int, org.jmol.modelset.Atom[], short[], byte[])
java.lang.String getState (java.util.Hashtable)
}
org/jmol/shapespecial/Polyhedra.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Polyhedra extends org.jmol.shape.AtomShape {
private static final float DEFAULT_DISTANCE_FACTOR
private static final float DEFAULT_FACECENTEROFFSET
private static final int EDGES_NONE
static final int EDGES_ALL
static final int EDGES_FRONT
private static final int MAX_VERTICES
private static final int FACE_COUNT_MAX
private org.jmol.modelset.Atom[] otherAtoms
int polyhedronCount
org.jmol.shapespecial.Polyhedra$Polyhedron[] polyhedrons
int drawEdges
private float radius
private int nVertices
float faceCenterOffset
float distanceFactor
boolean isCollapsed
private boolean iHaveCenterBitSet
private boolean bondedOnly
private boolean haveBitSetVertices
private java.util.BitSet centers
private java.util.BitSet bsVertices
private java.util.BitSet bsVertexCount
private short[] normixesT
private byte[] planesT
private static final javax.vecmath.Point3f randomPoint
private javax.vecmath.Vector3f align1
private javax.vecmath.Vector3f align2
private final javax.vecmath.Vector3f vAB
private final javax.vecmath.Vector3f vAC
private static float minDistanceForPlanarity
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void deletePolyhedra ()
private void setVisible (boolean)
private void buildPolyhedra ()
private org.jmol.shapespecial.Polyhedra$Polyhedron constructBondsPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron constructBitSetPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron constructRadiusPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron validatePolyhedronNew (org.jmol.modelset.Atom, int, org.jmol.modelset.Atom[])
private java.lang.String faceId (int, int, int)
private boolean isAligned (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
private boolean isPlanar (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
static void <clinit> ()
}
org/jmol/shapespecial/PolyhedraRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.PolyhedraRenderer extends org.jmol.shape.ShapeRenderer {
private int drawEdges
public void <init> ()
protected void render ()
private void render1 (org.jmol.shapespecial.Polyhedra$Polyhedron, short)
private void drawFace (short, org.jmol.modelset.Atom, org.jmol.modelset.Atom, org.jmol.modelset.Atom, boolean, boolean)
private void fillFace (short, org.jmol.modelset.Atom, org.jmol.modelset.Atom, org.jmol.modelset.Atom)
}
org/jmol/shapespecial/Vectors.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Vectors extends org.jmol.shape.AtomShape {
public void <init> ()
protected void initModelSet ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/VectorsRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.VectorsRenderer extends org.jmol.shape.ShapeRenderer {
final javax.vecmath.Point3f pointVectorEnd
final javax.vecmath.Point3f pointArrowHead
final javax.vecmath.Point3i screenVectorEnd
final javax.vecmath.Point3i screenArrowHead
final javax.vecmath.Vector3f headOffsetVector
int diameter
int headWidthPixels
float vectorScale
float headScale
boolean doShaft
static final float arrowHeadOffset
public void <init> ()
protected void render ()
boolean transform (short, org.jmol.modelset.Atom, javax.vecmath.Vector3f)
void renderVector (org.jmol.modelset.Atom)
}