Package jgromacs.data

Class 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 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