Examples of javax.vecmath.Vector3f

javax.vecmath.Vector3f

      rotatePrev2 = atom2.index;
    } else {
      atom1 = modelSet.atoms[rotatePrev1];
      atom2 = modelSet.atoms[rotatePrev2];
    }
    Vector3f v1 = new Vector3f(atom2.screenX - atom1.screenX, atom2.screenY
        - atom1.screenY, 0);
    Vector3f v2 = new Vector3f(deltaX, deltaY, 0);
    v1.cross(v1, v2);
    float degrees = (v1.z > 0 ? 1 : -1) * v2.length();
   
    BitSet bs = BitSetUtil.copy(bsBranch);
    bs.andNot(selectionManager.getMotionFixedAtoms());


    rotateAboutPointsInternal(atom1, atom2, 0, degrees, false, bs,

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    float dx, dy;
    return (float) Math.sqrt((dx = _x - location._x) * dx + (dy = _y - location._y) * dy);
  }


  public Vector3f getVector(Location location) {
    return new Vector3f(location._x - _x, location._y - _y, 0);  
  }

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          return false;
        pt3 = (args.length > 2
            && (args[2].tok == Token.bitset || args[2].tok == Token.point3f) ? ptValue(
            args[2], false)
            : null);
        Vector3f norm = new Vector3f(pt2);
        if (pt3 == null) {
          if (args.length == 2 || !ScriptVariable.bValue(args[2])) {
            // plane(<point1>,<point2>) or 
            // plane(<point1>,<point2>,false)
            pt3 = new Point3f(pt1);
            pt3.add(pt2);
            pt3.scale(0.5f);
            norm.sub(pt1);
            norm.normalize();
          } else {
            // plane(<point1>,<vLine>,true)
          }
          return addX(Measure.getPlaneThroughPoint(pt3, norm));
        }
        // plane(<point1>,<point2>,<point3>)
        // plane(<point1>,<point2>,<point3>,<pointref>)
        Vector3f vAB = new Vector3f();
        Vector3f vAC = new Vector3f();
        float nd = Measure.getDirectedNormalThroughPoints(pt1, pt2, pt3,
            (args.length == 4 ? ptValue(args[3], true) : null), norm, vAB, vAC);
        return addX(new Point4f(norm.x, norm.y, norm.z, nd));
      }
    }

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      return false;
    ScriptVariable x1 = args[0];
    ScriptVariable x2 = args[1];
    if (x1.tok != Token.point3f || x2.tok != Token.point3f)
      return false;
    Vector3f a = new Vector3f((Point3f) x1.value);
    Vector3f b = new Vector3f((Point3f) x2.value);
    a.cross(a, b);
    return addX(new Point3f(a));
  }

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        case 1:
          Matrix3f m3 = new Matrix3f();
          m4.get(m3);
          return addX(m3);
        case 2:
          Vector3f v3 = new Vector3f();
          m4.get(v3);
          return addX(v3);
        default:
          return false;
        }

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    }
    return true;
  }


  static Matrix4f getMatrix4f(Matrix3f matRotate, Tuple3f vTranslate) {
    return new Matrix4f(matRotate, vTranslate == null ? new Vector3f() : new Vector3f(vTranslate), 1);
  }

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      error(ERROR_coordinateOrNameOrExpressionRequired);
    return center;
  }


