Residue

java.lang.Object
- jgromacs.data.Residue

All Implemented Interfaces:

java.lang.Cloneable
```
public class Residue
extends java.lang.Object
implements java.lang.Cloneable
```
Objects of this class represent a single residue

Constructor Summary

Constructors
Constructor and Description
`Residue()` Constructs a new Residue object
`Residue(int index, java.lang.String name, ResidueType residueType)` Constructs a new Residue object of given index, name and residue type
`Residue(int index, java.lang.String name, java.lang.String chainID, ResidueType residueType)` Constructs a new Residue object of given index, name, chainID and residue type
`Residue(java.lang.String name)` Constructs a new Residue object of given name

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAtom(Atom atom)` Adds a new atom to the residue
`java.lang.Object`	`clone()` Returns an identical Residue object
`double`	`distanceAlphaCarbons(Residue other)` Returns the Euclidean distance of alpha-carbon atoms of this amino acid an another
`double`	`distanceClosest(Residue other)` Returns the Euclidean distance of the closest atoms of this amino acid and another
`double`	`distanceClosestHeavy(Residue other)` Returns the Euclidean distance of the closest heavy atoms of this amino acid and another
`boolean`	`equals(java.lang.Object other)` Returns true if the two residues are identical
`java.lang.String`	`get1LetterCode()` Returns the 1 letter code of residue type
`java.lang.String`	`get3LetterCode()` Returns the 3 letter code of residue type
`PointList`	`getAllAtomCoordinates()` Returns the coordinates of all atoms
`Atom`	`getAlphaCarbon()` Returns the alpha carbon atom if any (otherwise returns null)
`Point3D`	`getAlphaCarbonCoordinates()` Returns the position of alpha-carbon atom
`Atom`	`getAtom(int i)` Returns atom #i of the residue
`Atom`	`getAtomByIndex(int index)` Returns the atom of given index
`Atom`	`getAtomByName(java.lang.String name)` Returns the atom of name
`IndexSet`	`getAtomIndices()` Returns the index set of all atoms
`java.util.ArrayList<Atom>`	`getAtomsAsArrayList()` Returns the list of atoms as an ArrayList object
`IndexSet`	`getBackBoneAtomIndices()` Returns the index set of backbone atoms
`Atom`	`getBetaCarbon()` Returns the beta carbon atom if any (otherwise returns null)
`Atom`	`getCarbonylOxygen()` Returns the carbonyl oxygen atom of amino acid
`java.lang.String`	`getChainID()` Returns the chain ID of residue
`java.lang.String`	`getCombinedCode()` Returns residue index and the 3 letter code of residue type
`Atom`	`getCTerminalCarbon()` Returns the C-terminal carbon atom of amino acid
`Atom`	`getDeltaCarbon()` Returns the delta carbon atom if any (otherwise returns null)
`Atom`	`getEpsilonCarbon()` Returns the epsilon carbon atom if any (otherwise returns null)
`Atom`	`getGammaCarbon()` Returns the gamma carbon atom if any (otherwise returns null)
`IndexSet`	`getHeavyAtomIndices()` Returns the index set of heavy atoms
`IndexSet`	`getHydrogenAtomIndices()` Returns the index set of hydrogen atoms
`int`	`getIndex()` Returns the index of residue
`IndexSet`	`getMainChainAtomIndices()` Returns the index set of main chain atoms
`IndexSet`	`getMainChainPlusCbAtomIndices()` Returns the index set of main chain atoms and beta carbon atom
`IndexSet`	`getMainChainPlusHAtomIndices()` Returns the index set of main chain atoms and hydrogen atoms
`java.lang.String`	`getName()` Returns the name of residue
`Atom`	`getNTerminalNitrogen()` Returns the N-terminal nitrogen atom of amino acid
`int`	`getNumberOfAtoms()` Returns the number of atoms in the residue
`ResidueType`	`getResidueType()` Returns the type of residue
`IndexSet`	`getSideChainAtomIndices()` Returns the index set of side chain atoms
`IndexSet`	`getSideChainMinusHAtomIndices()` Returns the index set of side chain atoms except of hydrogen atoms
`Atom`	`getZetaCarbon()` Returns the zeta carbon atom if any (otherwise returns null)
`int`	`hashCode()` Returns hash code
`boolean`	`isAminoAcid()` Returns true if it is an amino acid
`boolean`	`isAtomIn(Atom atom)` Returns true if the given atom is in the residue
`boolean`	`isOther()` Returns true if it is not an amino acid neither a water molecule
`boolean`	`isWater()` Returns true if it is a water molecule
`void`	`removeAtom(Atom atom)` Removes the given atom from the residue
`void`	`removeAtom(int i)` Removes atom #i from the residue
`void`	`removeAtomByIndex(int index)` Removes atom of given index from the residue
`void`	`setAllAtomCoordinates(PointList pointlist)` Sets the coordinates of all atoms
`void`	`setAtom(int i, Atom atom)` Replaces atom #i of the residue with the given atom
`void`	`setAtomCoordinates(int i, Point3D coordinates)` Sets the coordinates of atom #i
`void`	`setAtomOfIndexCoordinates(int index, Point3D coordinates)` Sets the coordinates of atom of given index
`void`	`setChainID(java.lang.String chainID)` Sets the chain ID of residue
`void`	`setIndex(int index)` Sets the index of residue
`void`	`setName(java.lang.String name)` Sets the name of residue
`void`	`setResidueType(ResidueType residueType)` Sets the type of residue
`java.lang.String`	`toString()` Returns the String representation of residue
`java.lang.String`	`toStringInfo()` Returns summary information about the residue

