org.jmol.util
Class Measure
java.lang.Object
org.jmol.util.Measure
public final class Measure
- extends java.lang.Object
Method Summary |
static void |
calcAveragePoint(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC)
|
static void |
calcAveragePointN(javax.vecmath.Point3f[] points,
int nPoints,
javax.vecmath.Point3f averagePoint)
|
static void |
calcBestAxisThroughPoints(javax.vecmath.Point3f[] points,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection,
int nTriesMax)
|
static void |
calcNormalizedNormal(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNormNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
|
static Quaternion |
calculateQuaternionRotation(javax.vecmath.Point3f[][] centerAndPoints,
float[] retStddev,
boolean doReport)
|
static void |
calcXYNormalToLine(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Vector3f vNormNorm)
|
static float |
computeAngle(javax.vecmath.Tuple3f pointA,
javax.vecmath.Tuple3f pointB,
javax.vecmath.Tuple3f pointC,
boolean asDegrees)
|
static float |
computeAngle(javax.vecmath.Tuple3f pointA,
javax.vecmath.Tuple3f pointB,
javax.vecmath.Tuple3f pointC,
javax.vecmath.Vector3f vectorBA,
javax.vecmath.Vector3f vectorBC,
boolean asDegrees)
|
static java.lang.Object |
computeHelicalAxis(java.lang.String id,
int tokType,
javax.vecmath.Point3f a,
javax.vecmath.Point3f b,
Quaternion dq)
|
static float |
computeTorsion(javax.vecmath.Tuple3f p1,
javax.vecmath.Tuple3f p2,
javax.vecmath.Tuple3f p3,
javax.vecmath.Tuple3f p4,
boolean asDegrees)
|
static float |
distanceToPlane(javax.vecmath.Point4f plane,
float d,
javax.vecmath.Point3f pt)
|
static float |
distanceToPlane(javax.vecmath.Point4f plane,
javax.vecmath.Point3f pt)
|
static float |
distanceToPlane(javax.vecmath.Vector3f norm,
float w,
javax.vecmath.Point3f pt)
|
static float |
findAxis(javax.vecmath.Point3f[] points,
int nPoints,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection)
|
static javax.vecmath.Point3f[] |
getCenterAndPoints(java.util.List vPts)
|
static float |
getDirectedNormalThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Point3f ptRef,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
|
static boolean |
getNormalFromCenter(javax.vecmath.Point3f ptCenter,
javax.vecmath.Point3f ptA,
javax.vecmath.Point3f ptB,
javax.vecmath.Point3f ptC,
boolean isOutward,
javax.vecmath.Vector3f normal)
|
static float |
getNormalThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
|
static javax.vecmath.Point4f |
getPlaneThroughPoint(javax.vecmath.Point3f pt,
javax.vecmath.Vector3f normal)
|
static javax.vecmath.Point4f |
getPlaneThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
|
static float |
getRmsd(javax.vecmath.Point3f[][] centerAndPoints,
Quaternion q)
|
static float |
getTransformMatrix4(java.util.List ptsA,
java.util.List ptsB,
javax.vecmath.Matrix4f m,
javax.vecmath.Point3f centerA)
|
static void |
moveToPlane(javax.vecmath.Point4f plane,
javax.vecmath.Point3f a)
|
static void |
projectOntoAxis(javax.vecmath.Point3f point,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection)
|
static java.util.List |
transformPoints(java.util.List vPts,
javax.vecmath.Matrix4f m4,
javax.vecmath.Point3f center)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
radiansPerDegree
public static final float radiansPerDegree
- See Also:
- Constant Field Values
Measure
public Measure()
computeAngle
public static float computeAngle(javax.vecmath.Tuple3f pointA,
javax.vecmath.Tuple3f pointB,
javax.vecmath.Tuple3f pointC,
javax.vecmath.Vector3f vectorBA,
javax.vecmath.Vector3f vectorBC,
boolean asDegrees)
computeAngle
