Package org.jmol.util

Class Measure

java.lang.Object

org.jmol.util.Measure

public final class Measure
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static float	radiansPerDegree

Constructor Summary

Constructors

Constructor	Description
Measure()

Method Summary

Modifier and Type	Method	Description
static void	calcAveragePoint(Point3f pointA, Point3f pointB, Point3f pointC)
static void	calcAveragePointN(Point3f[] points, int nPoints, Point3f averagePoint)
static void	calcBestAxisThroughPoints(Point3f[] points, Point3f axisA, Vector3f axisUnitVector, Vector3f vectorProjection, int nTriesMax)
static void	calcNormalizedNormal(Point3f pointA, Point3f pointB, Point3f pointC, Vector3f vNormNorm, Vector3f vAB, Vector3f vAC)
static Quaternion	calculateQuaternionRotation(Point3f[][] centerAndPoints, float[] retStddev)
static float	computeAngle(Tuple3f pointA, Tuple3f pointB, Tuple3f pointC, Vector3f vectorBA, Vector3f vectorBC, boolean asDegrees)
static float	computeAngleABC(Tuple3f pointA, Tuple3f pointB, Tuple3f pointC, boolean asDegrees)
static java.lang.Object	computeHelicalAxis(java.lang.String id, int tokType, Point3f a, Point3f b, Quaternion dq)
static float	computeTorsion(Tuple3f p1, Tuple3f p2, Tuple3f p3, Tuple3f p4, boolean asDegrees)
static float	distanceToPlane(Point4f plane, Point3f pt)
static float	distanceToPlane(Vector3f norm, float w, Point3f pt)
static float	distanceToPlaneD(Point4f plane, float d, Point3f pt)
static float	findAxis(Point3f[] points, int nPoints, Point3f axisA, Vector3f axisUnitVector, Vector3f vectorProjection)
static void	getBisectingPlane(Point3f pointA, Vector3f vAB, Point3f ptTemp, Vector3f vTemp, Point4f plane)
static Point3f[]	getCenterAndPoints(java.util.List<Point3f> vPts)
static float	getDirectedNormalThroughPoints(Point3f pointA, Point3f pointB, Point3f pointC, Point3f ptRef, Vector3f vNorm, Vector3f vAB, Vector3f vAC)
static Point3f	getIntersection(Point3f pt1, Vector3f v, Point4f plane, Point3f ptRet, Vector3f tempNorm, Vector3f vTemp)
static java.util.List<java.lang.Object>	getIntersectionPP(Point4f plane1, Point4f plane2)
static boolean	getNormalFromCenter(Point3f ptCenter, Point3f ptA, Point3f ptB, Point3f ptC, boolean isOutward, Vector3f normal)
static float	getNormalThroughPoints(Point3f pointA, Point3f pointB, Point3f pointC, Vector3f vNorm, Vector3f vAB, Vector3f vAC)
static void	getNormalToLine(Point3f pointA, Point3f pointB, Vector3f vNormNorm)
static void	getPlaneProjection(Point3f pt, Point4f plane, Point3f ptProj, Vector3f vNorm)
static void	getPlaneThroughPoint(Point3f pt, Vector3f normal, Point4f plane)
static void	getPlaneThroughPoints(Point3f pointA, Point3f pointB, Point3f pointC, Vector3f vNorm, Vector3f vAB, Vector3f vAC, Point4f plane)
static float	getRmsd(Point3f[][] centerAndPoints, Quaternion q)
static float	getTransformMatrix4(java.util.List<Point3f> ptsA, java.util.List<Point3f> ptsB, Matrix4f m, Point3f centerA)
static boolean	isInTetrahedron(Point3f pt, Point3f ptA, Point3f ptB, Point3f ptC, Point3f ptD, Point4f plane, Vector3f vTemp, Vector3f vTemp2, Vector3f vTemp3, boolean fullyEnclosed)
static void	projectOntoAxis(Point3f point, Point3f axisA, Vector3f axisUnitVector, Vector3f vectorProjection)
static java.util.List<Point3f>	transformPoints(java.util.List<Point3f> vPts, Matrix4f m4, Point3f center)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

radiansPerDegree

public static final float radiansPerDegree

See Also:

Constant Field Values

Constructor Detail

Measure

public Measure()

Method Detail

computeAngle

public static float computeAngle(Tuple3f pointA,
                                 Tuple3f pointB,
                                 Tuple3f pointC,
                                 Vector3f vectorBA,
                                 Vector3f vectorBC,
                                 boolean asDegrees)

computeAngleABC

public static float computeAngleABC(Tuple3f pointA,
                                    Tuple3f pointB,
                                    Tuple3f pointC,
                                    boolean asDegrees)

computeTorsion

public static float computeTorsion(Tuple3f p1,
                                   Tuple3f p2,
                                   Tuple3f p3,
                                   Tuple3f p4,
                                   boolean asDegrees)

computeHelicalAxis

public static java.lang.Object computeHelicalAxis(java.lang.String id,
                                                  int tokType,
                                                  Point3f a,
                                                  Point3f b,
                                                  Quaternion dq)

