jgromacs.data
Class Atom

java.lang.Object
  extended by jgromacs.data.Atom
All Implemented Interfaces:
java.lang.Cloneable

public class Atom
extends java.lang.Object
implements java.lang.Cloneable

Objects of this class represent a single atom


Constructor Summary
Atom()
          Constructs a new Atom object
 
Method Summary
 java.lang.Object clone()
          Returns an identical Atom object
 double distance(Atom other)
          Returns the Euclidean distance between this atom and another atom
 boolean equals(java.lang.Object other)
          Returns true if the two atoms are identical
 AtomType getAtomType()
          Returns the type of atom
 double getBvalue()
          Returns the B-value of atom
 Point3D getCoordinates()
          Returns the coordinates of atom
 int getIndex()
          Returns the index of atom
 java.lang.String getName()
          Returns the name of atom
 double getOccupancy()
          Returns the occupancy of atom
 double getXCoordinate()
          Returns the X coordinate of atom
 double getYCoordinate()
          Returns the Y coordinate of atom
 double getZCoordinate()
          Returns the Z coordinate of atom
 int hashCode()
          Returns hash code
 boolean isAlphaCarbon()
          Returns true if it is an alpha carbon atom
 boolean isBackboneAtom()
          Returns true if it is a backbone atom
 boolean isBetaCarbon()
          Returns true if it is a beta carbon atom
 boolean isCarbonylOxygen()
          Returns true if it is a carbonyl oxygen atom
 boolean isCTerminalCarbon()
          Returns true if it is a C-terminal carbon atom
 boolean isDeltaCarbon()
          Returns true if it is a delta carbon atom
 boolean isEpsilonCarbon()
          Returns true if it is an epsilon carbon atom
 boolean isGammaCarbon()
          Returns true if it is a gamma carbon atom
 boolean isHeavyAtom()
          Returns true if it is a heavy atom (not hydrogen)
 boolean isHydrogenAtom()
          Returns true if the atom is a Hydrogen
 boolean isMainChainAtom()
          Returns true if it is a main chain atom
 boolean isMainChainHydrogenAtom()
          Returns true if it is a main chain hydrogen atom
 boolean isMainChainPlusCbAtom()
          Returns true if it is a main chain or beta carbon atom
 boolean isMainChainPlusHAtom()
          Returns true if it is a main chain or hydrogen atom
 boolean isNTerminalNitrogen()
          Returns true if it is an N-terminal nitrogen atom
 boolean isSideChainAtom()
          Returns true if it is a side chain atom
 boolean isSideChainMinusHAtom()
          Returns true if it is a side chain atom but not hydrogen
 boolean isTerminalOxygen()
          Returns true if it is a terminal oxygen atom
 boolean isZetaCarbon()
          Returns true if it is a zeta carbon atom
 void setAtomType(AtomType atomType)
          Sets the type of atom
 void setBvalue(double bvalue)
          Sets the B-value of atom
 void setCoordinates(Point3D coordinates)
          Sets the coordinates of atom
 void setIndex(int index)
          Sets the index of atom
 void setName(java.lang.String name)
          Sets the name of atom
 void setOccupancy(double occupancy)
          Sets the occupancy of atom
 void setXCoordinate(double x)
          Sets the X coordinate of atom
 void setYCoordinate(double y)
          Sets the Y coordinate of atom
 void setZCoordinate(double z)
          Sets the Z coordinate of atom
 java.lang.String toString()
          Returns the String representation of atom
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Atom

