Class Util

java.lang.Object
org.jmol.minimize.Util
public class Util extends Object

  • Field Details

  • Constructor Details

    • Util

      public Util()

  • Method Details

    • sub

      public static void sub(double[] a, double[] b, V3d result)

    • putCoord

      public static void putCoord(V3d v, double[] c)

    • distance2

      public static double distance2(double[] a, double[] b)

    • distance2V

      public static double distance2V(V3d a, V3d b)

    • getAngleRadiansABC

      public static double getAngleRadiansABC(double[] a, double[] b, double[] c)

    • isApprox

      public static boolean isApprox(V3d a, V3d b, double precision)

    • canBeSquared

      public static boolean canBeSquared(double x)

    • isNegligible

      public static boolean isNegligible(double a, double b)

    • isFinite

      public static boolean isFinite(double a)

    • isNegligible3

      public static boolean isNegligible3(double a, double b, double precision)

    • isNear

      public static boolean isNear(double a, double b)

    • isNear3

      public static boolean isNear3(double a, double b, double epsilon)

    • isNearZero

      public static boolean isNearZero(double a)

    • isNearZero2

      public static boolean isNearZero2(double a, double epsilon)

    • canBeNormalized

      public static boolean canBeNormalized(V3d a)

    • pointPlaneAngleRadians

      public static double pointPlaneAngleRadians(V3d a, V3d b, V3d c, V3d d, V3d v1, V3d v2, V3d norm, boolean fixTheta)
      calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
      Parameters:
      a -
      b -
      c -
      d -
      v1 -
      v2 -
      norm -
      fixTheta -
      Returns:
      Wilson angle

    • getTorsionAngleRadians

      public static double getTorsionAngleRadians(double[] a, double[] b, double[] c, double[] d, V3d r1, V3d r2, V3d r3)

    • restorativeForceAndDistance

      public static double restorativeForceAndDistance(V3d a, V3d b, V3d vab)

    • restorativeForceAndAngleRadians

      public static double restorativeForceAndAngleRadians(V3d i, V3d j, V3d k)

    • restorativeForceAndOutOfPlaneAngleRadians

      public static double restorativeForceAndOutOfPlaneAngleRadians(V3d i, V3d j, V3d k, V3d l, V3d an, V3d bn, V3d cn)

    • restorativeForceAndTorsionAngleRadians

      public static double restorativeForceAndTorsionAngleRadians(V3d i, V3d j, V3d k, V3d l)