getPlaneThroughPoints

public static void getPlaneThroughPoints(Point3f pointA,
                                         Point3f pointB,
                                         Point3f pointC,
                                         Vector3f vNorm,
                                         Vector3f vAB,
                                         Vector3f vAC,
                                         Point4f plane)

getPlaneThroughPoint

public static void getPlaneThroughPoint(Point3f pt,
                                        Vector3f normal,
                                        Point4f plane)

distanceToPlane

public static float distanceToPlane(Point4f plane,
                                    Point3f pt)

distanceToPlaneD

public static float distanceToPlaneD(Point4f plane,
                                     float d,
                                     Point3f pt)

distanceToPlane

public static float distanceToPlane(Vector3f norm,
                                    float w,
                                    Point3f pt)

calcNormalizedNormal

public static void calcNormalizedNormal(Point3f pointA,
                                        Point3f pointB,
                                        Point3f pointC,
                                        Vector3f vNormNorm,
                                        Vector3f vAB,
                                        Vector3f vAC)

getDirectedNormalThroughPoints

public static float getDirectedNormalThroughPoints(Point3f pointA,
                                                   Point3f pointB,
                                                   Point3f pointC,
                                                   Point3f ptRef,
                                                   Vector3f vNorm,
                                                   Vector3f vAB,
                                                   Vector3f vAC)

getNormalThroughPoints

public static float getNormalThroughPoints(Point3f pointA,
                                           Point3f pointB,
                                           Point3f pointC,
                                           Vector3f vNorm,
                                           Vector3f vAB,
                                           Vector3f vAC)

getPlaneProjection

public static void getPlaneProjection(Point3f pt,
                                      Point4f plane,
                                      Point3f ptProj,
                                      Vector3f vNorm)

getNormalFromCenter

public static boolean getNormalFromCenter(Point3f ptCenter,
                                          Point3f ptA,
                                          Point3f ptB,
                                          Point3f ptC,
                                          boolean isOutward,
                                          Vector3f normal)

Parameters:

ptCenter -

ptA -

ptB -

ptC -

isOutward -

normal -

Returns:

true if winding is proper; false if not

getNormalToLine

public static void getNormalToLine(Point3f pointA,
                                   Point3f pointB,
                                   Vector3f vNormNorm)

getBisectingPlane

public static void getBisectingPlane(Point3f pointA,
                                     Vector3f vAB,
                                     Point3f ptTemp,
                                     Vector3f vTemp,
                                     Point4f plane)

projectOntoAxis

public static void projectOntoAxis(Point3f point,
                                   Point3f axisA,
                                   Vector3f axisUnitVector,
                                   Vector3f vectorProjection)

calcBestAxisThroughPoints

public static void calcBestAxisThroughPoints(Point3f[] points,
                                             Point3f axisA,
                                             Vector3f axisUnitVector,
                                             Vector3f vectorProjection,
                                             int nTriesMax)

findAxis

public static float findAxis(Point3f[] points,
                             int nPoints,
                             Point3f axisA,
                             Vector3f axisUnitVector,
                             Vector3f vectorProjection)

calcAveragePoint

public static void calcAveragePoint(Point3f pointA,
                                    Point3f pointB,
                                    Point3f pointC)

calcAveragePointN

public static void calcAveragePointN(Point3f[] points,
                                     int nPoints,
                                     Point3f averagePoint)

getCenterAndPoints

public static Point3f[] getCenterAndPoints(java.util.List<Point3f> vPts)

getTransformMatrix4

public static float getTransformMatrix4(java.util.List<Point3f> ptsA,
                                        java.util.List<Point3f> ptsB,
                                        Matrix4f m,
                                        Point3f centerA)

calculateQuaternionRotation

public static Quaternion calculateQuaternionRotation(Point3f[][] centerAndPoints,
                                                     float[] retStddev)

getRmsd

public static float getRmsd(Point3f[][] centerAndPoints,
                            Quaternion q)

transformPoints

public static java.util.List<Point3f> transformPoints(java.util.List<Point3f> vPts,
                                                      Matrix4f m4,
                                                      Point3f center)

isInTetrahedron

public static boolean isInTetrahedron(Point3f pt,
                                      Point3f ptA,
                                      Point3f ptB,
                                      Point3f ptC,
                                      Point3f ptD,
                                      Point4f plane,
                                      Vector3f vTemp,
                                      Vector3f vTemp2,
                                      Vector3f vTemp3,
                                      boolean fullyEnclosed)

getIntersectionPP

public static java.util.List<java.lang.Object> getIntersectionPP(Point4f plane1,
                                                                 Point4f plane2)

Parameters:

plane1 -

plane2 -

Returns:

[ point, vector ] or []

getIntersection

public static Point3f getIntersection(Point3f pt1,
                                      Vector3f v,
                                      Point4f plane,
                                      Point3f ptRet,
                                      Vector3f tempNorm,
                                      Vector3f vTemp)

Parameters:

pt1 - point on line

v - unit vector of line

plane -

ptRet - point of intersection of line with plane

tempNorm -

vTemp -

Returns:

ptRte