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) }