  private Point4f planeParameter(int i) throws ScriptException {
    Vector3f vAB = new Vector3f();
    Vector3f vAC = new Vector3f();
    Point4f plane = null;
    boolean isNegated = (tokAt(i) == Token.minus);
    if (isNegated)
      i++;
    if (i < statementLength)
      switch (getToken(i).tok) {
      case Token.point4f:
        plane = (Point4f) theToken.value;
        break;
      case Token.dollarsign:
        String id = objectNameParameter(++i);
        if (isSyntaxCheck)
          return new Point4f();
        int shapeType = shapeManager.getShapeIdFromObjectName(id);
        switch (shapeType) {
        case JmolConstants.SHAPE_DRAW:
          setShapeProperty(JmolConstants.SHAPE_DRAW, "thisID", id);
          Point3f[] points = (Point3f[]) getShapeProperty(
              JmolConstants.SHAPE_DRAW, "vertices");
          if (points == null || points.length < 3 || points[0] == null
              || points[1] == null || points[2] == null)
            break;
          plane = Measure.getPlaneThroughPoints(points[0], points[1],
              points[2], new Vector3f(), vAB, vAC);
          break;
        case JmolConstants.SHAPE_ISOSURFACE:
          setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "thisID", id);
          plane = (Point4f) getShapeProperty(JmolConstants.SHAPE_ISOSURFACE,
              "plane");
          break;
        }
        break;
      case Token.x:
        if (!checkToken(++i) || getToken(i++).tok != Token.opEQ)
          evalError("x=?", null);
        plane = new Point4f(1, 0, 0, -floatParameter(i));
        break;
      case Token.y:
        if (!checkToken(++i) || getToken(i++).tok != Token.opEQ)
          evalError("y=?", null);
        plane = new Point4f(0, 1, 0, -floatParameter(i));
        break;
      case Token.z:
        if (!checkToken(++i) || getToken(i++).tok != Token.opEQ)
          evalError("z=?", null);
        plane = new Point4f(0, 0, 1, -floatParameter(i));
        break;
      case Token.identifier:
      case Token.string:
        String str = parameterAsString(i);
        if (str.equalsIgnoreCase("xy"))
          return new Point4f(0, 0, 1, 0);
        if (str.equalsIgnoreCase("xz"))
          return new Point4f(0, 1, 0, 0);
        if (str.equalsIgnoreCase("yz"))
          return new Point4f(1, 0, 0, 0);
        iToken += 2;
        break;
      case Token.leftbrace:
        if (!isPoint3f(i)) {
          plane = getPoint4f(i);
          break;
        }
        // fall through
      case Token.bitset:
      case Token.expressionBegin:
        Point3f pt1 = atomCenterOrCoordinateParameter(i);
        if (getToken(++iToken).tok == Token.comma)
          ++iToken;
        Point3f pt2 = atomCenterOrCoordinateParameter(iToken);
        if (getToken(++iToken).tok == Token.comma)
          ++iToken;
        Point3f pt3 = atomCenterOrCoordinateParameter(iToken);
        i = iToken;
        Vector3f norm = new Vector3f();
        float w = Measure.getNormalThroughPoints(pt1, pt2, pt3, norm, vAB, vAC);
        plane = new Point4f(norm.x, norm.y, norm.z, w);
        if (!isSyntaxCheck && Logger.debugging)
          Logger.debug("points: " + pt1 + pt2 + pt3 + " defined plane: "
              + plane);

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      Logger.info("defined plane: " + p);
    return p;
  }


  protected Point4f getHklPlane(Point3f pt) {
    Vector3f vAB = new Vector3f();
    Vector3f vAC = new Vector3f();
    Point3f pt1 = new Point3f(pt.x == 0 ? 1 : 1 / pt.x, 0, 0);
    Point3f pt2 = new Point3f(0, pt.y == 0 ? 1 : 1 / pt.y, 0);
    Point3f pt3 = new Point3f(0, 0, pt.z == 0 ? 1 : 1 / pt.z);
    // trick for 001 010 100 is to define the other points on other edges
    if (pt.x == 0 && pt.y == 0 && pt.z == 0) {
      return null;
    } else if (pt.x == 0 && pt.y == 0) {
      pt1.set(1, 0, pt3.z);
      pt2.set(0, 1, pt3.z);
    } else if (pt.y == 0 && pt.z == 0) {
      pt2.set(pt1.x, 0, 1);
      pt3.set(pt1.x, 1, 0);
    } else if (pt.z == 0 && pt.x == 0) {
      pt3.set(0, pt2.y, 1);
      pt1.set(1, pt2.y, 0);
    } else if (pt.x == 0) {
      pt1.set(1, pt2.y, 0);
    } else if (pt.y == 0) {
      pt2.set(0, 1, pt3.z);
    } else if (pt.z == 0) {
      pt3.set(pt1.x, 0, 1);
    }
    // base this one on the currently defined unit cell
    viewer.toCartesian(pt1, false);
    viewer.toCartesian(pt2, false);
    viewer.toCartesian(pt3, false);
    Vector3f plane = new Vector3f();
    float w = Measure.getNormalThroughPoints(pt1, pt2, pt3, plane, vAB, vAC);
    return new Point4f(plane.x, plane.y, plane.z, w);
  }