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Residue
```
public Residue()
```
    Constructs a new Residue object
  - Residue
```
public Residue(java.lang.String name)
```
    Constructs a new Residue object of given name
  - Residue
```
public Residue(int index,
               java.lang.String name,
               ResidueType residueType)
```
    Constructs a new Residue object of given index, name and residue type
  - Residue
```
public Residue(int index,
               java.lang.String name,
               java.lang.String chainID,
               ResidueType residueType)
```
    Constructs a new Residue object of given index, name, chainID and residue type
- Method Detail
  - getIndex
```
public int getIndex()
```
    Returns the index of residue
    
    Returns:
    
    index of the residue
  - setIndex
```
public void setIndex(int index)
```
    Sets the index of residue
    
    Parameters:
    
    index - index of the residue
  - getName
```
public java.lang.String getName()
```
    Returns the name of residue
    
    Returns:
    
    name of the residue
  - setName
```
public void setName(java.lang.String name)
```
    Sets the name of residue
    
    Parameters:
    
    name - name of the residue
  - getResidueType
```
public ResidueType getResidueType()
```
    Returns the type of residue
    
    Returns:
    
    residue type
  - setResidueType
```
public void setResidueType(ResidueType residueType)
```
    Sets the type of residue
    
    Parameters:
    
    residueType - residue type
  - getChainID
```
public java.lang.String getChainID()
```
    Returns the chain ID of residue
    
    Returns:
    
    chain ID of residue
  - setChainID
```
public void setChainID(java.lang.String chainID)
```
    Sets the chain ID of residue
    
    Parameters:
    
    chainID - chain ID
  - getNumberOfAtoms
```
public int getNumberOfAtoms()
```
    Returns the number of atoms in the residue
    
    Returns:
    
    number of atoms
  - getAtomsAsArrayList
```
public java.util.ArrayList<Atom> getAtomsAsArrayList()
```
    Returns the list of atoms as an ArrayList object
    
    Returns:
    
    list of atoms as an ArrayList
  - getAtom
```
public Atom getAtom(int i)
```
    Returns atom #i of the residue
    
    Returns:
    
    atom #i
  - getAtomByIndex
```
public Atom getAtomByIndex(int index)
```
    Returns the atom of given index
    
    Parameters:
    
    index - index of atom
    
    Returns:
    
    atom of given index
  - getAtomByName
```
public Atom getAtomByName(java.lang.String name)
```
    Returns the atom of name
    
    Parameters:
    
    name - name of atom
    
    Returns:
    
    atom of given name
  - get1LetterCode
```
public java.lang.String get1LetterCode()
```
    Returns the 1 letter code of residue type
    
    Returns:
    
    1 letter code
  - get3LetterCode
```
public java.lang.String get3LetterCode()
```
    Returns the 3 letter code of residue type
    
    Returns:
    
    3 letter code
  - getCombinedCode
```
public java.lang.String getCombinedCode()
```
    Returns residue index and the 3 letter code of residue type
    
