Package org.biojava.bio.structure

Class AtomImpl

  • All Implemented Interfaces:
    Atom
    public class AtomImpl
extends java.lang.Object
implements Atom
    Implementation of an Atom of a PDB file. currently the coordinates of an atom are represented by a double[3] array.
    Since:
    1.4
    Version:
    %I% %G%
    Author:
    Andreas Prlic

    • Constructor Summary

      Constructors 
      Constructor Description
      AtomImpl()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.Object clone()
      returns and identical copy of this object .
      java.lang.Character getAltLoc()
      get alternate Location.
      double[] getCoords()
      get the coordinates as a double[3] array .
      java.lang.String getFullName()
      get full name of atom e.g.
      long getId()
      Get the Hibernate database ID.
      java.lang.String getName()
      Gets this object's name.
      double getOccupancy()
      get occupancy.
      Group getParent()
      Returns the parent Group of the Atom.
      java.lang.String getPDBline()
      get the whole line .
      int getPDBserial()
      get PDB atom number.
      double getTempFactor()
      get set temp factor.
      double getX()
      Get the X coordinate.
      double getY()
      Get the Y coordinate.
      double getZ()
      Get the Z coordinate.
      void setAltLoc​(java.lang.Character c)
      set alternate Location.
      void setCoords​(double[] c)
      the coordinates.
      void setFullName​(java.lang.String s)
      set full name of atom e.g.
      void setId​(long id)
      Set the Hibernate database ID.
      void setName​(java.lang.String s)
      trimmed version of atom name, e.g.
      void setOccupancy​(double occu)
      set occupancy.
      void setParent​(Group parent)
      Sets the back-reference to its parent Group.
      void setPDBline​(java.lang.String s)
      store the whole line.
      void setPDBserial​(int i)
      set PDB atom number.
      void setTempFactor​(double temp)
      get set temp factor .
      void setX​(double x)
      Set the X coordinate.
      void setY​(double y)
      Set the Y coordinate.
      void setZ​(double z)
      Set the Z coordinate.
      java.lang.String toString()
      string representation.

      • Methods inherited from class java.lang.Object

        equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • AtomImpl

        public AtomImpl()

    • Method Detail

      • getId

        public long getId()
        Get the Hibernate database ID.
        Returns:
        the id
        See Also:
        setId(long)

      • setId

        public void setId​(long id)
        Set the Hibernate database ID.
        Parameters:
        id - the hibernate id
        See Also:
        getId()

      • setName

        public void setName​(java.lang.String s)
        trimmed version of atom name, e.g. "CA"
        Specified by:
        setName in interface Atom
        Parameters:
        s - a String specifying the name value
        See Also:
        getName()

      • getName

        public java.lang.String getName()
        Gets this object's name.
        Specified by:
        getName in interface Atom
        Returns:
        a String representing the name value
        See Also:
        setName(java.lang.String)

      • setFullName

        public void setFullName​(java.lang.String s)
        set full name of atom e.g. " CA " .
        Specified by:
        setFullName in interface Atom
        Parameters:
        s - a String specifying the full name value
        See Also:
        getFullName()

      • getFullName

        public java.lang.String getFullName()
        get full name of atom e.g. " CA ".
        Specified by:
        getFullName in interface Atom
        Returns:
        a String representing the full name value
        See Also:
        setFullName(java.lang.String)

      • setPDBserial

        public void setPDBserial​(int i)
        set PDB atom number.
        Specified by:
        setPDBserial in interface Atom
        Parameters:
        i - an int specifying the PDBserial value
        See Also:
        getPDBserial()

      • getPDBserial

        public int getPDBserial()
        get PDB atom number.
        Specified by:
        getPDBserial in interface Atom
        Returns:
        an int representing the PDBserial value
        See Also:
        setPDBserial(int)

      • setCoords

        public void setCoords​(double[] c)
        the coordinates.
        Specified by:
        setCoords in interface Atom
        Parameters:
        c - an array of doubles specifying the coords value
        See Also:
        getCoords()

