jprotein.data.datatype
Class Atom1

java.lang.Object
  extended by jprotein.data.datatype.Atom1

public class Atom1
extends java.lang.Object


Constructor Summary
Atom1(java.lang.String symbol, javax.vecmath.Point3f coord)
           
 
Method Summary
 float distance(Atom atom)
           
 float distance(javax.vecmath.Point3f point)
           
 float distance(Residue3D residue)
           
 double getAtomAccessibleSurfaceArea()
           
 int getAtomIndex()
           
static int getAtomIndex(char symbol)
           
 double getAtomSurfaceArea()
           
 javax.vecmath.Point3f getCoordinates()
           
 java.lang.String getName()
           
 double getPercentAccessibility()
           
 javax.vecmath.Point3f getProjection(int i)
           
 float getRadius()
           
static float getRadius(char symbol)
           
 char getSymbol()
           
 void initAccess()
           
 boolean isAccessible(int i)
           
 boolean isSideChainAtom()
           
 void setAccessibility(Atom atom)
           
 void setAccessibility(Atom atom, float probeRadius)
           
 void setAccessibility(Atom atom, float probeRadius, float noise)
           
 void setAccessible(boolean b, int i)
           
 void setCoordinates(javax.vecmath.Point3f coord)
           
 void setName(java.lang.String name)
           
 void setSymbol(char symbol)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Atom1

public Atom1(java.lang.String symbol,
             javax.vecmath.Point3f coord)
Method Detail

getAtomIndex

public static int getAtomIndex(char symbol)

getAtomIndex

public int getAtomIndex()

getCoordinates

public javax.vecmath.Point3f getCoordinates()

setCoordinates

public void setCoordinates(javax.vecmath.Point3f coord)

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

getRadius

public static float getRadius(char symbol)

getRadius

public float getRadius()

getSymbol

public char getSymbol()

setSymbol

public void setSymbol(char symbol)

isSideChainAtom

public boolean isSideChainAtom()

distance

public float distance(Atom atom)

distance

public float distance(Residue3D residue)

distance

public float distance(javax.vecmath.Point3f point)

getPercentAccessibility

public double getPercentAccessibility()

getAtomSurfaceArea

public double getAtomSurfaceArea()

getAtomAccessibleSurfaceArea

public double getAtomAccessibleSurfaceArea()

setAccessibility

public void setAccessibility(Atom atom)

setAccessibility

public void setAccessibility(Atom atom,
                             float probeRadius)

setAccessibility

public void setAccessibility(Atom atom,
                             float probeRadius,
                             float noise)

setAccessible

public void setAccessible(boolean b,
                          int i)

isAccessible

public boolean isAccessible(int i)

initAccess

public void initAccess()

getProjection

public javax.vecmath.Point3f getProjection(int i)