    Returns:
    
    combined code
  - addAtom
```
public void addAtom(Atom atom)
```
    Adds a new atom to the residue
    
    Parameters:
    
    atom - new atom
  - setAtom
```
public void setAtom(int i,
                    Atom atom)
```
    Replaces atom #i of the residue with the given atom
    
    Parameters:
    
    atom - new atom
  - removeAtom
```
public void removeAtom(int i)
```
    Removes atom #i from the residue
  - removeAtom
```
public void removeAtom(Atom atom)
```
    Removes the given atom from the residue
    
    Parameters:
    
    atom - the atom to be removed
  - removeAtomByIndex
```
public void removeAtomByIndex(int index)
```
    Removes atom of given index from the residue
    
    Parameters:
    
    index - index of atom to be removed
  - getNTerminalNitrogen
```
public Atom getNTerminalNitrogen()
```
    Returns the N-terminal nitrogen atom of amino acid
    
    Returns:
    
    N-terminal nitrogen atom
  - getAlphaCarbon
```
public Atom getAlphaCarbon()
```
    Returns the alpha carbon atom if any (otherwise returns null)
    
    Returns:
    
    alpha carbon atom
  - getBetaCarbon
```
public Atom getBetaCarbon()
```
    Returns the beta carbon atom if any (otherwise returns null)
    
    Returns:
    
    beta carbon atom
  - getGammaCarbon
```
public Atom getGammaCarbon()
```
    Returns the gamma carbon atom if any (otherwise returns null)
    
    Returns:
    
    gamma carbon atom
  - getDeltaCarbon
```
public Atom getDeltaCarbon()
```
    Returns the delta carbon atom if any (otherwise returns null)
    
    Returns:
    
    delta carbon atom
  - getEpsilonCarbon
```
public Atom getEpsilonCarbon()
```
    Returns the epsilon carbon atom if any (otherwise returns null)
    
    Returns:
    
    epsilon carbon atom
  - getZetaCarbon
```
public Atom getZetaCarbon()
```
    Returns the zeta carbon atom if any (otherwise returns null)
    
    Returns:
    
    zeta carbon atom
  - getCTerminalCarbon
```
public Atom getCTerminalCarbon()
```
    Returns the C-terminal carbon atom of amino acid
    
    Returns:
    
    C-terminal carbon atom
  - getCarbonylOxygen
```
public Atom getCarbonylOxygen()
```
    Returns the carbonyl oxygen atom of amino acid
    
    Returns:
    
    carbonyl oxygen atom
  - getAtomIndices
```
public IndexSet getAtomIndices()
```
    Returns the index set of all atoms
    
    Returns:
    
    index set of all atoms
  - getHydrogenAtomIndices
```
public IndexSet getHydrogenAtomIndices()
```
    Returns the index set of hydrogen atoms
    
    Returns:
    
    index set of hydrogen atoms
  - getHeavyAtomIndices
```
public IndexSet getHeavyAtomIndices()
```
    Returns the index set of heavy atoms
    
    Returns:
    
    index set of heavy atoms
  - getBackBoneAtomIndices
```
public IndexSet getBackBoneAtomIndices()
```
    Returns the index set of backbone atoms
    
    Returns:
    
    index set of backbone atoms
  - getMainChainAtomIndices
```
public IndexSet getMainChainAtomIndices()
```
    Returns the index set of main chain atoms
    
    Returns:
    
    index set of main chain atoms
  - getMainChainPlusCbAtomIndices
```
public IndexSet getMainChainPlusCbAtomIndices()
```
    Returns the index set of main chain atoms and beta carbon atom
    
    Returns:
    
    index set of main chain atoms and beta carbon atom
  - getMainChainPlusHAtomIndices
```
public IndexSet getMainChainPlusHAtomIndices()
```
    Returns the index set of main chain atoms and hydrogen atoms
    
    Returns:
    
    index set of main chain atoms and hydrogen atoms
  - getSideChainAtomIndices
```
public IndexSet getSideChainAtomIndices()
```
    Returns the index set of side chain atoms
    
    Returns:
    
    index set of side chain atoms
  - getSideChainMinusHAtomIndices
```
public IndexSet getSideChainMinusHAtomIndices()
```
    Returns the index set of side chain atoms except of hydrogen atoms
    