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  private void move() throws ScriptException {
    if (statementLength > 11)
      error(ERROR_badArgumentCount);
    // rotx roty rotz zoom transx transy transz slab seconds fps
    Vector3f dRot = new Vector3f(floatParameter(1), floatParameter(2),
        floatParameter(3));
    float dZoom = floatParameter(4);
    Vector3f dTrans = new Vector3f(intParameter(5), intParameter(6),
        intParameter(7));
    float dSlab = floatParameter(8);
    float floatSecondsTotal = floatParameter(9);
    int fps = (statementLength == 11 ? intParameter(10) : 30);
    if (isSyntaxCheck)

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        refresh();
      viewer.moveTo(f, null, JmolConstants.axisZ, 0, null, 100, 0, 0, 0, null,
          Float.NaN, Float.NaN, Float.NaN);
      return;
    }
    Vector3f axis = new Vector3f(Float.NaN, 0, 0);
    Point3f center = null;
    int i = 1;
    float floatSecondsTotal = (isFloatParameter(i) ? floatParameter(i++) : 2.0f);
    float degrees = 90;
    BitSet bsCenter = null;
    switch (getToken(i).tok) {
    case Token.quaternion:
      Quaternion q;
      boolean isMolecular = false;
      if (tokAt(++i) == Token.molecular) {
        // see comment below
        isMolecular = true;
        i++;
      }
      if (tokAt(i) == Token.bitset || tokAt(i) == Token.expressionBegin) {
        isMolecular = true;
        center = centerParameter(i);
        if (!(expressionResult instanceof BitSet))
          error(ERROR_invalidArgument);
        bsCenter = (BitSet) expressionResult;
        q = (isSyntaxCheck ? new Quaternion() : viewer
            .getAtomQuaternion(bsCenter.nextSetBit(0)));
      } else {
        q = getQuaternionParameter(i);
      }
      i = iToken + 1;
      if (q == null)
        error(ERROR_invalidArgument);
      AxisAngle4f aa = q.toAxisAngle4f();
      axis.set(aa.x, aa.y, aa.z);
      /*
       * The quaternion angle for an atom represents the angle by which the
       * reference frame must be rotated to match the frame defined for the
       * residue.
       * 
       * However, to "moveTo" this frame as the REFERENCE frame, what we have to
       * do is take that quaternion frame and rotate it BACKWARD by that many
       * degrees. Then it will match the reference frame, which is ultimately
       * our window frame.
       * 
       * We only apply this for molecular-type quaternions, because in general
       * the orientation quaternion refers to how the reference plane has been
       * changed (the orientation matrix)
       */
      degrees = (isMolecular ? -1 : 1) * (float) (aa.angle * 180.0 / Math.PI);
      break;
    case Token.point4f:
    case Token.point3f:
    case Token.leftbrace:
      // {X, Y, Z} deg or {x y z deg}
      if (isPoint3f(i)) {
        axis.set(getPoint3f(i, true));
        i = iToken + 1;
        degrees = floatParameter(i++);
      } else {
        Point4f pt4 = getPoint4f(i);
        i = iToken + 1;
        axis.set(pt4.x, pt4.y, pt4.z);
        degrees = (pt4.x == 0 && pt4.y == 0 && pt4.z == 0 ? Float.NaN : pt4.w);
      }
      break;
    case Token.front:
      axis.set(1, 0, 0);
      degrees = 0f;
      checkLength(++i);
      break;
    case Token.back:
      axis.set(0, 1, 0);
      degrees = 180f;
      checkLength(++i);
      break;
    case Token.left:
      axis.set(0, 1, 0);
      checkLength(++i);
      break;
    case Token.right:
      axis.set(0, -1, 0);
      checkLength(++i);
      break;
    case Token.top:
      axis.set(1, 0, 0);
      checkLength(++i);
      break;
    case Token.bottom:
      axis.set(-1, 0, 0);
      checkLength(++i);
      break;
    default:
      // X Y Z deg
      axis = new Vector3f(floatParameter(i++), floatParameter(i++),
          floatParameter(i++));
      degrees = floatParameter(i++);
    }
    if (Float.isNaN(axis.x) || Float.isNaN(axis.y) || Float.isNaN(axis.z))
      axis.set(0, 0, 0);
    else if (axis.length() == 0 && degrees == 0)
      degrees = Float.NaN;
    boolean isChange = !viewer.isInPosition(axis, degrees);
    // optional zoom
    float zoom = (isFloatParameter(i) ? floatParameter(i++) : Float.NaN);
    // optional xTrans yTrans

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