      • getCoords

        public double[] getCoords()
        get the coordinates as a double[3] array .
        Specified by:
        getCoords in interface Atom
        Returns:
        an array of doubles representing the coords value
        See Also:
        setCoords(double[])

      • setX

        public void setX​(double x)
        Description copied from interface: Atom
        Set the X coordinate.
        Specified by:
        setX in interface Atom
        Parameters:
        x - a double
        See Also:
        Atom.getX()

      • setY

        public void setY​(double y)
        Description copied from interface: Atom
        Set the Y coordinate.
        Specified by:
        setY in interface Atom
        Parameters:
        y - a double
        See Also:
        Atom.getY()

      • setZ

        public void setZ​(double z)
        Description copied from interface: Atom
        Set the Z coordinate.
        Specified by:
        setZ in interface Atom
        Parameters:
        z - a double
        See Also:
        Atom.getZ()

      • getX

        public double getX()
        Get the X coordinate.
        Specified by:
        getX in interface Atom
        Returns:
        a double
        See Also:
        setX(double)

      • getY

        public double getY()
        Get the Y coordinate.
        Specified by:
        getY in interface Atom
        Returns:
        a double
        See Also:
        setY(double)

      • getZ

        public double getZ()
        Get the Z coordinate.
        Specified by:
        getZ in interface Atom
        Returns:
        a double
        See Also:
        setZ(double)

      • setAltLoc

        public void setAltLoc​(java.lang.Character c)
        set alternate Location.
        Specified by:
        setAltLoc in interface Atom
        Parameters:
        c - a Character object specifying the alt loc value
        See Also:
        getAltLoc()

      • getAltLoc

        public java.lang.Character getAltLoc()
        get alternate Location.
        Specified by:
        getAltLoc in interface Atom
        Returns:
        a Character object representing the alt loc value
        See Also:
        setAltLoc(java.lang.Character)

      • setPDBline

        public void setPDBline​(java.lang.String s)
        store the whole line.
        Specified by:
        setPDBline in interface Atom
        Parameters:
        s - a String specifying the PDBline value
        See Also:
        getPDBline()

      • toString

        public java.lang.String toString()
        string representation.
        Overrides:
        toString in class java.lang.Object

      • setOccupancy

        public void setOccupancy​(double occu)
        Description copied from interface: Atom
        set occupancy.
        Specified by:
        setOccupancy in interface Atom
        Parameters:
        occu - a double specifying the occupancy value
        See Also:
        Atom.getOccupancy()

      • getOccupancy

        public double getOccupancy()
        Description copied from interface: Atom
        get occupancy.
        Specified by:
        getOccupancy in interface Atom
        Returns:
        a double representing the occupancy value
        See Also:
        Atom.setOccupancy(double)

      • setTempFactor

        public void setTempFactor​(double temp)
        Description copied from interface: Atom
        get set temp factor .
        Specified by:
        setTempFactor in interface Atom
        Parameters:
        temp - a double specifying the temp factor value
        See Also:
        Atom.getTempFactor()

      • getTempFactor

        public double getTempFactor()
        Description copied from interface: Atom
        get set temp factor.
        Specified by:
        getTempFactor in interface Atom
        Returns:
        a double representing the temp factor value
        See Also:
        Atom.setTempFactor(double)

      • clone

        public java.lang.Object clone()
        returns and identical copy of this object .
        Specified by:
        clone in interface Atom
        Overrides:
        clone in class java.lang.Object
        Returns:
        and identical copy of this object

      • setParent

        public void setParent​(Group parent)
        Description copied from interface: Atom
        Sets the back-reference to its parent Group.
        Specified by:
        setParent in interface Atom
        Parameters:
        parent - the parent Group
        See Also:
        Atom.getParent()

      • getParent

        public Group getParent()
        Description copied from interface: Atom
        Returns the parent Group of the Atom. returns null if the referenced object is not Group
        Specified by:
        getParent in interface Atom
        Returns:
        Group the parent Group of the Atom, or null
        See Also:
        Atom.setParent(Group)