meshi.geometry
Class Angle

java.lang.Object
  meshi.geometry.Angle

All Implemented Interfaces:

Updateable

Direct Known Subclasses:

QuickAndDirtyAngle

public class Angle
extends java.lang.Object
implements Updateable

--------------------------- Angle -----------------------------------

Field Summary

private double	angle
protected int	angleCode
protected java.lang.String	angleName
protected java.lang.String	angleResName
protected int	angleResNum
Atom	atom1
Atom	atom2
Atom	atom3
protected AtomPair	atomPair1
protected AtomPair	atomPair2
private double	cosAngle
private double	dangleDx1
private double	dangleDx2
private double	dangleDx3
private double	dangleDy1
private double	dangleDy2
private double	dangleDy3
private double	dangleDz1
private double	dangleDz2
private double	dangleDz3
Distance	DISTANCE1
Distance	DISTANCE2
protected DistanceMatrix	distanceMatrix
private int	numberOfUpdates
private double	sinAngle

Constructor Summary

Angle(Atom atom1, Atom atom2, Atom atom3, DistanceMatrix distanceMatrix)

Angle(AtomPair atomPair1, AtomPair atomPair2, DistanceMatrix distanceMatrix)

Method Summary

double	acos(double cos) Calculate the arc-cosine function.
double	angle()
protected void	assignName() Assigns a meaningful name to an angle.
Atom	atom1()
Atom	atom2()
Atom	atom3()
AtomPair	atomPair1()
AtomPair	atomPair2()
double	cosAngle()
double	dangleDx1()
double	dangleDx2()
double	dangleDx3()
double	dangleDy1()
double	dangleDy2()
double	dangleDy3()
double	dangleDz1()
double	dangleDz2()
double	dangleDz3()
static double	deg2rad(double ang)
boolean	frozen()
int	getAngleCode()
java.lang.String	getAngleName()
java.lang.String	getAngleResName()
int	getAngleResNum()
AtomPair	hinge(Angle other)
boolean	proper(Angle other)
static double	rad2deg(double ang)
AtomPair	sharedAtomPair(Angle other)
double	sinAngle()
java.lang.String	toString()
protected void	update()
void	update(int numberOfUpdates)

Methods inherited from class java.lang.Object

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

Field Detail

atom1

public final Atom atom1

atom2

public final Atom atom2

atom3

public final Atom atom3

angleName

protected java.lang.String angleName

angleCode

protected int angleCode

angleResNum

protected int angleResNum

angleResName

protected java.lang.String angleResName

atomPair1

protected AtomPair atomPair1

atomPair2

protected AtomPair atomPair2

DISTANCE1

public final Distance DISTANCE1

DISTANCE2

public final Distance DISTANCE2

angle

private double angle

dangleDx1

private double dangleDx1

dangleDy1

private double dangleDy1

dangleDz1

private double dangleDz1

dangleDx2

private double dangleDx2

dangleDy2

private double dangleDy2

dangleDz2

private double dangleDz2

dangleDx3

private double dangleDx3

dangleDy3

private double dangleDy3

dangleDz3

private double dangleDz3

cosAngle

private double cosAngle

sinAngle

private double sinAngle

distanceMatrix

protected DistanceMatrix distanceMatrix

numberOfUpdates

private int numberOfUpdates

Constructor Detail

Angle

public Angle(Atom atom1,
             Atom atom2,
             Atom atom3,
             DistanceMatrix distanceMatrix)

Angle

public Angle(AtomPair atomPair1,
             AtomPair atomPair2,
             DistanceMatrix distanceMatrix)

Method Detail

atom1

public Atom atom1()

atom2

public Atom atom2()

atom3

public Atom atom3()

atomPair1

public AtomPair atomPair1()

atomPair2

public AtomPair atomPair2()

sharedAtomPair

public AtomPair sharedAtomPair(Angle other)

proper

public boolean proper(Angle other)

hinge

public AtomPair hinge(Angle other)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

angle

public double angle()

dangleDx1

public double dangleDx1()

dangleDy1

public double dangleDy1()

dangleDz1

public double dangleDz1()

dangleDx2

public double dangleDx2()

dangleDy2

public double dangleDy2()

dangleDz2

public double dangleDz2()

dangleDx3

public double dangleDx3()

dangleDy3

public double dangleDy3()

dangleDz3

public double dangleDz3()

cosAngle

public double cosAngle()

sinAngle

public double sinAngle()

update

public void update(int numberOfUpdates)
            throws UpdateableException

Specified by:

update in interface Updateable

Throws:

UpdateableException

update

protected void update()

acos

public double acos(double cos)

Calculate the arc-cosine function. This method simply calls Math.acos, extending classes however may use approximations in order to save time.

Parameters:

cos - value

Returns:

arccos value

frozen

public boolean frozen()

deg2rad

public static double deg2rad(double ang)

rad2deg

public static double rad2deg(double ang)

getAngleName

public java.lang.String getAngleName()

getAngleCode

public int getAngleCode()

getAngleResNum

public int getAngleResNum()

getAngleResName

public java.lang.String getAngleResName()

assignName

protected void assignName()

Assigns a meaningful name to an angle. This method assigns (if possible): - name to the angle object. - number corresponding to this name. - the number in the chain of the center atom residue to which this amgle belong - the name of the center atom residue to which this angle belong The names to numbers conversion is: Three consecutive Ca's - 0