ffe.lang
Class AtomUtils

java.lang.Object
  ffe.lang.AtomUtils

public final class AtomUtils

extends java.lang.Object

The AtomUtils class is a simple math library that operates on 3-coordinate vectors. The main design objectives were speed and no memory consumption.

Field Summary

static float	BUFF Length in Angstroms that is added to Atomic Radii when determining if two Atoms are within bonding distance
static javax.vecmath.Color3f[]	colorlist
static java.util.Hashtable	colorlookup Colors for display routines
static int	DOUBLEBOND Bonding Character
static int	SINGLEBOND Bonding Character
static int	SP Atomic Bonding Hybridization
static int	SP2 Atomic Bonding Hybridization
static int	SP3 Atomic Bonding Hybridization
static int	TRIPLEBOND Bonding Character

Constructor Summary

AtomUtils()

Method Summary

static double	angle(double[] i, double[] j)
static float	angle(float[] i, float[] j)
static double	bondangle(double[] i, double[] j, double[] k) Finds the angle formed by three atoms
static float	bondangle(float[] i, float[] j, float[] k) Finds the angle formed by three atoms
static void	cross(double[] a, double[] b, double[] ret) Finds the cross-product between two vectors
static void	cross(float[] a, float[] b, float[] ret) Finds the cross-product between two vectors
static void	diff(double[] a, double[] b, double[] ret) Finds the difference between two vectors
static void	diff(float[] a, float[] b, float[] ret) Finds the difference between two vectors
static double	dihedralangle(double[] a, double[] b, double[] c, double[] d) Finds the dihedral angle formed between 4 atoms
static float	dihedralangle(float[] a, float[] b, float[] c, float[] d) Finds the dihedral angle formed between 4 atoms
static double	dist(double[] a, double[] b) Finds the distance between two vectors
static float	dist(float[] a, float[] b) Finds the distance between two vectors
static double	dot(double[] a, double[] b) Finds the dot product between two vectors
static float	dot(float[] a, float[] b) Finds the dot product between two vectors
static void	norm(double[] n, double[] ret) Normalizes a vector
static void	norm(float[] n, float[] ret) Normalizes a vector
static void	printVector(double[] v)
static double	r(double[] d) Finds the length of a vector
static float	r(float[] d) Finds the length of a vector
static void	scalar(double[] n, double a, double[] ret) Scales a vector
static void	scalar(float[] n, float a, float[] ret) Scales a vector
static void	sum(double[] a, double[] b, double[] ret)
static void	sum(float[] a, float[] b, float[] ret)

Methods inherited from class java.lang.Object

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

Field Detail

BUFF

public static final float BUFF

Length in Angstroms that is added to Atomic Radii when determining if two Atoms are within bonding distance

See Also:

Constant Field Values

SP

public static final int SP

Atomic Bonding Hybridization

See Also:

Constant Field Values

SP2

public static final int SP2

Atomic Bonding Hybridization

See Also:

Constant Field Values

SP3

public static final int SP3

Atomic Bonding Hybridization

See Also:

Constant Field Values

SINGLEBOND

public static final int SINGLEBOND

Bonding Character

See Also:

Constant Field Values

DOUBLEBOND

public static final int DOUBLEBOND

Bonding Character

See Also:

Constant Field Values

TRIPLEBOND

public static final int TRIPLEBOND

Bonding Character

See Also:

Constant Field Values

colorlookup

public static final java.util.Hashtable colorlookup

Colors for display routines

colorlist

public static final javax.vecmath.Color3f[] colorlist

Constructor Detail

AtomUtils

public AtomUtils()

Method Detail

r

public static float r(float[] d)

Finds the length of a vector

Parameters:

d - A vector to find the length of.

Returns:

Length of vector d.

norm

public static void norm(float[] n,
                        float[] ret)

Normalizes a vector

Parameters:

n - A vector to be normalized.

Returns:

Normalized vector.

scalar

public static void scalar(float[] n,
                          float a,
                          float[] ret)

Scales a vector

Parameters:

n - A vector to be scaled

a - A scaler value

Returns:

Vector n scaled by a

dist

public static float dist(float[] a,
                         float[] b)

Finds the distance between two vectors

Parameters:

a - First vector

b - Second vector

diff

public static void diff(float[] a,
                        float[] b,
                        float[] ret)

Finds the difference between two vectors

Parameters:

a - First vector

b - Second vector

ret - Return Values

sum

public static void sum(float[] a,
                       float[] b,
                       float[] ret)

dot

public static float dot(float[] a,
                        float[] b)

Finds the dot product between two vectors

Parameters:

a - First vector

b - Second vector

Returns:

The dot product of a and b

cross

public static void cross(float[] a,
                         float[] b,
                         float[] ret)

Finds the cross-product between two vectors

Parameters:

a - First vector

b - Second vector

ret - The cross-product a x b

bondangle

public static float bondangle(float[] i,
                              float[] j,
                              float[] k)

Finds the angle formed by three atoms

Parameters:

i - Atom position vector

j - Atom position vector (central atom)

k - Atom position vector

Returns:

The angle in the range [ -pi, pi ]

angle

public static float angle(float[] i,
                          float[] j)

dihedralangle

public static float dihedralangle(float[] a,
                                  float[] b,
                                  float[] c,
                                  float[] d)

Finds the dihedral angle formed between 4 atoms

Parameters:

a - Atom position vector

b - Atom position vector

c - Atom position vector

d - Atom position vector

Returns:

The dihedral angle in the range [ -pi, pi ]

r

public static double r(double[] d)

Finds the length of a vector

Parameters:

d - A vector to find the length of.

Returns:

Length of vector d.

norm

public static void norm(double[] n,
                        double[] ret)

Normalizes a vector

Parameters:

n - A vector to be normalized.

Returns:

Normalized vector.

scalar

public static void scalar(double[] n,
                          double a,
                          double[] ret)

Scales a vector

Parameters:

n - A vector to be scaled

a - A scaler value

Returns:

Vector n scaled by a

dist

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

Finds the distance between two vectors

Parameters:

a - First vector

b - Second vector

diff

public static void diff(double[] a,
                        double[] b,
                        double[] ret)

Finds the difference between two vectors

Parameters:

a - First vector

b - Second vector

ret - Return Values

sum

public static void sum(double[] a,
                       double[] b,
                       double[] ret)

dot

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

Finds the dot product between two vectors

Parameters:

a - First vector

b - Second vector

Returns:

The dot product of a and b

cross

public static void cross(double[] a,
                         double[] b,
                         double[] ret)

Finds the cross-product between two vectors

Parameters:

a - First vector

b - Second vector

ret - The cross-product a x b

bondangle

public static double bondangle(double[] i,
                               double[] j,
                               double[] k)

Finds the angle formed by three atoms

Parameters:

i - Atom position vector

j - Atom position vector (central atom)

k - Atom position vector

Returns:

The angle in the range [ -pi, pi ]

angle

public static double angle(double[] i,
                           double[] j)

printVector

public static void printVector(double[] v)

dihedralangle

public static double dihedralangle(double[] a,
                                   double[] b,
                                   double[] c,
                                   double[] d)

Finds the dihedral angle formed between 4 atoms

Parameters:

a - Atom position vector

b - Atom position vector

c - Atom position vector

d - Atom position vector

Returns:

The dihedral angle in the range [ -pi, pi ]