public static float computeAngle(javax.vecmath.Tuple3f pointA,
javax.vecmath.Tuple3f pointB,
javax.vecmath.Tuple3f pointC,
boolean asDegrees)
computeTorsion
public static float computeTorsion(javax.vecmath.Tuple3f p1,
javax.vecmath.Tuple3f p2,
javax.vecmath.Tuple3f p3,
javax.vecmath.Tuple3f p4,
boolean asDegrees)
computeHelicalAxis
public static java.lang.Object computeHelicalAxis(java.lang.String id,
int tokType,
javax.vecmath.Point3f a,
javax.vecmath.Point3f b,
Quaternion dq)
getPlaneThroughPoints
public static javax.vecmath.Point4f getPlaneThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
getPlaneThroughPoint
public static javax.vecmath.Point4f getPlaneThroughPoint(javax.vecmath.Point3f pt,
javax.vecmath.Vector3f normal)
distanceToPlane
public static float distanceToPlane(javax.vecmath.Point4f plane,
javax.vecmath.Point3f pt)
distanceToPlane
public static float distanceToPlane(javax.vecmath.Point4f plane,
float d,
javax.vecmath.Point3f pt)
distanceToPlane
public static float distanceToPlane(javax.vecmath.Vector3f norm,
float w,
javax.vecmath.Point3f pt)
calcNormalizedNormal
public static void calcNormalizedNormal(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNormNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
getDirectedNormalThroughPoints
public static float getDirectedNormalThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Point3f ptRef,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
getNormalThroughPoints
public static float getNormalThroughPoints(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC,
javax.vecmath.Vector3f vNorm,
javax.vecmath.Vector3f vAB,
javax.vecmath.Vector3f vAC)
moveToPlane
public static void moveToPlane(javax.vecmath.Point4f plane,
javax.vecmath.Point3f a)
getNormalFromCenter
public static boolean getNormalFromCenter(javax.vecmath.Point3f ptCenter,
javax.vecmath.Point3f ptA,
javax.vecmath.Point3f ptB,
javax.vecmath.Point3f ptC,
boolean isOutward,
javax.vecmath.Vector3f normal)
- Parameters:
ptCenter
- ptA
- ptB
- ptC
- isOutward
- normal
-
- Returns:
- true if winding is proper; false if not
calcXYNormalToLine
public static void calcXYNormalToLine(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Vector3f vNormNorm)
projectOntoAxis
public static void projectOntoAxis(javax.vecmath.Point3f point,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection)
calcBestAxisThroughPoints
public static void calcBestAxisThroughPoints(javax.vecmath.Point3f[] points,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection,
int nTriesMax)
findAxis
public static float findAxis(javax.vecmath.Point3f[] points,
int nPoints,
javax.vecmath.Point3f axisA,
javax.vecmath.Vector3f axisUnitVector,
javax.vecmath.Vector3f vectorProjection)
calcAveragePoint
public static void calcAveragePoint(javax.vecmath.Point3f pointA,
javax.vecmath.Point3f pointB,
javax.vecmath.Point3f pointC)
calcAveragePointN
public static void calcAveragePointN(javax.vecmath.Point3f[] points,
int nPoints,
javax.vecmath.Point3f averagePoint)
getCenterAndPoints
public static javax.vecmath.Point3f[] getCenterAndPoints(java.util.List vPts)
getTransformMatrix4
public static float getTransformMatrix4(java.util.List ptsA,
java.util.List ptsB,
javax.vecmath.Matrix4f m,
javax.vecmath.Point3f centerA)
calculateQuaternionRotation
public static Quaternion calculateQuaternionRotation(javax.vecmath.Point3f[][] centerAndPoints,
float[] retStddev,
boolean doReport)
getRmsd
public static float getRmsd(javax.vecmath.Point3f[][] centerAndPoints,
Quaternion q)
transformPoints
public static java.util.List transformPoints(java.util.List vPts,
javax.vecmath.Matrix4f m4,
javax.vecmath.Point3f center)