Package jgromacs.data

Class Residue

java.lang.Object
jgromacs.data.Residue
All Implemented Interfaces:
Cloneable

public class Residue extends Object implements Cloneable
Objects of this class represent a single residue
  • Constructor Details

    • Residue

      public Residue()
      Constructs a new Residue object
    • Residue

      public Residue(String name)
      Constructs a new Residue object of given name
    • Residue

      public Residue(int index, String name, ResidueType residueType)
      Constructs a new Residue object of given index, name and residue type
    • Residue

      public Residue(int index, String name, String chainID, ResidueType residueType)
      Constructs a new Residue object of given index, name, chainID and residue type
  • Method Details

    • 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 String getName()
      Returns the name of residue
      Returns:
      name of the residue
    • setName

      public void setName(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 String getChainID()
      Returns the chain ID of residue
      Returns:
      chain ID of residue
    • setChainID

      public void setChainID(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 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(String name)
      Returns the atom of name
      Parameters:
      name - name of atom
      Returns:
      atom of given name
    • get1LetterCode

      public String get1LetterCode()
      Returns the 1 letter code of residue type
      Returns:
      1 letter code
    • get3LetterCode

      public String get3LetterCode()
      Returns the 3 letter code of residue type
      Returns:
      3 letter code
    • getCombinedCode

      public 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 Object clone()
      Returns an identical Residue object
      Overrides:
      clone in class Object
      Returns:
      clone of the residue
    • toString

      public String toString()
      Returns the String representation of residue
      Overrides:
      toString in class Object
      Returns:
      String representation
    • toStringInfo

      public String toStringInfo()
      Returns summary information about the residue
      Returns:
      summary information
    • equals

      public boolean equals(Object other)
      Returns true if the two residues are identical
      Overrides:
      equals in class Object
      Parameters:
      other - the other residue
    • hashCode

      public int hashCode()
      Returns hash code
      Overrides:
      hashCode in class Object