public Atom()
Constructs a new Atom object

Method Detail

getAtomType

public AtomType getAtomType()
Returns the type of atom

Returns:
Type of the atom

getIndex

public int getIndex()
Returns the index of atom

Returns:
Index of the atom

setIndex

public void setIndex(int index)
Sets the index of atom

Parameters:
index - index of the atom

getName

public java.lang.String getName()
Returns the name of atom

Returns:
Name of the atom

setName

public void setName(java.lang.String name)
Sets the name of atom

Parameters:
name - name of the atom

setAtomType

public void setAtomType(AtomType atomType)
Sets the type of atom

Parameters:
atomType - type of the atom

getCoordinates

public Point3D getCoordinates()
Returns the coordinates of atom

Returns:
Coordinates of atom

setCoordinates

public void setCoordinates(Point3D coordinates)
Sets the coordinates of atom

Parameters:
coordinates - coordinates of the atom

getXCoordinate

public double getXCoordinate()
Returns the X coordinate of atom

Returns:
X coordinate of atom

setXCoordinate

public void setXCoordinate(double x)
Sets the X coordinate of atom

Parameters:
x - X coordinate of the atom

getYCoordinate

public double getYCoordinate()
Returns the Y coordinate of atom

Returns:
Y coordinate of atom

setYCoordinate

public void setYCoordinate(double y)
Sets the Y coordinate of atom

Parameters:
y - Y coordinate of the atom

getZCoordinate

public double getZCoordinate()
Returns the Z coordinate of atom

Returns:
Z coordinate of atom

setZCoordinate

public void setZCoordinate(double z)
Sets the Z coordinate of atom

Parameters:
z - Z coordinate of the atom

getOccupancy

public double getOccupancy()
Returns the occupancy of atom

Returns:
occupancy of atom

setOccupancy

public void setOccupancy(double occupancy)
Sets the occupancy of atom

Parameters:
occupancy - occupancy of the atom

getBvalue

public double getBvalue()
Returns the B-value of atom

Returns:
B-value of atom

setBvalue

public void setBvalue(double bvalue)
Sets the B-value of atom

Parameters:
bvalue - B-value of the atom

isHydrogenAtom

public boolean isHydrogenAtom()
Returns true if the atom is a Hydrogen


isHeavyAtom

public boolean isHeavyAtom()
Returns true if it is a heavy atom (not hydrogen)


isAlphaCarbon

public boolean isAlphaCarbon()
Returns true if it is an alpha carbon atom


isCTerminalCarbon

public boolean isCTerminalCarbon()
Returns true if it is a C-terminal carbon atom


isBetaCarbon

public boolean isBetaCarbon()
Returns true if it is a beta carbon atom


isGammaCarbon

public boolean isGammaCarbon()
Returns true if it is a gamma carbon atom


isDeltaCarbon

public boolean isDeltaCarbon()
Returns true if it is a delta carbon atom


isEpsilonCarbon

public boolean isEpsilonCarbon()
Returns true if it is an epsilon carbon atom


isZetaCarbon

public boolean isZetaCarbon()
Returns true if it is a zeta carbon atom


isCarbonylOxygen

public boolean isCarbonylOxygen()
Returns true if it is a carbonyl oxygen atom


isTerminalOxygen

public boolean isTerminalOxygen()
Returns true if it is a terminal oxygen atom


isNTerminalNitrogen

public boolean isNTerminalNitrogen()
Returns true if it is an N-terminal nitrogen atom


isBackboneAtom

public boolean isBackboneAtom()
Returns true if it is a backbone atom


isMainChainAtom

public boolean isMainChainAtom()
Returns true if it is a main chain atom


isMainChainHydrogenAtom

public boolean isMainChainHydrogenAtom()
Returns true if it is a main chain hydrogen atom


isMainChainPlusHAtom

public boolean isMainChainPlusHAtom()
Returns true if it is a main chain or hydrogen atom


isMainChainPlusCbAtom

public boolean isMainChainPlusCbAtom()
Returns true if it is a main chain or beta carbon atom


isSideChainAtom

public boolean isSideChainAtom()
Returns true if it is a side chain atom


isSideChainMinusHAtom

public boolean isSideChainMinusHAtom()
Returns true if it is a side chain atom but not hydrogen


distance

public double distance(Atom other)
Returns the Euclidean distance between this atom and another atom

Parameters:
other - another atom
Returns:
distance between atoms

toString

public java.lang.String toString()
Returns the String representation of atom

Overrides:
toString in class java.lang.Object
Returns:
String representation

clone

public java.lang.Object clone()
Returns an identical Atom object

Overrides:
clone in class java.lang.Object
Returns:
clone of the atom

equals

public boolean equals(java.lang.Object other)
Returns true if the two atoms are identical

Overrides:
equals in class java.lang.Object
Parameters:
other - the other atom

hashCode

public int hashCode()
Returns hash code

Overrides:
hashCode in class java.lang.Object