Atom

java.lang.Object
- 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

Constructors
Constructor and Description

Atom()
Constructs a new Atom object

Constructors
Constructor and Description
`Atom()` Constructs a new Atom object

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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
finalize, 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

Class Atom

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Atom

Method Detail

getAtomType

getIndex

setIndex

getName

setName

setAtomType

getCoordinates

setCoordinates

getXCoordinate

setXCoordinate

getYCoordinate

setYCoordinate

getZCoordinate

setZCoordinate

getOccupancy

setOccupancy

getBvalue

setBvalue

isHydrogenAtom

isHeavyAtom

isAlphaCarbon

isCTerminalCarbon

isBetaCarbon

isGammaCarbon

isDeltaCarbon

isEpsilonCarbon

isZetaCarbon

isCarbonylOxygen

isTerminalOxygen

isNTerminalNitrogen

isBackboneAtom

isMainChainAtom

isMainChainHydrogenAtom

isMainChainPlusHAtom

isMainChainPlusCbAtom

isSideChainAtom

isSideChainMinusHAtom

distance

toString

clone

equals

hashCode