    Returns:
    
    index set of side chain atoms except of hydrogens
  - setAtomCoordinates
```
public void setAtomCoordinates(int i,
                               Point3D coordinates)
```
    Sets the coordinates of atom #i
    
    Parameters:
    
    coordinates - new atomic coordinates
  - setAtomOfIndexCoordinates
```
public void setAtomOfIndexCoordinates(int index,
                                      Point3D coordinates)
```
    Sets the coordinates of atom of given index
    
    Parameters:
    
    coordinates - new atomic coordinates
  - setAllAtomCoordinates
```
public void setAllAtomCoordinates(PointList pointlist)
```
    Sets the coordinates of all atoms
    
    Parameters:
    
    pointlist - list of new atomic coordinates
  - getAllAtomCoordinates
```
public PointList getAllAtomCoordinates()
```
    Returns the coordinates of all atoms
    
    Returns:
    
    list of atomic coordinates
  - getAlphaCarbonCoordinates
```
public Point3D getAlphaCarbonCoordinates()
```
    Returns the position of alpha-carbon atom
    
    Returns:
    
    position of alpha-carbon atom
  - distanceAlphaCarbons
```
public double distanceAlphaCarbons(Residue other)
```
    Returns the Euclidean distance of alpha-carbon atoms of this amino acid an another
    
    Parameters:
    
    other - other amino acid
    
    Returns:
    
    Euclidean distance of alpha-carbon atoms
  - distanceClosest
```
public double distanceClosest(Residue other)
```
    Returns the Euclidean distance of the closest atoms of this amino acid and another
    
    Parameters:
    
    other - other amino acid
    
    Returns:
    
    Euclidean distance of closest atoms
  - distanceClosestHeavy
```
public double distanceClosestHeavy(Residue other)
```
    Returns the Euclidean distance of the closest heavy atoms of this amino acid and another
    
    Parameters:
    
    other - other amino acid
    
    Returns:
    
    Euclidean distance of closest heavy atoms
  - isAminoAcid
```
public boolean isAminoAcid()
```
    Returns true if it is an amino acid
  - isWater
```
public boolean isWater()
```
    Returns true if it is a water molecule
  - isOther
```
public boolean isOther()
```
    Returns true if it is not an amino acid neither a water molecule
  - isAtomIn
```
public boolean isAtomIn(Atom atom)
```
    Returns true if the given atom is in the residue
    
    Parameters:
    
    atom - the atom to search for
  - clone
```
public java.lang.Object clone()
```
    Returns an identical Residue object
    
    Overrides:
    
    clone in class java.lang.Object
    
    Returns:
    
    clone of the residue
  - toString
```
public java.lang.String toString()
```
    Returns the String representation of residue
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    String representation
  - toStringInfo
```
public java.lang.String toStringInfo()
```
    Returns summary information about the residue
    
    Returns:
    
    summary information
  - equals
```
public boolean equals(java.lang.Object other)
```
    Returns true if the two residues are identical
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    
    other - the other residue
  - hashCode
```
public int hashCode()
```
    Returns hash code
    
    Overrides:
    
    hashCode in class java.lang.Object

Class Residue

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Residue

Residue

Residue

Residue

Method Detail

getIndex

setIndex

getName

setName

getResidueType

setResidueType

getChainID

setChainID

getNumberOfAtoms

getAtomsAsArrayList

getAtom

getAtomByIndex

getAtomByName

get1LetterCode

get3LetterCode

getCombinedCode

addAtom

setAtom

removeAtom

removeAtom

removeAtomByIndex

getNTerminalNitrogen

getAlphaCarbon

getBetaCarbon

getGammaCarbon

getDeltaCarbon

getEpsilonCarbon

getZetaCarbon

getCTerminalCarbon

getCarbonylOxygen

getAtomIndices

getHydrogenAtomIndices

getHeavyAtomIndices

getBackBoneAtomIndices

getMainChainAtomIndices

getMainChainPlusCbAtomIndices

getMainChainPlusHAtomIndices

getSideChainAtomIndices

getSideChainMinusHAtomIndices

setAtomCoordinates

setAtomOfIndexCoordinates

setAllAtomCoordinates

getAllAtomCoordinates

getAlphaCarbonCoordinates

distanceAlphaCarbons

distanceClosest

distanceClosestHeavy

isAminoAcid

isWater

isOther

isAtomIn

clone

toString

toStringInfo

equals

hashCode